Drugs and pesticide residues in broiler feed can compromise the therapeutic and production benefits of antibiotic(ANT)application and affect gene expression.In this study,we analyzed the expression of 13 key pancreati...Drugs and pesticide residues in broiler feed can compromise the therapeutic and production benefits of antibiotic(ANT)application and affect gene expression.In this study,we analyzed the expression of 13 key pancreatic genes and blood physiology parameters after administering one maximum residue limit of herbicide glyphosate(GLY),two ANTs,and one anticoccidial drug(AD).A total of 260 Ross 308 broilers aged 1-40 d were divided into the following four groups of 65 birds each:control group,which was fed the main diet(MD),and three experimental groups,which were fed MD supplemented with GLY,GLY+ANTs(enrofloxacin and colistin methanesulfonate),and GLY+AD(ammonium maduramicin),respectively.The results showed that the addition of GLY,GLY+ANTs,and GLY+AD caused significant changes in the expression of several genes of physiological and economic importance.In particular,genes related to inflammation and apoptosis(interleukin 6(IL6),prostaglandin-endoperoxide synthase 2(PTGS2),and caspase 6(CASP6))were downregulated by up to 99.1%,and those related to antioxidant protection(catalase(CAT),superoxide dismutase 1(SOD1)and peroxiredoxin 6(PRDX6))by up to 98.6%,compared to controls.There was also a significant decline in the values of immunological characteristics in the blood serum observed in the experimental groups,and certain changes in gene expression were concordant with changes in the functioning of the pancreas and blood.The changes revealed in gene expression and blood indices in response to GLY,ANTs,and AD provide insights into the possible mechanisms of action of these agents at the molecular level.Specifically,these changes may be indicative of physiological mechanisms to overcome the negative effects of GLY,GLY+ANTs,and GLY+AD in broilers.展开更多
Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive...Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive thyroid-related cell lines cultured under simulated microgravity.Methods:Five thyroid-related cell lines—normal thyrocytes(Nthy-ori 3-1),papillary thyroid cancer(PTC)cells(SNU-790,TPC-1),poorly differentiated thyroid cancer cell(BCPAP),and anaplastic thyroid cancer cell(SNU-80)—were cultured under simulated microgravity(10-3 g)using a clinostat.Differentially expressed genes(DEGs)were analyzed using cDNA microarray,followed by functional annotation and assessment of aggressiveness via Transwell migration and invasion assays.Results:DEG analysis under simulated microgravity revealed distinct gene expression profiles by gravity condition,with 2980 DEGs in SNU-790,1033 in BCPAP,562 in TPC-1,477 in Nthy-ori 3-1,and 246 in SNU-80,as confirmed by hierarchical clustering.In PTC cell lines(SNU-790,TPC-1),G2–M phase–related genes were upregulated.In non-PTC cell lines(BCPAP,SNU-80),genes associated with innate immune response,Toll-like receptor signaling,were upregulated,whereas Hypoxia-Inducible Factor 1-alpha(HIF-1α)signaling-related genes were downregulated.Additionally,under simulated microgravity,significant migration was observed in SNU-790(3×104 cells)and BCPAP(2×104 and 3×104),while significant invasion occurred in SNU-790,Nthy-ori 3-1,and BCPAP at a seeding density of 2×104.Other conditions showed no significant differences.Conclusion:This study comprehensively evaluates the effects of simulated microgravity using a diverse panel of thyroid-related cell lines.Thesefindings provide valuable insight into how microgravity could influence cancer biology,emphasizing the importance of further research on cancer behavior in space environments and its implications for human health during long-term space missions.展开更多
Highlights●Natural variations in the SGT3 promoter TATA box repeats directly modulate gene expression and SGAs content in tubers,providing a novel molecular marker for low-steroidal glycoalkaloids(SGAs)breeding.●The...Highlights●Natural variations in the SGT3 promoter TATA box repeats directly modulate gene expression and SGAs content in tubers,providing a novel molecular marker for low-steroidal glycoalkaloids(SGAs)breeding.●The SGT3 promoter haplotype with(TA)10exhibits signifcantly higher transcriptional activity,correlating with high SGAs content,while the(TA)13haplotype is linked to low SGAs in natural germplasms.展开更多
Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression...Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression in rice remains unclear.Here,we construct a map of 137,629 polymorphic STRs in the rice(Oryza sativa L.)genome using a population-scale resequencing dataset.A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency,mutational patterns,chromosomal distribution,and functional properties of STRs are correlated with the sequences and lengths of repeat motifs.Leveraging a transcriptome dataset from 127 rice accessions,we identify 44,672 expression STRs(eSTRs)by modeling gene expression in response to the length variation of STRs.These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures.Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits.By editing the(ACT)_(7) STR in OsFD1 promoter,we further experimentally validate its role in regulating gene expression and phenotype.Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.展开更多
Gallbladder cancer(GBC)is a lethal biliary tract malignancy,which is infrequent in most developed countries,but common in many developing countries in specific geographical regions of the world.Non-specific symptoms l...Gallbladder cancer(GBC)is a lethal biliary tract malignancy,which is infrequent in most developed countries,but common in many developing countries in specific geographical regions of the world.Non-specific symptoms leading to late diagnosis is one of the primary factors contributing to poor prognosis in GBC.An understanding of the complex relationship between molecular genetics and epidemiological variances in the incidence rates of GBC is thus of utmost importance.Present review summarizes recent updates on population-specific dysregulated genetic expressions in the genesis of GBC,highlighting the pattern of ethno-geographic variations and on advances in targeted therapies conducted till date;points out the lacunae that deserve further attention and suggest possible new directions for future clinical trials in GBC.The review calls for the need of genetic screening of each GBC patients and for more extensive clinical trials on targeted therapies to move towards the goal of personalized medicine,bringing about more favourable survival outcomes.展开更多
N^(6)-Methyladenosine(m^(6)A)is the most common modification in the transcriptome of biological RNA and plays roles that include maintaining the stability and transportation of mRNA,mRNA precursor shearing,polyadenyla...N^(6)-Methyladenosine(m^(6)A)is the most common modification in the transcriptome of biological RNA and plays roles that include maintaining the stability and transportation of mRNA,mRNA precursor shearing,polyadenylation,and the initiation of translation.With the improving understanding of RNA methylation,m^(6)A modification is known to play vital roles in plant development and growth.The multi-petalization of flowering plants has high ornamental and research value in horticultural landscapes.However,the mechanism of RNA methylation in flower formation in Magnolia wufengensis,a classical multi-petalizational plant,remains unclear.This study compared and analyzed RNA m^(6)A methylation and the transcriptome in floral buds of two varieties with large differences in tepal number at the early stage of development.It was found that the degree of RNA m^(6)A methylation and relative expression levels of MawuAGL6-2,MawuPI-4,and MawuAGL9 in‘Jiaodan’with 36 tepals were significantly higher than those in‘Jiaohong’with 9 tepals during the development of floral organ primordia.Combined with quantitative real-time PCR,the expression levels of MawuAGL6-2,MawuPI-4,and MawuAGL9were positively correlated with the number of tepals.Transgenic experiments showed that MawuAGL6-1/2,and MawuPI-4 can increase the number of petals in Arabidopsis.Moreover,MawuAGL6-2 and MawuPI-4 can restore the missing petal phenotype of mutant Arabidopsis.Yeast two hybrid and yeast three hybrid indicated that MawuAGL6-2,MawuAP3-1/2,and MawuPI-4 could interact with each other under the mediation of the class E protein MawuAGL9.Based on these results,it is hypothesized that m^(6)A methylation influences the multi-petalization of Magnolia wufengensis by affecting the expression levels of MawuAGL6-2,MawuAP3-1/2,MawuPI-4,and MawuAGL9.These findings provide a better understanding of the molecular mechanisms of epigenetic modifications in flower developmental diversity.展开更多
DNA microarray technology is an extremely effective technique for studying gene expression patterns in cells, and the main challenge currently faced by this technology is how to analyze the large amount of gene expres...DNA microarray technology is an extremely effective technique for studying gene expression patterns in cells, and the main challenge currently faced by this technology is how to analyze the large amount of gene expression data generated. To address this, this paper employs a mixed-effects model to analyze gene expression data. In terms of data selection, 1176 genes from the white mouse gene expression dataset under two experimental conditions were chosen, setting up two conditions: pneumococcal infection and no infection, and constructing a mixed-effects model. After preprocessing the gene chip information, the data were imported into the model, preliminary results were calculated, and permutation tests were performed to biologically validate the preliminary results using GSEA. The final dataset consists of 20 groups of gene expression data from pneumococcal infection, which categorizes functionally related genes based on the similarity of their expression profiles, facilitating the study of genes with unknown functions.展开更多
Urea is a major end product of nitrogen catabolism,serving as an osmolyte to regulate osmotic stress in fish exposed to varying water environments.It has been well known that urea transporters(UTs)facilitate the rapid...Urea is a major end product of nitrogen catabolism,serving as an osmolyte to regulate osmotic stress in fish exposed to varying water environments.It has been well known that urea transporters(UTs)facilitate the rapid movement of urea across cell membranes.However,researches on ut genes were predominantly focused on elasmobranchs and early developmental stages of fish.In this investigation,a total of three ut genes were identified in spotted sea bass.Phylogenetic,homology,and syntenic analyses were conducted to validate the annotation and assess the evolutionary relationships among ut genes.Both ut-a and ut-b genes have retained their evolutionary stability,demonstrating a significant level of homology between them.To gain deeper insights into the evolution of ut genes in spotted sea bass,we performed selective pressure analysis using site,branch,and branch-site models.The results suggested that positive selection likely played a significant role in shaping the evolution of the ut gene family.Furthermore,tissue-specific expression analyses revealed high expression levels of ut genes in osmoregulatory tissues such as the gill and kidney.Additionally,all three ut genes exhibited salinity-related expression patterns in gill and kidney tissues during both seawater-to-freshwater(SF)and freshwater-to-seawater(FS)adaptation.In situ hybridization results demonstrated the localization of both ut-a and ut-c mRNAs on the gill lamellae and adjacent gill filament epithelium.In summary,our study establishes a solid foundation for future research elucidating the evolutionary relationships and functional significance of ut genes during salinity acclimation in spotted sea bass and other teleost species.展开更多
Glutathione-S-transferase(GST,EC2.5.1.18)multifunctional protease is important for detoxification,defense against biotic and abiotic stresses,and secondary metabolic material transport for plant growth and development...Glutathione-S-transferase(GST,EC2.5.1.18)multifunctional protease is important for detoxification,defense against biotic and abiotic stresses,and secondary metabolic material transport for plant growth and development.In this study,71 members of the BpGST family were identified from the entire Betula platyphylla Suk.genome.Most of the members encode proteins with amino acid lengths ranging from 101 to 875 and were localized to the cytoplasm by a prediction.BpGSTs can be divided into seven subfamilies,with a majority of birch U and F subfamily members according to gene structure,conserved motifs and evolutionary analysis.GST family genes showed collinearity with 22 genes in Oryza sativa L.,and three genes in Arabidopsis thaliana;promoter cis-acting elements predicted that the GST gene family is functional in growth,hormone regulation,and abiotic stress response.Most members of the F subfamily of GST(BpGSTFs)were expressed in roots,stems,leaves,and petioles,with the most expression observed in leaves.On the basis of the expression profiles of F subfamily genes(BpGSTF1 to BpGSTF13)during salt,mannitol and ABA stress,BpGSTF proteins seem to have multiple functions depending on the type of abiotic stress;for instance,BpGSTs may function at different times during abiotic stress.This study enhances understanding of the GST gene family and provides a basis for further exploration of their function in birch.展开更多
Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyz...Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyzed the global gene expression profile of adipose-derived mesenchymal stem cells(ASCs)using microarray analysis and compared it with stromal vascular fraction(SVF)cells.Results:Microarray analysis revealed that ASCs express elevated levels of genes related to the extracellular matrix(ECM;extracellular matrix)and collagen,which are critical components of tissue remodeling and wound healing.Additionally,genes associated with cell growth,differentiation,motility,and plasticity were highly expressed.When compared to stromal vascular fraction(SVF)cells,ASCs demonstrated enrichment of genes involved in anti-inflammatory responses,immune modulation,tissue repair,cell adhesion,and migration processes.Gene Set Enrichment Analysis(GSEA;Gene Set Enrichment Analysis)showed activation of pathways related to angiogenesis,such as vascular endothelial growth factor(VEGF),Integrin,Wnt signaling pathways,transforming growth factor-beta(TGF-β),extracellular matrix(ECM),and matrix metalloproteinase(MMP),highlighting the significant angiogenic potential of ASCs.Gene Ontology(GO;Gene Ontology)analysis further linked ASCs to biological processes associated with the regulation of cell proliferation and muscle cell differentiation.Conclusion:These findings collectively underscore the suitability of adipose-derived mesenchymal stem cells(ASCs)as a promising candidate for regenerative medicine,particularly in applications involving tissue repair,immune modulation,and promotion of angiogenesis.展开更多
Background Mobile element variants(MEVs)have a significant and complex impact on genomic diversity and phe-notypic traits.However,the quantity,distribution,and relationship with gene expression and complex traits of M...Background Mobile element variants(MEVs)have a significant and complex impact on genomic diversity and phe-notypic traits.However,the quantity,distribution,and relationship with gene expression and complex traits of MEVs in the pig genome remain poorly understood.Results We constructed the most comprehensive porcine MEV library based on high-depth whole genome sequencing(WGS)data from 747 pigs across 59 breeds worldwide.This database identified a total of 147,993 poly-morphic MEVs,including 121,099 short interspersed nuclear elements(SINEs),26,053 long interspersed nuclear elements(LINEs),802 long terminal repeats(LTRs),and 39 other transposons,among which 54%are newly discovered.We found that MEVs are unevenly distributed across the genome and are strongly influenced by negative selec-tion effects.Importantly,we identified 514,530,and 584 candidate MEVs associated with population differentiation,domestication,and breed formation,respectively.For example,a significantly differentiated MEV is located in the ATRX intron between Asian and European pigs,whereas ATRX is also differentially expressed between Asian and European pigs in muscle tissue.In addition,we identified 4,169 expressed MEVs(eMEVs)significantly associated with gene expression and 6,914 splicing MEVs(sMEVs)associated with gene splicing based on RNA-seq data from 266 porcine liver tissues.These eMEVs and sMEVs explain 6.24%and 9.47%,respectively,of the observed cis-heritability and high-light the important role of MEVs in the regulation of gene expression.Finally,we provide a high-quality SNP–MEV reference haplotype panel to impute MEV genotypes from genome-wide SNPs.Notably,we identified a candidate MEV significantly associated with total teat number,demonstrating the functionality of this reference panel.Conclusions The present investigation demonstrated the importance of MEVs in pigs in terms of population diversity,gene expression and phenotypic traits,which may provide useful resources and theoretical support for pig genetics and breeding.展开更多
Given the growing concern over global warming and the critical role of carbon dioxide(CO_(2))in this phenomenon,the study of CO_(2)-induced alterations in coal strength has garnered significant attention due to its im...Given the growing concern over global warming and the critical role of carbon dioxide(CO_(2))in this phenomenon,the study of CO_(2)-induced alterations in coal strength has garnered significant attention due to its implications for carbon sequestration.A large number of experiments have proved that CO_(2) interaction time(T),saturation pressure(P)and other parameters have significant effects on coal strength.However,accurate evaluation of CO_(2)-induced alterations in coal strength is still a difficult problem,so it is particularly important to establish accurate and efficient prediction models.This study explored the application of advancedmachine learning(ML)algorithms and Gene Expression Programming(GEP)techniques to predict CO_(2)-induced alterations in coal strength.Sixmodels were developed,including three metaheuristic-optimized XGBoost models(GWO-XGBoost,SSA-XGBoost,PO-XGBoost)and three GEP models(GEP-1,GEP-2,GEP-3).Comprehensive evaluations using multiple metrics revealed that all models demonstrated high predictive accuracy,with the SSA-XGBoost model achieving the best performance(R2—Coefficient of determination=0.99396,RMSE—Root Mean Square Error=0.62102,MAE—Mean Absolute Error=0.36164,MAPE—Mean Absolute Percentage Error=4.8101%,RPD—Residual Predictive Deviation=13.4741).Model interpretability analyses using SHAP(Shapley Additive exPlanations),ICE(Individual Conditional Expectation),and PDP(Partial Dependence Plot)techniques highlighted the dominant role of fixed carbon content(FC)and significant interactions between FC and CO_(2) saturation pressure(P).Theresults demonstrated that the proposedmodels effectively address the challenges of CO_(2)-induced strength prediction,providing valuable insights for geological storage safety and environmental applications.展开更多
In order to solve the black-box modeling problem and improve the prediction accuracy of model,two distinguished models for tensile strength(Ts)and yield strength(Ys)of hot-rolled strip steel are established based on t...In order to solve the black-box modeling problem and improve the prediction accuracy of model,two distinguished models for tensile strength(Ts)and yield strength(Ys)of hot-rolled strip steel are established based on the industrial hot-rolled data and the algorithm of gene expression programming(GEP).Firstly,the industrial data of hot-rolled strip steel are preprocessed using the Pauta criterion,so as to eliminate outliers.The key input variables that affect Ys and Ts are selected by using the method of the maximal information coefficient(MIC).Secondly,the explicit prediction models of Ys and Ts are established using GEP.Subsequently,the model results based on GEP are compared with those based on the support vector regression(SVR)and the back propagation neural network(BPNN).Finally,the mathematical expression models for Ys and Ts obtained by GEP are used to further analyse the specific relationships between the chemical composition and mechanical property.It is shown that the errors of Ys and Ts based on GEP are less than 4%,and the coefficient of determination(R^(2))of Ys and Ts based on GEP is above 0.9,which has strong prediction performance.The prediction accuracy of GEP can achieve the same level with SVR and BPNN.It is worth mentioning that the proposed model can not only show the explicit relationship between the chemical composition,production process,and mechanical property of strip steel,but also occupy high prediction accuracy,which can make reliable reference for strip steel product design and optimisation.展开更多
Assessing the stability of pillars in underground mines(especially in deep underground mines)is a critical concern during both the design and the operational phases of a project.This study mainly focuses on developing...Assessing the stability of pillars in underground mines(especially in deep underground mines)is a critical concern during both the design and the operational phases of a project.This study mainly focuses on developing two practical models to predict pillar stability status.For this purpose,two robust models were developed using a database including 236 case histories from seven underground hard rock mines,based on gene expression programming(GEP)and decision tree-support vector machine(DT-SVM)hybrid algorithms.The performance of the developed models was evaluated based on four common statistical criteria(sensitivity,specificity,Matthews correlation coefficient,and accuracy),receiver operating characteristic(ROC)curve,and testing data sets.The results showed that the GEP and DT-SVM models performed exceptionally well in assessing pillar stability,showing a high level of accuracy.The DT-SVM model,in particular,outperformed the GEP model(accuracy of 0.914,sensitivity of 0.842,specificity of 0.929,Matthews correlation coefficient of 0.767,and area under the ROC of 0.897 for the test data set).Furthermore,upon comparing the developed models with the previous ones,it was revealed that both models can effectively determine the condition of pillar stability with low uncertainty and acceptable accuracy.This suggests that these models could serve as dependable tools for project managers,aiding in the evaluation of pillar stability during the design and operational phases of mining projects,despite the inherent challenges in this domain.展开更多
The forkhead box(FOX)family represents a class of transcription factors characterized by a distinctive winged helical structure.Forkhead box A1(FOXA1),a member of the forkhead box A(FOXA)subfamily within the FOX gene ...The forkhead box(FOX)family represents a class of transcription factors characterized by a distinctive winged helical structure.Forkhead box A1(FOXA1),a member of the forkhead box A(FOXA)subfamily within the FOX gene family,was the first forkhead protein identified in mammals.It serves as a pivotal transcription factor in tissue-specific differentiation and functions.Upon activation,owing to its unique structural domains,FOXA1 can interact with nucleosomes to open chromatin,thereby facilitating the recruitment of other transcription factors.These factorsmay act independently or synergistically with recruited transcription factors to regulate gene expression.Consequently,FOXA1 and other FOXA subfamily members with similar functions are referred to as“pioneer factors.”In recent years,studies on FOXA1 have advanced our understanding of its crucial role in gene regulation and involvement in disease processes.However,owing to their tissue-specific effects and varying biological behaviors in different environmental contexts,the underlying mechanisms remain elusive.Weused the PubMed database to better understand the complexmechanisms of FOXA1.By using keywords such as“FOXA1”and“transcription factor,”an extensive literature was retrieved,and many of the most relevant publications were screened.The selected studies were then thoroughly synthesized and summarized.This review synthesizes recent findings on FOXA1,encompassing its structural characteristics,domain functions,roles in embryonic development and the maintenance of adult organ morphology and function,interactions with histone posttranslational modifications in gene regulation,and the influence of its posttranslational modifications on gene expression.We also explore the involvement of FOXA1 in various diseases.By elucidating the biological mechanisms and disease-related roles of FOXA1,this review aims to provide insights for future research on its complex mechanisms and potential therapeutic targets.展开更多
Correction to:J.Iron Steel Res.Int.https://doi.org/10.1007/s42243-025-01545-x The publication of this article unfortunately contained mistakes.Equation(14)was not correct.The corrected equation is given below.
Hydrangea macrophylla is a popular ornamental shrub with a lot of economic and aesthetic value.It is known for its different flower shapes(lacecap and mophead)and the way its flowers change color depending on the pH o...Hydrangea macrophylla is a popular ornamental shrub with a lot of economic and aesthetic value.It is known for its different flower shapes(lacecap and mophead)and the way its flowers change color depending on the pH of the soil.Even though it is important for gardening,we still don’t know much about the molecular processes that lead to flower growth.The purpose of this study was to find and study SNP-related genes and transcription factors that are connected to the growth of H.macrophylla flowers.Genome-wide SNP analysis identified 11 SNPs associated with MYB transcription factors and 10 SNPs linked to a MADS-box SEP1 gene,highlighting their potential role in inflorescence-type regulation.These SNPs provide genomic resources for functional validation and markerassisted breeding in Hydrangea macrophylla.We found the MYB and MADS-box gene families,which are important for pigmentation and flower organ identity,through an analysis of the transcriptome and gene expression.The MYB family has 731R-MYBs,105 R2R3-MYBs,and 43R-MYBs.TheMADS-box family had 42 Type I(M-type)members and 36 Type II(MIKC-type)members.Motif and phylogenetic analysis showed that certain domains were preserved.For example,R2R3-MYBs and MIKC-type MADS genes are grouped with Arabidopsis orthologs,which suggests that their functions are also preserved.There was a clear link between the greatest expression ofMADS-box genes and the distinct phases of floral bud differentiation.Some MYB genes,on the other hand,showed alternative expression patterns that may help petals or sepals develop.qRT-PCR validation of representative MYB and MADS-box genes corroborated the transcriptome-based expression profiles,supporting their role in flower development and inflorescence-type regulation.展开更多
As a critical component of the in situ stress state,determination of the minimum horizontal principal stress plays a significant role in both geotechnical and petroleum engineering.To this end,a gene expression progra...As a critical component of the in situ stress state,determination of the minimum horizontal principal stress plays a significant role in both geotechnical and petroleum engineering.To this end,a gene expression programming(GEP)algorithm-based model,in which the data of borehole breakout size,vertical principal stress,and rock strength characteristics are used as the inputs,is proposed to predict the minimum horizontal principal stress.Seventy-nine(79)samples with seven features are collected to construct the minimum horizontal principal stress dataset used for training models.Twenty-four(24)GEP model hyperparameter sets were configured to explore the key parameter combinations among the inputs and their potential relationships with the minimum horizontal principal stresses.Model performance was evaluated using root mean squared error(RMSE),mean absolute error(MAE),mean absolute percentage error(MAPE),and coefficient of determination(R^(2)).By comparing predictive performance and parameter composition,two models were selected from 24 GEP models that demonstrated excellent predictive performance and simpler parameter composition.Compared with prevalent models,the results indicate that the two selected GEP models have better performance on the test set(R^(2)=0.9568 and 0.9621).Additionally,the results conducted by SHapley Additive exPlanations(SHAP)sensitivity analysis and Local Interpretable Model-agnostic Explanations(LIME)demonstrate that the vertical principal stress is the most influential parameter in both GEP models.The two GEP models have simple parameter compositions as well as stable and excellent prediction performance,which is a viable method for predicting the minimum horizontal principal stresses.展开更多
It has recently become evident that the de novo emergence of genes is widespread and documented for a variety of organisms.De novo genes frequently emerge in proximity to existing genes,forming gene overlaps.Here,we p...It has recently become evident that the de novo emergence of genes is widespread and documented for a variety of organisms.De novo genes frequently emerge in proximity to existing genes,forming gene overlaps.Here,we present an analysis of the evolutionary history of a putative de novo gene,lawc,which overlaps with the conserved Trf2 gene,which encodes a general transcription factor in Drosophila melanogaster.We demonstrate that lawc emerged approximately 68 million years ago in the 5'-untranslated region(UTR)of Trf2 and displays an extensive spatiotemporal expression pattern.One of the most remarkable features of the lawc evolutionary history is that its emergence was facilitated by the engagement of Drosophilidae-specific short,highly conserved regions located in Trf2 introns.This represents a unique example of putative de novo gene birth involving conserved DNA regions localized in introns of conserved genes.The observed lawc expression pattern may be due to the overlap of lawc with the 5'-UTR of Trf2.This study not only enriches our understanding of gene evolution but also highlights the complex interplay between genetic conservation and innovation.展开更多
AIM:To identify key genes and inflammatory signaling pathways involved in the anti-inflammatory effects of Hedysarum polybotrys polysaccharide(HPS)in a rat model of endotoxin-induced uveitis(EIU).METHODS:EIU was induc...AIM:To identify key genes and inflammatory signaling pathways involved in the anti-inflammatory effects of Hedysarum polybotrys polysaccharide(HPS)in a rat model of endotoxin-induced uveitis(EIU).METHODS:EIU was induced in Wistar rats through subcutaneous injection of lipopolysaccharide(LPS,200μg)and the rats were then randomly assigned to EIU group(n=5)and the HPS intervention group(n=5).HPS(400 mg/kg,intraperitoneally)or its carrier was administered 24h and 1h prior to EIU induction.Eyes were examined and enucleated 24h post-induction,and total RNA was extracted from the iris-ciliary body.Gene expression microarrays were used to identify differentially expressed genes(DEGs),followed by bioinformatics analyses,including gene ontology(GO)and pathway analysis.Key findings were not experimentally validated at the mRNA or protein level.RESULTS:A total of 322 DEGs were identified,comprising 254 mRNA and 68 lncRNA genes.GO analysis revealed significant functional categories,including response to LPS.Pathway analysis identified key signaling pathways involved in uveitis,such as cytokine-cytokine receptor interactions.Notably,16 mRNA and 7 lncRNA DEGs emerged as central nodes in the gene correlation network.CONCLUSION:HPS exerts its anti-inflammatory effects through coordinated signaling pathways,offering insights into potential therapeutic targets for managing uveitis.展开更多
基金supported by the Russian Science Foundation(No.22-16-00128),“Investigation of the Toxic Effect of Glyphosates on the Functional State of the Bird Intestinal Microbial Community,Their Growth and Development,and the Development of a Biological Product Based on the Glyphosate Degrading Strain”.
文摘Drugs and pesticide residues in broiler feed can compromise the therapeutic and production benefits of antibiotic(ANT)application and affect gene expression.In this study,we analyzed the expression of 13 key pancreatic genes and blood physiology parameters after administering one maximum residue limit of herbicide glyphosate(GLY),two ANTs,and one anticoccidial drug(AD).A total of 260 Ross 308 broilers aged 1-40 d were divided into the following four groups of 65 birds each:control group,which was fed the main diet(MD),and three experimental groups,which were fed MD supplemented with GLY,GLY+ANTs(enrofloxacin and colistin methanesulfonate),and GLY+AD(ammonium maduramicin),respectively.The results showed that the addition of GLY,GLY+ANTs,and GLY+AD caused significant changes in the expression of several genes of physiological and economic importance.In particular,genes related to inflammation and apoptosis(interleukin 6(IL6),prostaglandin-endoperoxide synthase 2(PTGS2),and caspase 6(CASP6))were downregulated by up to 99.1%,and those related to antioxidant protection(catalase(CAT),superoxide dismutase 1(SOD1)and peroxiredoxin 6(PRDX6))by up to 98.6%,compared to controls.There was also a significant decline in the values of immunological characteristics in the blood serum observed in the experimental groups,and certain changes in gene expression were concordant with changes in the functioning of the pancreas and blood.The changes revealed in gene expression and blood indices in response to GLY,ANTs,and AD provide insights into the possible mechanisms of action of these agents at the molecular level.Specifically,these changes may be indicative of physiological mechanisms to overcome the negative effects of GLY,GLY+ANTs,and GLY+AD in broilers.
文摘Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive thyroid-related cell lines cultured under simulated microgravity.Methods:Five thyroid-related cell lines—normal thyrocytes(Nthy-ori 3-1),papillary thyroid cancer(PTC)cells(SNU-790,TPC-1),poorly differentiated thyroid cancer cell(BCPAP),and anaplastic thyroid cancer cell(SNU-80)—were cultured under simulated microgravity(10-3 g)using a clinostat.Differentially expressed genes(DEGs)were analyzed using cDNA microarray,followed by functional annotation and assessment of aggressiveness via Transwell migration and invasion assays.Results:DEG analysis under simulated microgravity revealed distinct gene expression profiles by gravity condition,with 2980 DEGs in SNU-790,1033 in BCPAP,562 in TPC-1,477 in Nthy-ori 3-1,and 246 in SNU-80,as confirmed by hierarchical clustering.In PTC cell lines(SNU-790,TPC-1),G2–M phase–related genes were upregulated.In non-PTC cell lines(BCPAP,SNU-80),genes associated with innate immune response,Toll-like receptor signaling,were upregulated,whereas Hypoxia-Inducible Factor 1-alpha(HIF-1α)signaling-related genes were downregulated.Additionally,under simulated microgravity,significant migration was observed in SNU-790(3×104 cells)and BCPAP(2×104 and 3×104),while significant invasion occurred in SNU-790,Nthy-ori 3-1,and BCPAP at a seeding density of 2×104.Other conditions showed no significant differences.Conclusion:This study comprehensively evaluates the effects of simulated microgravity using a diverse panel of thyroid-related cell lines.Thesefindings provide valuable insight into how microgravity could influence cancer biology,emphasizing the importance of further research on cancer behavior in space environments and its implications for human health during long-term space missions.
基金financially supported by the Guangdong Major Project of Basic and Applied Basic Research,China(2021B0301030004)the National Natural Science Foundation of China(32360757,U2202206 and 32361143517)the Yunnan Fundamental Research Projects,China(202201AT070037,202501AS070012)。
文摘Highlights●Natural variations in the SGT3 promoter TATA box repeats directly modulate gene expression and SGAs content in tubers,providing a novel molecular marker for low-steroidal glycoalkaloids(SGAs)breeding.●The SGT3 promoter haplotype with(TA)10exhibits signifcantly higher transcriptional activity,correlating with high SGAs content,while the(TA)13haplotype is linked to low SGAs in natural germplasms.
基金supported by the National Natural Science Foundation of China(32172010)the Major Program of Guangdong Basic and Applied Basic Research(2019B030302006).
文摘Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression in rice remains unclear.Here,we construct a map of 137,629 polymorphic STRs in the rice(Oryza sativa L.)genome using a population-scale resequencing dataset.A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency,mutational patterns,chromosomal distribution,and functional properties of STRs are correlated with the sequences and lengths of repeat motifs.Leveraging a transcriptome dataset from 127 rice accessions,we identify 44,672 expression STRs(eSTRs)by modeling gene expression in response to the length variation of STRs.These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures.Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits.By editing the(ACT)_(7) STR in OsFD1 promoter,we further experimentally validate its role in regulating gene expression and phenotype.Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.
文摘Gallbladder cancer(GBC)is a lethal biliary tract malignancy,which is infrequent in most developed countries,but common in many developing countries in specific geographical regions of the world.Non-specific symptoms leading to late diagnosis is one of the primary factors contributing to poor prognosis in GBC.An understanding of the complex relationship between molecular genetics and epidemiological variances in the incidence rates of GBC is thus of utmost importance.Present review summarizes recent updates on population-specific dysregulated genetic expressions in the genesis of GBC,highlighting the pattern of ethno-geographic variations and on advances in targeted therapies conducted till date;points out the lacunae that deserve further attention and suggest possible new directions for future clinical trials in GBC.The review calls for the need of genetic screening of each GBC patients and for more extensive clinical trials on targeted therapies to move towards the goal of personalized medicine,bringing about more favourable survival outcomes.
基金supported by the National Natural Science Foundation of China(Grant No.31570651)。
文摘N^(6)-Methyladenosine(m^(6)A)is the most common modification in the transcriptome of biological RNA and plays roles that include maintaining the stability and transportation of mRNA,mRNA precursor shearing,polyadenylation,and the initiation of translation.With the improving understanding of RNA methylation,m^(6)A modification is known to play vital roles in plant development and growth.The multi-petalization of flowering plants has high ornamental and research value in horticultural landscapes.However,the mechanism of RNA methylation in flower formation in Magnolia wufengensis,a classical multi-petalizational plant,remains unclear.This study compared and analyzed RNA m^(6)A methylation and the transcriptome in floral buds of two varieties with large differences in tepal number at the early stage of development.It was found that the degree of RNA m^(6)A methylation and relative expression levels of MawuAGL6-2,MawuPI-4,and MawuAGL9 in‘Jiaodan’with 36 tepals were significantly higher than those in‘Jiaohong’with 9 tepals during the development of floral organ primordia.Combined with quantitative real-time PCR,the expression levels of MawuAGL6-2,MawuPI-4,and MawuAGL9were positively correlated with the number of tepals.Transgenic experiments showed that MawuAGL6-1/2,and MawuPI-4 can increase the number of petals in Arabidopsis.Moreover,MawuAGL6-2 and MawuPI-4 can restore the missing petal phenotype of mutant Arabidopsis.Yeast two hybrid and yeast three hybrid indicated that MawuAGL6-2,MawuAP3-1/2,and MawuPI-4 could interact with each other under the mediation of the class E protein MawuAGL9.Based on these results,it is hypothesized that m^(6)A methylation influences the multi-petalization of Magnolia wufengensis by affecting the expression levels of MawuAGL6-2,MawuAP3-1/2,MawuPI-4,and MawuAGL9.These findings provide a better understanding of the molecular mechanisms of epigenetic modifications in flower developmental diversity.
文摘DNA microarray technology is an extremely effective technique for studying gene expression patterns in cells, and the main challenge currently faced by this technology is how to analyze the large amount of gene expression data generated. To address this, this paper employs a mixed-effects model to analyze gene expression data. In terms of data selection, 1176 genes from the white mouse gene expression dataset under two experimental conditions were chosen, setting up two conditions: pneumococcal infection and no infection, and constructing a mixed-effects model. After preprocessing the gene chip information, the data were imported into the model, preliminary results were calculated, and permutation tests were performed to biologically validate the preliminary results using GSEA. The final dataset consists of 20 groups of gene expression data from pneumococcal infection, which categorizes functionally related genes based on the similarity of their expression profiles, facilitating the study of genes with unknown functions.
基金supported by the National Natural Science Foundation of China(No.32072947)the China Agriculture Research System(No.CARS-47)。
文摘Urea is a major end product of nitrogen catabolism,serving as an osmolyte to regulate osmotic stress in fish exposed to varying water environments.It has been well known that urea transporters(UTs)facilitate the rapid movement of urea across cell membranes.However,researches on ut genes were predominantly focused on elasmobranchs and early developmental stages of fish.In this investigation,a total of three ut genes were identified in spotted sea bass.Phylogenetic,homology,and syntenic analyses were conducted to validate the annotation and assess the evolutionary relationships among ut genes.Both ut-a and ut-b genes have retained their evolutionary stability,demonstrating a significant level of homology between them.To gain deeper insights into the evolution of ut genes in spotted sea bass,we performed selective pressure analysis using site,branch,and branch-site models.The results suggested that positive selection likely played a significant role in shaping the evolution of the ut gene family.Furthermore,tissue-specific expression analyses revealed high expression levels of ut genes in osmoregulatory tissues such as the gill and kidney.Additionally,all three ut genes exhibited salinity-related expression patterns in gill and kidney tissues during both seawater-to-freshwater(SF)and freshwater-to-seawater(FS)adaptation.In situ hybridization results demonstrated the localization of both ut-a and ut-c mRNAs on the gill lamellae and adjacent gill filament epithelium.In summary,our study establishes a solid foundation for future research elucidating the evolutionary relationships and functional significance of ut genes during salinity acclimation in spotted sea bass and other teleost species.
基金supported by the National Key Research and Development Program of China(No.2021YFD2200304)FundamentalResearch Funds for the Central Universities(2572022DQ08)the National Natural Science Foundation of China(No32171738).
文摘Glutathione-S-transferase(GST,EC2.5.1.18)multifunctional protease is important for detoxification,defense against biotic and abiotic stresses,and secondary metabolic material transport for plant growth and development.In this study,71 members of the BpGST family were identified from the entire Betula platyphylla Suk.genome.Most of the members encode proteins with amino acid lengths ranging from 101 to 875 and were localized to the cytoplasm by a prediction.BpGSTs can be divided into seven subfamilies,with a majority of birch U and F subfamily members according to gene structure,conserved motifs and evolutionary analysis.GST family genes showed collinearity with 22 genes in Oryza sativa L.,and three genes in Arabidopsis thaliana;promoter cis-acting elements predicted that the GST gene family is functional in growth,hormone regulation,and abiotic stress response.Most members of the F subfamily of GST(BpGSTFs)were expressed in roots,stems,leaves,and petioles,with the most expression observed in leaves.On the basis of the expression profiles of F subfamily genes(BpGSTF1 to BpGSTF13)during salt,mannitol and ABA stress,BpGSTF proteins seem to have multiple functions depending on the type of abiotic stress;for instance,BpGSTs may function at different times during abiotic stress.This study enhances understanding of the GST gene family and provides a basis for further exploration of their function in birch.
基金supported through National Research Foundation(NRF)of Korea grants funded by the Korean Government(No.NRF-2022R1F1A1064405)the research fund of Catholic Kwandong University and Catholic Kwandong University International St.Mary’s Hospital for S.-W Kim.
文摘Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyzed the global gene expression profile of adipose-derived mesenchymal stem cells(ASCs)using microarray analysis and compared it with stromal vascular fraction(SVF)cells.Results:Microarray analysis revealed that ASCs express elevated levels of genes related to the extracellular matrix(ECM;extracellular matrix)and collagen,which are critical components of tissue remodeling and wound healing.Additionally,genes associated with cell growth,differentiation,motility,and plasticity were highly expressed.When compared to stromal vascular fraction(SVF)cells,ASCs demonstrated enrichment of genes involved in anti-inflammatory responses,immune modulation,tissue repair,cell adhesion,and migration processes.Gene Set Enrichment Analysis(GSEA;Gene Set Enrichment Analysis)showed activation of pathways related to angiogenesis,such as vascular endothelial growth factor(VEGF),Integrin,Wnt signaling pathways,transforming growth factor-beta(TGF-β),extracellular matrix(ECM),and matrix metalloproteinase(MMP),highlighting the significant angiogenic potential of ASCs.Gene Ontology(GO;Gene Ontology)analysis further linked ASCs to biological processes associated with the regulation of cell proliferation and muscle cell differentiation.Conclusion:These findings collectively underscore the suitability of adipose-derived mesenchymal stem cells(ASCs)as a promising candidate for regenerative medicine,particularly in applications involving tissue repair,immune modulation,and promotion of angiogenesis.
基金National Key Research and Development Program of China(2022YFF1000103)Postdoctoral Fellowship Program of CPSF under Grant Number GZC20240620.
文摘Background Mobile element variants(MEVs)have a significant and complex impact on genomic diversity and phe-notypic traits.However,the quantity,distribution,and relationship with gene expression and complex traits of MEVs in the pig genome remain poorly understood.Results We constructed the most comprehensive porcine MEV library based on high-depth whole genome sequencing(WGS)data from 747 pigs across 59 breeds worldwide.This database identified a total of 147,993 poly-morphic MEVs,including 121,099 short interspersed nuclear elements(SINEs),26,053 long interspersed nuclear elements(LINEs),802 long terminal repeats(LTRs),and 39 other transposons,among which 54%are newly discovered.We found that MEVs are unevenly distributed across the genome and are strongly influenced by negative selec-tion effects.Importantly,we identified 514,530,and 584 candidate MEVs associated with population differentiation,domestication,and breed formation,respectively.For example,a significantly differentiated MEV is located in the ATRX intron between Asian and European pigs,whereas ATRX is also differentially expressed between Asian and European pigs in muscle tissue.In addition,we identified 4,169 expressed MEVs(eMEVs)significantly associated with gene expression and 6,914 splicing MEVs(sMEVs)associated with gene splicing based on RNA-seq data from 266 porcine liver tissues.These eMEVs and sMEVs explain 6.24%and 9.47%,respectively,of the observed cis-heritability and high-light the important role of MEVs in the regulation of gene expression.Finally,we provide a high-quality SNP–MEV reference haplotype panel to impute MEV genotypes from genome-wide SNPs.Notably,we identified a candidate MEV significantly associated with total teat number,demonstrating the functionality of this reference panel.Conclusions The present investigation demonstrated the importance of MEVs in pigs in terms of population diversity,gene expression and phenotypic traits,which may provide useful resources and theoretical support for pig genetics and breeding.
基金partially supported by the National Natural Science Foundation of China(42177164,52474121)the Outstanding Youth Project of Hunan Provincial Department of Education(23B0008).
文摘Given the growing concern over global warming and the critical role of carbon dioxide(CO_(2))in this phenomenon,the study of CO_(2)-induced alterations in coal strength has garnered significant attention due to its implications for carbon sequestration.A large number of experiments have proved that CO_(2) interaction time(T),saturation pressure(P)and other parameters have significant effects on coal strength.However,accurate evaluation of CO_(2)-induced alterations in coal strength is still a difficult problem,so it is particularly important to establish accurate and efficient prediction models.This study explored the application of advancedmachine learning(ML)algorithms and Gene Expression Programming(GEP)techniques to predict CO_(2)-induced alterations in coal strength.Sixmodels were developed,including three metaheuristic-optimized XGBoost models(GWO-XGBoost,SSA-XGBoost,PO-XGBoost)and three GEP models(GEP-1,GEP-2,GEP-3).Comprehensive evaluations using multiple metrics revealed that all models demonstrated high predictive accuracy,with the SSA-XGBoost model achieving the best performance(R2—Coefficient of determination=0.99396,RMSE—Root Mean Square Error=0.62102,MAE—Mean Absolute Error=0.36164,MAPE—Mean Absolute Percentage Error=4.8101%,RPD—Residual Predictive Deviation=13.4741).Model interpretability analyses using SHAP(Shapley Additive exPlanations),ICE(Individual Conditional Expectation),and PDP(Partial Dependence Plot)techniques highlighted the dominant role of fixed carbon content(FC)and significant interactions between FC and CO_(2) saturation pressure(P).Theresults demonstrated that the proposedmodels effectively address the challenges of CO_(2)-induced strength prediction,providing valuable insights for geological storage safety and environmental applications.
基金supported by the National Natural Science Foundation of China(Grant Nos.52074187 and 52274388)Liaoning Province Artificial Intelligence Innovation and Development Plan Project(Major Science and Technology Project)(2023JH26-10100002)the National Key Research and Development Program of China(No.2022YFB3304800).
文摘In order to solve the black-box modeling problem and improve the prediction accuracy of model,two distinguished models for tensile strength(Ts)and yield strength(Ys)of hot-rolled strip steel are established based on the industrial hot-rolled data and the algorithm of gene expression programming(GEP).Firstly,the industrial data of hot-rolled strip steel are preprocessed using the Pauta criterion,so as to eliminate outliers.The key input variables that affect Ys and Ts are selected by using the method of the maximal information coefficient(MIC).Secondly,the explicit prediction models of Ys and Ts are established using GEP.Subsequently,the model results based on GEP are compared with those based on the support vector regression(SVR)and the back propagation neural network(BPNN).Finally,the mathematical expression models for Ys and Ts obtained by GEP are used to further analyse the specific relationships between the chemical composition and mechanical property.It is shown that the errors of Ys and Ts based on GEP are less than 4%,and the coefficient of determination(R^(2))of Ys and Ts based on GEP is above 0.9,which has strong prediction performance.The prediction accuracy of GEP can achieve the same level with SVR and BPNN.It is worth mentioning that the proposed model can not only show the explicit relationship between the chemical composition,production process,and mechanical property of strip steel,but also occupy high prediction accuracy,which can make reliable reference for strip steel product design and optimisation.
文摘Assessing the stability of pillars in underground mines(especially in deep underground mines)is a critical concern during both the design and the operational phases of a project.This study mainly focuses on developing two practical models to predict pillar stability status.For this purpose,two robust models were developed using a database including 236 case histories from seven underground hard rock mines,based on gene expression programming(GEP)and decision tree-support vector machine(DT-SVM)hybrid algorithms.The performance of the developed models was evaluated based on four common statistical criteria(sensitivity,specificity,Matthews correlation coefficient,and accuracy),receiver operating characteristic(ROC)curve,and testing data sets.The results showed that the GEP and DT-SVM models performed exceptionally well in assessing pillar stability,showing a high level of accuracy.The DT-SVM model,in particular,outperformed the GEP model(accuracy of 0.914,sensitivity of 0.842,specificity of 0.929,Matthews correlation coefficient of 0.767,and area under the ROC of 0.897 for the test data set).Furthermore,upon comparing the developed models with the previous ones,it was revealed that both models can effectively determine the condition of pillar stability with low uncertainty and acceptable accuracy.This suggests that these models could serve as dependable tools for project managers,aiding in the evaluation of pillar stability during the design and operational phases of mining projects,despite the inherent challenges in this domain.
基金supported by grants from the National Natural Science Foundation of China (No.82470042)Liaoning Provincial Joint Science and Technology Plan (No.2023JH2/101800021)+1 种基金Basic Scientific Research Project of Liaoning Provincial Department of Education (No.LJKMZ20221186)Shenyang Municipal Public Health Research and Development Special Project (No.LJKMZ20221186)
文摘The forkhead box(FOX)family represents a class of transcription factors characterized by a distinctive winged helical structure.Forkhead box A1(FOXA1),a member of the forkhead box A(FOXA)subfamily within the FOX gene family,was the first forkhead protein identified in mammals.It serves as a pivotal transcription factor in tissue-specific differentiation and functions.Upon activation,owing to its unique structural domains,FOXA1 can interact with nucleosomes to open chromatin,thereby facilitating the recruitment of other transcription factors.These factorsmay act independently or synergistically with recruited transcription factors to regulate gene expression.Consequently,FOXA1 and other FOXA subfamily members with similar functions are referred to as“pioneer factors.”In recent years,studies on FOXA1 have advanced our understanding of its crucial role in gene regulation and involvement in disease processes.However,owing to their tissue-specific effects and varying biological behaviors in different environmental contexts,the underlying mechanisms remain elusive.Weused the PubMed database to better understand the complexmechanisms of FOXA1.By using keywords such as“FOXA1”and“transcription factor,”an extensive literature was retrieved,and many of the most relevant publications were screened.The selected studies were then thoroughly synthesized and summarized.This review synthesizes recent findings on FOXA1,encompassing its structural characteristics,domain functions,roles in embryonic development and the maintenance of adult organ morphology and function,interactions with histone posttranslational modifications in gene regulation,and the influence of its posttranslational modifications on gene expression.We also explore the involvement of FOXA1 in various diseases.By elucidating the biological mechanisms and disease-related roles of FOXA1,this review aims to provide insights for future research on its complex mechanisms and potential therapeutic targets.
文摘Correction to:J.Iron Steel Res.Int.https://doi.org/10.1007/s42243-025-01545-x The publication of this article unfortunately contained mistakes.Equation(14)was not correct.The corrected equation is given below.
基金funded by Science and Technology Research Project of Shanghai Greening and City Appearance Administration in 2023(G232406).
文摘Hydrangea macrophylla is a popular ornamental shrub with a lot of economic and aesthetic value.It is known for its different flower shapes(lacecap and mophead)and the way its flowers change color depending on the pH of the soil.Even though it is important for gardening,we still don’t know much about the molecular processes that lead to flower growth.The purpose of this study was to find and study SNP-related genes and transcription factors that are connected to the growth of H.macrophylla flowers.Genome-wide SNP analysis identified 11 SNPs associated with MYB transcription factors and 10 SNPs linked to a MADS-box SEP1 gene,highlighting their potential role in inflorescence-type regulation.These SNPs provide genomic resources for functional validation and markerassisted breeding in Hydrangea macrophylla.We found the MYB and MADS-box gene families,which are important for pigmentation and flower organ identity,through an analysis of the transcriptome and gene expression.The MYB family has 731R-MYBs,105 R2R3-MYBs,and 43R-MYBs.TheMADS-box family had 42 Type I(M-type)members and 36 Type II(MIKC-type)members.Motif and phylogenetic analysis showed that certain domains were preserved.For example,R2R3-MYBs and MIKC-type MADS genes are grouped with Arabidopsis orthologs,which suggests that their functions are also preserved.There was a clear link between the greatest expression ofMADS-box genes and the distinct phases of floral bud differentiation.Some MYB genes,on the other hand,showed alternative expression patterns that may help petals or sepals develop.qRT-PCR validation of representative MYB and MADS-box genes corroborated the transcriptome-based expression profiles,supporting their role in flower development and inflorescence-type regulation.
基金partially supported by the National Natural Science Foundation of China(Grant Nos.42177164 and 52474121)the Distinguished Youth Science Foundation of Hunan Province of China(Grant No.2022JJ10073).
文摘As a critical component of the in situ stress state,determination of the minimum horizontal principal stress plays a significant role in both geotechnical and petroleum engineering.To this end,a gene expression programming(GEP)algorithm-based model,in which the data of borehole breakout size,vertical principal stress,and rock strength characteristics are used as the inputs,is proposed to predict the minimum horizontal principal stress.Seventy-nine(79)samples with seven features are collected to construct the minimum horizontal principal stress dataset used for training models.Twenty-four(24)GEP model hyperparameter sets were configured to explore the key parameter combinations among the inputs and their potential relationships with the minimum horizontal principal stresses.Model performance was evaluated using root mean squared error(RMSE),mean absolute error(MAE),mean absolute percentage error(MAPE),and coefficient of determination(R^(2)).By comparing predictive performance and parameter composition,two models were selected from 24 GEP models that demonstrated excellent predictive performance and simpler parameter composition.Compared with prevalent models,the results indicate that the two selected GEP models have better performance on the test set(R^(2)=0.9568 and 0.9621).Additionally,the results conducted by SHapley Additive exPlanations(SHAP)sensitivity analysis and Local Interpretable Model-agnostic Explanations(LIME)demonstrate that the vertical principal stress is the most influential parameter in both GEP models.The two GEP models have simple parameter compositions as well as stable and excellent prediction performance,which is a viable method for predicting the minimum horizontal principal stresses.
基金funded by a grant from the Russian Science Foundation № 24-24-00354
文摘It has recently become evident that the de novo emergence of genes is widespread and documented for a variety of organisms.De novo genes frequently emerge in proximity to existing genes,forming gene overlaps.Here,we present an analysis of the evolutionary history of a putative de novo gene,lawc,which overlaps with the conserved Trf2 gene,which encodes a general transcription factor in Drosophila melanogaster.We demonstrate that lawc emerged approximately 68 million years ago in the 5'-untranslated region(UTR)of Trf2 and displays an extensive spatiotemporal expression pattern.One of the most remarkable features of the lawc evolutionary history is that its emergence was facilitated by the engagement of Drosophilidae-specific short,highly conserved regions located in Trf2 introns.This represents a unique example of putative de novo gene birth involving conserved DNA regions localized in introns of conserved genes.The observed lawc expression pattern may be due to the overlap of lawc with the 5'-UTR of Trf2.This study not only enriches our understanding of gene evolution but also highlights the complex interplay between genetic conservation and innovation.
基金Supported by the National Natural Science Fundation of China(No.82101107No.81471575).
文摘AIM:To identify key genes and inflammatory signaling pathways involved in the anti-inflammatory effects of Hedysarum polybotrys polysaccharide(HPS)in a rat model of endotoxin-induced uveitis(EIU).METHODS:EIU was induced in Wistar rats through subcutaneous injection of lipopolysaccharide(LPS,200μg)and the rats were then randomly assigned to EIU group(n=5)and the HPS intervention group(n=5).HPS(400 mg/kg,intraperitoneally)or its carrier was administered 24h and 1h prior to EIU induction.Eyes were examined and enucleated 24h post-induction,and total RNA was extracted from the iris-ciliary body.Gene expression microarrays were used to identify differentially expressed genes(DEGs),followed by bioinformatics analyses,including gene ontology(GO)and pathway analysis.Key findings were not experimentally validated at the mRNA or protein level.RESULTS:A total of 322 DEGs were identified,comprising 254 mRNA and 68 lncRNA genes.GO analysis revealed significant functional categories,including response to LPS.Pathway analysis identified key signaling pathways involved in uveitis,such as cytokine-cytokine receptor interactions.Notably,16 mRNA and 7 lncRNA DEGs emerged as central nodes in the gene correlation network.CONCLUSION:HPS exerts its anti-inflammatory effects through coordinated signaling pathways,offering insights into potential therapeutic targets for managing uveitis.
