We identified a wheat(Triticum aestivum L.) multi-pistil mutant from an F_2 breeding population in 2012, named 12 TP(three pistils in one floret). Genetic analysis showed that one dominant gene locus controlled the mu...We identified a wheat(Triticum aestivum L.) multi-pistil mutant from an F_2 breeding population in 2012, named 12 TP(three pistils in one floret). Genetic analysis showed that one dominant gene locus controlled the multi-pistil trait. Using homozygous normal and multi-pistil lines(near-isogenic lines; NILs) derived from the original mutant 12 TP, a simple sequence repeat(SSR) marker assay located the 12 TP locus on chromosome arm 2 DL. Four SSR markers were linked to 12 TP and their order was Xcfd233→Xcfd62-12 TP→Xwmc41→Xcfd168 at 15.85, 10.47, 2.89, and 10.37 cM, respectively. The average genetic expressivity of the trait ‘three pistils in one floret' was more than 98% in seven homozygous 12 TP lines; however, the average genetic expressivity in heterozygous F_1 plants was about 49%. Thus, the 12 TP is a semi-dominant gene locus, which differ from all previously reported multi-pistil mutants. Mutant 12 TP is a new useful germplasm for study of wheat floral development and for breeding of high yield wheat.展开更多
Diminished social pleasure has been reported in people with schizophrenia and autism spectrum disorder(ASD).Previous studies suggested that emotional expressivity is closely correlated with social pleasure.However,the...Diminished social pleasure has been reported in people with schizophrenia and autism spectrum disorder(ASD).Previous studies suggested that emotional expressivity is closely correlated with social pleasure.However,the underlying psychological mechanisms between traits related to schizophrenia and ASD,emotional expressivity,and social pleasure remain unclear.This study aimed to investigate the relationship between subclinical schizotypal and autistic traits,facial expressions,and social pleasure.Eighty-six healthy participants(mean age=20.35±0.26 years,44 males)were recruited to complete an emotion elicitation task and an autobiographical recalling task,while their facial expressions were videotaped for computerized analysis using the FaceReader.The intensity of different facial expressions(happy,sad,angry,surprised,scared,and disgusted),valence,and arousal were extracted.The self-report Multidimensional Schizotypy Scale(MSS),Autism-Spectrum Quotient(AQ),and Anticipatory and Consummatory Interpersonal Pleasure Scale(ACIPS)were administered to measure subclinical traits and social pleasure.Partial correlation analysis and moderation analysis were performed.Both schizotypal and autistic traits were negatively correlated with social pleasure.The moderation effects of angry facial expression for both schizotypal and autistic traits on their associations with social pleasure were significant.In addition,scared and surprised facial expressions moderated the associations between positive and negative dimensions of schizotypy and social pleasure,while arousal moderated the associations between autistic traits and social pleasure.Our study identified different moderating effects of facial emotion expressions on schizotypal and social anhedonia and autistic traits and social anhedonia,thereby revealing possible different psychopathological mechanisms underlying similar social anhedonia in subclinical populations.展开更多
Mytilus contain abundant antimicrobial peptides(AMPs)that play a key role in the innate immunity.However,heterologous production of these AMPs remains challenging due to their short sequences,multiple disulfide bonds,...Mytilus contain abundant antimicrobial peptides(AMPs)that play a key role in the innate immunity.However,heterologous production of these AMPs remains challenging due to their short sequences,multiple disulfide bonds,and high content of cationic amino acids,which hinder functional expression in prokaryotic systems such as Escherichia coli.To establish a eukaryotic recombinant expression system for the AMPs of mussel and obtain recombinant mussel AMPs for subsequent studies,we reported the successful recombinant expression of myticofensin B1,a novel defensin-like AMP identified previously in Mytiluscoruscus,using the eukaryotic host Pichia pastoris.The codon-optimized gene encoding the mature myticofensin-B1(composed of 65 amino acid residues,including 6 conserved cysteine residues)was cloned into a pPICZαA vector and expressed in P.pastoris GS115.Structural fidelity of the recombinant peptide was confirmed by liquid chromatography-tandem mass spectrometry(LC-MS/MS),showing a molecular weight of 8849.9 Da,which was consistent with the theoretical prediction.Functional assays demonstrated a broad-spectrum antimicrobial activity of the recombinant myticofensin-B1,with stronger inhibition against Gram-negative bacteria.Scanning electron microscopy revealed different effects of the recombinant myticofensin-B1 against different bacteria.In addition,the recombinant myticofensin-B1 exhibited a very low hemolytic activity against sheep red blood cells and weak cytotoxicity against human A549 lung cancer cells.This study establishes P.pastoris as a powerful platform to produce functional mussel AMP and highlights the potential of the recombinant myticofensin-B1 as a therapeutic agent for aquaculture pathogens and infections.展开更多
Betalain,an economically valuable water-soluble natural plant pigment,is prized for its strong antioxidant activity,making it popular as a dietary supplement and a visual marker for plant transformation.However,market...Betalain,an economically valuable water-soluble natural plant pigment,is prized for its strong antioxidant activity,making it popular as a dietary supplement and a visual marker for plant transformation.However,market demand significantly outstrips current production capacity.This study reports the development of an efficient push-and-pull multigene strategy based on polycistronic expression and metabolic flux regulation to enhance betalain biosynthesis in transgenic maize(Zea mays L.)endosperm.We engineered a novel enhanced RUBY(eRUBY)system derived from the original polycistronic RUBY construct(CYP76AD1P2ADODA1P2ADOPA5GT unit,abbreviated CDG)by introducing arogenate dehydrogenase(ADHα)to increase the L-tyrosine substrate supply.All the genes were driven by the endosperm-specific promoter.Fusion of ADHαinto a single polycistronic eRUBY construct(CDGA)produced significantly higher betanin(6.88 mg g−1 dry weight)and isobetanin(1.81 mg g−1 dry weight)levels than in CDG+A,which stacked the ADHαcassette independently with CDG.The high betalain accumulation in CDGA lines(which also exhibited higher transgene copy number)resulted in a 2.85–7.58-fold improvement in endosperm antioxidant capacity compared to WT(versus 2.48–2.80-fold in CDG+A).Importantly,transgenic plants maintained a normal phenotype.Transcriptome and metabolome analyses further indicated that metabolism of phenylalanine,alanine,aspartate,and glutamate contributes to betalain production.Hybridization with sweet corn successfully created a high-sugar eRUBY maize variety.Collectively,these results demonstrate the successful development of a novel maize germplasm with significantly enhanced nutritional value through high betalain accumulation.展开更多
Quantitative real-time PCR(qPCR)is widely used for gene expression analysis,but its accuracy critically depends on stable internal reference genes for normalization.In marine invertebrates,especially non-model taxa su...Quantitative real-time PCR(qPCR)is widely used for gene expression analysis,but its accuracy critically depends on stable internal reference genes for normalization.In marine invertebrates,especially non-model taxa such as cephalopods,systematic evaluation of reference genes is limited,leading to potential bias.The cuttlefish Sepiella japonica is ecologically and economically important in China,yet previous molecular studies have often relied on single unvalidated reference genes,which may compromise data reliability.This study aimed to systematically evaluate the stability of five commonly used reference genes(18S,ef-1α,ef-1γ,gapdh,andβ-actin)across multiple tissues and sexes of S.japonica,and to identify the most suitable reference genes and optimal number for qPCR normalization.Fifteen to sixteen tissue types were collected from ten healthy adults(five males and five females).Total RNA was extracted,reverse-transcribed,and analyzed by qPCR.Gene stability was assessed using four algorithms(geNorm,NormFinder,BestKeeper,andΔCt)integrated with RefFinder,and the optimal gene number was determined using geNorm pairwise variation(V_(n/n+1)<0.15).Four transcriptome-derived genes(creld2,cd109,acy1,and miox)were used for validation.The C_(t)values of the five genes ranged from 15.47 to 20.83.β-actin and gapdh showed pronounced variability in expression stability among tissues and sexes,indicating their limited suitability for normalization.18S exhibited the highest expression(mean C_(t):15.47-16.29)and lowest variability but displayed sex-biased expression,whereas ef-1αand ef-1γremained consistently stable across most tissues in both sexes,with ef-1αbeing the most robust and showing no sex-related bias.Although specific rankings varied among tissues and sexes,the comprehensive results indicated that ef-1αand ef-1γpossessed the highest overall stability,followed by 18S,whileβ-actin and gapdh were the least stable.The final comprehensive rankings were ef-1γ>ef-1α>18S>gapdh>β-actin(male)and ef-1α>ef-1γ>18S>gapdh>β-actin(female).geNorm analysis(V2/3<0.15)indicated that two genes,mainly ef-1αand ef-1γ,were generally sufficient for reliable normalization in most tissues.Validation confirmed that normalization using the stable ef-1αand ef-1γaccurately reflected the expression differences among tissues,whereasβ-actin and gapdh can bias or confound statistical analyses.ef-1αand ef-1γare identified as the most reliable reference gene combination for qPCR analysis in S.japonica,while 18S can serve as an auxiliary gene for within-sex comparisons.The use ofβ-actin or gapdh alone is not recommended.This study establishes a systematic framework for selecting reliable reference genes in S.japonica,thereby facilitating robust qPCR normalization and providing a foundation for future gene expression research in S.japonica and other cephalopods.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
Although both abscisic acid(ABA)and methyl jasmonate(MeJA)play significant roles in regulating the development and quality of grape(Vitis vinifera L.)berries,the regulatory effects and mechanisms of the combined appli...Although both abscisic acid(ABA)and methyl jasmonate(MeJA)play significant roles in regulating the development and quality of grape(Vitis vinifera L.)berries,the regulatory effects and mechanisms of the combined application of ABA and MeJA remain unclear.To further explore the optimal combination of these hormones for regulating the development of grape quality,combined ABA and MeJA treatments were carried out in this study,with‘Jumeigui’grape used as the material.The results indicated that the combined treatment of high-ABA and low-MeJA(HA+LM)increased the sugar-acid ratio,promoted the accumulation of phenolic substances in grape skins,and resulted in anthocyanin content 168.9%higher than that of the control,significantly enhancing coloration.Additionally,the combined treatment of low-ABA and low-MeJA(LA+LM)was more conducive to the accumulation of phenols in grape,especially phenolic acid and resveratrol,as the total phenolic content increased by 38.96%relative to that of the control.Moreover,the expressions of aroma-related genes were upregulated by the combined high-MeJA treatments.The combined treatment of high-ABA and high-MeJA(HA+HM)markedly increased terpene biosynthesis,followed by the LA+HM treatment,increasing the intensity of the rose flavor characteristics of the‘Jumeigui’grape.Therefore,the combination of MeJA and ABA at different concentrations had distinct effects on fruit quality and appropriate combinations can be selected according to the specific needs for the targeted metabolites.展开更多
[Objectives]To investigate the structure and function of the lipoxygenase(LOX)gene family in Physcomitrella patens.[Methods]This study employed bioinformatics methods to identify and predict LOX gene family members.Qu...[Objectives]To investigate the structure and function of the lipoxygenase(LOX)gene family in Physcomitrella patens.[Methods]This study employed bioinformatics methods to identify and predict LOX gene family members.Quantitative real-time PCR(qRT-PCR)was utilized to analyze the expression patterns of LOX genes at different stages of Botrytis cinerea infection.[Results]The P.patens LOX gene family comprises eight putative proteins,including two 12-LOX-type members and six 13-LOX-type members.Among the eight LOX proteins,PpLOX7 exhibited the lowest molecular weight and shortest amino acid sequence.PpLOX7 was identified as a basic protein with an isoelectric point(pI)of 8.54,while all other members were acidic.Subcellular localization analysis indicated that PpLOX7 was localized to the chloroplast,whereas the remaining members were distributed in the cytoplasm.Secondary structure prediction showed that all eight proteins were predominantly composed of random coils andα-helixes.Chromosomal mapping revealed that the LOX genes were distributed across 7 of the 27 chromosomes in P.patens,with PpLOX1 and PpLOX2 tandemly arranged on chromosome 15.The qRT-PCR analysis demonstrated distinct expression patterns among the eight PpLOX genes following B.cinerea infection.PpLOX1-3 and PpLOX7 were upregulated to varying degrees,suggesting their potential involvement in the early defense response of P.patens against B.cinerea.Notably,PpLOX2 exhibited highly significant differential expression,making it a key candidate for further investigation.[Conclusions]This study provides foundational insights into the functional roles of the LOX gene family in P.patens during biotic stress responses.展开更多
Background:The mechanisms underlying the beneficial effects of exercise on the human placenta are poorly understood.The objective of the current study was to ascertain the influence of a supervised concurrent exercise...Background:The mechanisms underlying the beneficial effects of exercise on the human placenta are poorly understood.The objective of the current study was to ascertain the influence of a supervised concurrent exercise intervention from gestational Week 17 until birth on key cytokines involved in placental development and function.Secondary aims were to explore:(a)the moderating effects of fetal sex and maternal weight status;and(b)whether gestational weight gain,lifestyle behaviors(diet,sleep patterns,and physical activity),and physical fitness(strength and cardiorespiratory fitness)mediated the effects of exercise on placental cytokines.Methods:Seventy-six pregnant women(33±4 years,mean±SD),divided into exercise(n=40)and control(n=36)groups,participated in this study.The exercise group followed a 60-min,3 days/week(aerobic+resistance)training program of moderate-to-vigorous intensity.Placental cytokines—including granulocyte-macrophage colony-stimulating factor(GM-CSF),granulocyte colony-stimulating factor(G-CSF),plateletderived growth factor AA(PDGF-AA),epidermal growth factor(EGF),monocyte chemoattractant protein-1(MCP-1),fractalkine,interleukin(IL)-8,IL-6,IL-1β,interleukin 1-receptor antagonist(IL-1ra),IL-10,tumor necrosis factor alpha(TNF-a),and interferon gamma(IFN-γ)were analyzed using Luminex multi-analyte profiling(x MAP)technology.Results:The exercise group presented higher placental levels of G-CSF and lower concentrations of EGF and IL-1ra than the control group(p<0.05).Significant effects of exercise on placental G-CSF and TNF-a(p<0.05)and a trend toward lower IL-6(p=0.08)were observed only in female placentas.Additionally,a reduction in weight gain partially mediated the effects of exercise on G-CSF(p<0.05).Conclusion:Maternal exercise during pregnancy is related to increased placental levels of G-CSF and lower EGF and IL-1ra levels.Some exercise-induced effects are observed exclusively in female placentas,including increased G-CSF and lower TNF-a and IL-6 concentrations.Notably,the increased levels of G-CSF observed with exercise might be due to a more adequate gestational weight gain.展开更多
Objective To develop a depression recognition model by integrating the spirit-expression diagnostic framework of traditional Chinese medicine(TCM)with machine learning algorithms.The proposed model seeks to establish ...Objective To develop a depression recognition model by integrating the spirit-expression diagnostic framework of traditional Chinese medicine(TCM)with machine learning algorithms.The proposed model seeks to establish a TCM-informed tool for early depression screening,thereby bridging traditional diagnostic principles with modern computational approaches.Methods The study included patients with depression who visited the Shanghai Pudong New Area Mental Health Center from October 1,2022 to October 1,2023,as well as students and teachers from Shanghai University of Traditional Chinese Medicine during the same period as the healthy control group.Videos of 3–10 s were captured using a Xiaomi Pad 5,and the TCM spirit and expressions were determined by TCM experts(at least 3 out of 5 experts agreed to determine the category of TCM spirit and expressions).Basic information,facial images,and interview information were collected through a portable TCM intelligent analysis and diagnosis device,and facial diagnosis features were extracted using the Open CV computer vision library technology.Statistical analysis methods such as parametric and non-parametric tests were used to analyze the baseline data,TCM spirit and expression features,and facial diagnosis feature parameters of the two groups,to compare the differences in TCM spirit and expression and facial features.Five machine learning algorithms,including extreme gradient boosting(XGBoost),decision tree(DT),Bernoulli naive Bayes(BernoulliNB),support vector machine(SVM),and k-nearest neighbor(KNN)classification,were used to construct a depression recognition model based on the fusion of TCM spirit and expression features.The performance of the model was evaluated using metrics such as accuracy,precision,and the area under the receiver operating characteristic(ROC)curve(AUC).The model results were explained using the Shapley Additive exPlanations(SHAP).Results A total of 93 depression patients and 87 healthy individuals were ultimately included in this study.There was no statistically significant difference in the baseline characteristics between the two groups(P>0.05).The differences in the characteristics of the spirit and expressions in TCM and facial features between the two groups were shown as follows.(i)Quantispirit facial analysis revealed that depression patients exhibited significantly reduced facial spirit and luminance compared with healthy controls(P<0.05),with characteristic features such as sad expressions,facial erythema,and changes in the lip color ranging from erythematous to cyanotic.(ii)Depressed patients exhibited significantly lower values in facial complexion L,lip L,and a values,and gloss index,but higher values in facial complexion a and b,lip b,low gloss index,and matte index(all P<0.05).(iii)The results of multiple models show that the XGBoost-based depression recognition model,integrating the TCM“spirit-expression”diagnostic framework,achieved an accuracy of 98.61%and significantly outperformed four benchmark algorithms—DT,BernoulliNB,SVM,and KNN(P<0.01).(iv)The SHAP visualization results show that in the recognition model constructed by the XGBoost algorithm,the complexion b value,categories of facial spirit,high gloss index,low gloss index,categories of facial expression and texture features have significant contribution to the model.Conclusion This study demonstrates that integrating TCM spirit-expression diagnostic features with machine learning enables the construction of a high-precision depression detection model,offering a novel paradigm for objective depression diagnosis.展开更多
The fertile soil of the countryside is also rich in artistic inspiration.“If farmers pick up a brush,they can become artists.If one devotes oneself wholeheartedly to something,a stroke of genius will follow,”said Mi...The fertile soil of the countryside is also rich in artistic inspiration.“If farmers pick up a brush,they can become artists.If one devotes oneself wholeheartedly to something,a stroke of genius will follow,”said Miao Huixin,a cultural envoy to Shengfeng Village in Youchegang Town,Xiuzhou District,Jiaxing City,Zhejiang Province.展开更多
The development of skeletal muscle are complicated processes involving genes responsible for proper muscle morphology,contractility,cell proliferation,differentiation,interactions,migration,and death.The three-dimensi...The development of skeletal muscle are complicated processes involving genes responsible for proper muscle morphology,contractility,cell proliferation,differentiation,interactions,migration,and death.The three-dimensional chromatin architecture of skeletal muscle development has not been studied intensively although dynamic transcriptional regulation during differentiation of muscle cells is one of the most deeply studied processes.The RNA-seq was used to analyze the transcriptome pattern during chicken muscle development across 12 stages.Hi-C was used to build chromatin architectures during four representative stages.Ch IP-seq was conducted to identify enhancers and promoters in these four stages,which are occupied by histone H3K27ac and H3K4me3 peaks.Results show that large-scale genome architecture changes are mostly unidirectional,and coupled by complex on/off dynamic patterns of gene expression.Specifically,we observed 258.30 Mb of the genome undergoing A/B compartment switching.Notable alterations(316.57 Mb)of interaction frequencies within TADs were observed.Substantial aging-associated genes exhibited ascending connectivity with the compartment transition from repressive to active status during muscle development.Some muscle-related gene promoters that interacted with active enhancers during development,and some myopathy/aging-associated genes that were activated in aging muscle were founded.These results provide key insights into skeletal muscle development in vivo,and offer a valuable resource that allows in-depth functional characterization of candidate genes.展开更多
Mangicol-type sesterterpenoids possess potent anti-inflammatory activity,characterized by a 5-5-6-5tetracyclic carbon skeleton formed by mangicdiene synthase Fg MS.Two proposed mechanisms for mangicdiene formation inv...Mangicol-type sesterterpenoids possess potent anti-inflammatory activity,characterized by a 5-5-6-5tetracyclic carbon skeleton formed by mangicdiene synthase Fg MS.Two proposed mechanisms for mangicdiene formation involve either C6-C10 cyclization(path a) or C2-C10 cyclization(path b) after the C10carbocation formation,but neither has been experimentally validated.Here,we have identified a second mangicdiene synthase Man D,which is derived from Fusarium sp.JNU-XJ070152-01 and shares high amino acid sequence identity with Fg MS.Through heterologous expression of man D in Aspergillus oryzae NSAR1,we observed production not only of mangicdiene(1) and variecoltetraene(2),previously identified by expression of Fg MS in Escherichia coli,but also two novel sesterterpene skeletons fusadiene(3)and fusatriene(4).The identification of fusadiene and fusatriene supports the occurrence of two key carbocation intermediates in path b,thus experimentally confirming that mangicdiene is built via path b for the first time,consistent with previous density functional theory(DFT) calculation results.展开更多
[Objectives]The present study was conducted to investigate the change rule ofβ-fructofuranosidase gene expression and its enzyme activity in the midgut of 5 th instar silkworm(Bombyx mori),in order to provide a refer...[Objectives]The present study was conducted to investigate the change rule ofβ-fructofuranosidase gene expression and its enzyme activity in the midgut of 5 th instar silkworm(Bombyx mori),in order to provide a reference for illustrating the enzymatic mechanism of usingβ-fructofuranosidase to absorb sucrose nutrition from mulberry leaves.[Methods]Real-time fluorescent quantitative PCR was applied to analyze the expression of BmSuc1 and BmSuc2 in midgut of 5 th-instar silkworm larvae,meanwhile the activities ofβ-fructofuranosidase was determined.[Results]BmSuc1 was expressed in the midgut of 5 th-instar silkworm larvae at different developmental stages.Its expression was upregulated at the beginning of the 5 th instar and during the peak feeding period,whereas BmSuc2 expression remained very low throughout the entire 5 th instar.The activity ofβ-fructofuranosidase was relatively high during the peak feeding period of 5 th-instar larvae,showing a trend of increasing first and then decreasing.[Conclusions]The expression pattern of the BmSuc1 gene and the changes inβ-fructofuranosidase activity were generally consistent with the physiological process of sugar nutrient absorption and utilization from mulberry leaves in 5 th-instar silkworms.It suggests that BmSuc1,as a sucrose hydrolase gene,plays a major role in the digestion and absorption of sucrose nutrients from mulberry leaves in the midgut tissue.展开更多
The pathogenesis-related protein PR10 plays a vital role in plant growth,development,and stress responses.This study systematically identified and analyzed PR10 genes in cultivated peanut(Arachis hypogaea L.),examinin...The pathogenesis-related protein PR10 plays a vital role in plant growth,development,and stress responses.This study systematically identified and analyzed PR10 genes in cultivated peanut(Arachis hypogaea L.),examining their phylogenetic relationships,conserved motifs,gene structures,and syntenic relationships.The analysis identified 54 Ah PR10 genes,which were classified into eight groups based on phylogenetic relationships,supported by gene structure and conserved motif characterization.Analysis of chromosomal distribution and synteny demonstrated that segmental duplications played a crucial role in the expansion of the Ah PR10 gene family.The identified Ah PR10 genes exhibited both constitutive and inducible expression patterns.Significantly,Ah PR10-7,Ah PR10-33,and Ah PR10-41 demonstrated potential importance in peanut resistance to Aspergillus flavus.In vitro fungistatic experiments demonstrated that recombinant Ah PR10-33 effectively inhibited A.flavus mycelial growth.These findings provide valuable insights for future investigations into Ah PR10 functions in protecting peanut from A.flavus infection.展开更多
While methodology for determining the mode of evolution in coding sequences has been well established,evaluation of adaptation events in emerging types of phenotype data needs further development.Here,we propose an an...While methodology for determining the mode of evolution in coding sequences has been well established,evaluation of adaptation events in emerging types of phenotype data needs further development.Here,we propose an analysis framework(expression variance decomposition,EVaDe)for comparative single-cell expression data based on phenotypic evolution theory.After decomposing the gene expression variance into separate components,we use two strategies to identify genes exhibiting large between-taxon expression divergence and small within-cell-type expression noise in certain cell types,attributing this pattern to putative adaptive evolution.In a dataset of primate prefrontal cortex,we find that such humanspecific key genes enrich with neurodevelopment-related functions,while most other genes exhibit neutral evolution patterns.Specific neuron types are found to harbor more of these key genes than other cell types,thus likely to have experienced more extensive adaptation.Reassuringly,at the molecular sequence level,the key genes are significantly associated with the rapidly evolving conserved non-coding elements.An additional case analysis comparing the naked mole-rat(NMR)with the mouse suggests that innateimmunity-related genes and cell types have undergone putative expression adaptation in NMR.Overall,the EVaDe framework may effectively probe adaptive evolution mode in single-cell expression data.展开更多
The B-box(BBX)gene family plays a vital role in plant growth,development,and stress responses.This study aimed to characterize the SmBBX gene family in eggplant(Solanum melongena L.),addressing the lack of systematic ...The B-box(BBX)gene family plays a vital role in plant growth,development,and stress responses.This study aimed to characterize the SmBBX gene family in eggplant(Solanum melongena L.),addressing the lack of systematic bioinformatics and functional studies in this species.A total of 33 SmBBX genes were identified through genome-wide analysis.These genes were phylogenetically grouped into five major clades,with shared domain structures,motifs,and genomic architectures among clade members.The gene duplication analysis revealed segmental duplication as the primary mechanism underlying the expansion of SmBBX proteins in eggplant.Additionally,expression profiling across diverse tissues and abiotic stress conditions,combined with the construction of protein—protein interaction networks and luciferase complementation assay,provided valuable insights into the functional roles of SmBBX genes.SmBBX21-2 and SmBBX22 were identified as the key regulators of anthocyanin biosynthesis,activating the expression of SmCHS and SmDFR promoters.Functional validation via heterologous and homologous overexpression demonstrated that SmBBX22 promoted anthocyanin accumulation by upregulating the expression of structural genes(SmCHS,SmF3H,SmF3′5′H,SmDFR,and SmANS)and transcription factors(SmTT8 and SmHY5)important for anthocyanin biosynthesis.Furthermore,the integration of DNA affinity purification sequencing and RNA-seq data revealed the direct transcriptional targets of SmBBX22,including genes involved in secondary metabolism,hormone signaling,and developmental regulation.This highlighted the role of SmBBX22 in phenylpropanoid and flavonoid biosynthesis.This study lays the foundation for understanding the functional roles of BBX genes in eggplant and provides new directions for future research in plant metabolism and stress adaptation.展开更多
This study examined the potential response mechanisms of Ligilactobacillus salivarius AR612 to glucose stress through whole-genome and comparative transcriptome analysis.We obtained the basic genome information of L.s...This study examined the potential response mechanisms of Ligilactobacillus salivarius AR612 to glucose stress through whole-genome and comparative transcriptome analysis.We obtained the basic genome information of L.salivarius AR612.The full genome length of L.salivarius AR612 was 1970245 bp,with a GC content of 33.01%and 1894 coding genes.Moreover,we identified many genes associated with genetic adaptations to various stress factors,including temperature,p H,osmotic pressure,bile salts,and oxidative stress.Physiological analysis revealed that the growth and morphology of AR612 changed significantly under glucose stress,with a decrease in the maximum growth and irregular cell morphology.Furthermore,a comparison of transcriptome data indicated that glucose stress induced changes in the number of differential genes.Moreover,AR612 could respond to extracellular glucose stress by changing the expression of genes related to cell morphology,carbohydrate metabolism,amino acid metabolism,fatty acid synthesis,and nucleotide metabolism.This study provides valuable theoretical insights for future research on the adaptation of L.salivarius AR612 to nutritional stress and its application in industrial processes.展开更多
Due to the unique microstructure and diverse opsin genes of the trinocular compound eye,stomatopoda possess an extraordinary ability to perceive multiple properties of light.They not only can detect natural light(NL)a...Due to the unique microstructure and diverse opsin genes of the trinocular compound eye,stomatopoda possess an extraordinary ability to perceive multiple properties of light.They not only can detect natural light(NL)and linearly polarized light(LPL),but also are the only animals capable of recognizing circularly polarized light(CPL).Here,we integrated single-cell RNA sequencing,previously published Illumina data,and in-situ hybridization(ISH)to quantify and localize functional opsin genes in Oratosquilla oratoria,a common stomatopoda species in the China Sea.A total of high-quality 31777 cells were captured for the first time in the O.oratoria compound eye,which were classified into 25 cell subpopulations,and hypothesized that cluster 22 is a critical cell subpopulation responsible for light(whether NL,LPL,or CPL)response in O.oratoria.Furthermore,we propose that the long-wavelengthsensitive opsin gene(lws)gene family,retinol dehydrogenase(rdh),voltage-gated ion channel(vgic),arrestin(arr),and myosin(myo)collectively mediate the light response in O.oratoria.Considering that very few vision-related opsin genes show differential expression in right-handed CPL(RCPL)-vs.-dark(DL),which provides additional evidence that stomatopoda cannot recognize RCPL.Meanwhile,we believe that UV-stimulated scaffold protein A(uvssa)and red pigment concentrating hormone(rpch)play special contributions in the left-handed CPL(LCPL)environment response.ISH revealing that 16 lws,6 middle-wavelength-sensitive(mws),and 2 ultraviolet(uv)opsin genes were expressed in the photoreceptors of the O.oratoria compound eye.Although the inability to determine the functional types of cell subpopulations limits the resolution of opsin genes,these findings systematically elucidate the specific expression patterns of opsin genes in O.oratoria and represent a significant step toward refining the visual ecological theory of O.oratoria and other stomatopod species.展开更多
基金supported by the National Science Fund of China (31571646)the Special Fund for Key Agricultural Project in Henan Province, China in 2016 (161100110400)
文摘We identified a wheat(Triticum aestivum L.) multi-pistil mutant from an F_2 breeding population in 2012, named 12 TP(three pistils in one floret). Genetic analysis showed that one dominant gene locus controlled the multi-pistil trait. Using homozygous normal and multi-pistil lines(near-isogenic lines; NILs) derived from the original mutant 12 TP, a simple sequence repeat(SSR) marker assay located the 12 TP locus on chromosome arm 2 DL. Four SSR markers were linked to 12 TP and their order was Xcfd233→Xcfd62-12 TP→Xwmc41→Xcfd168 at 15.85, 10.47, 2.89, and 10.37 cM, respectively. The average genetic expressivity of the trait ‘three pistils in one floret' was more than 98% in seven homozygous 12 TP lines; however, the average genetic expressivity in heterozygous F_1 plants was about 49%. Thus, the 12 TP is a semi-dominant gene locus, which differ from all previously reported multi-pistil mutants. Mutant 12 TP is a new useful germplasm for study of wheat floral development and for breeding of high yield wheat.
基金supported by National Natural Science Foundation of China,31871114,32061160468Natural Science Foundation of Shandong Province,ZR2021MC103.
文摘Diminished social pleasure has been reported in people with schizophrenia and autism spectrum disorder(ASD).Previous studies suggested that emotional expressivity is closely correlated with social pleasure.However,the underlying psychological mechanisms between traits related to schizophrenia and ASD,emotional expressivity,and social pleasure remain unclear.This study aimed to investigate the relationship between subclinical schizotypal and autistic traits,facial expressions,and social pleasure.Eighty-six healthy participants(mean age=20.35±0.26 years,44 males)were recruited to complete an emotion elicitation task and an autobiographical recalling task,while their facial expressions were videotaped for computerized analysis using the FaceReader.The intensity of different facial expressions(happy,sad,angry,surprised,scared,and disgusted),valence,and arousal were extracted.The self-report Multidimensional Schizotypy Scale(MSS),Autism-Spectrum Quotient(AQ),and Anticipatory and Consummatory Interpersonal Pleasure Scale(ACIPS)were administered to measure subclinical traits and social pleasure.Partial correlation analysis and moderation analysis were performed.Both schizotypal and autistic traits were negatively correlated with social pleasure.The moderation effects of angry facial expression for both schizotypal and autistic traits on their associations with social pleasure were significant.In addition,scared and surprised facial expressions moderated the associations between positive and negative dimensions of schizotypy and social pleasure,while arousal moderated the associations between autistic traits and social pleasure.Our study identified different moderating effects of facial emotion expressions on schizotypal and social anhedonia and autistic traits and social anhedonia,thereby revealing possible different psychopathological mechanisms underlying similar social anhedonia in subclinical populations.
基金supported by the National Natural Science Foundation of China(32271580,42020104009)the Fundamental Research Funds for Zhejiang Provincial Universities and Research Institutes(JX6311101923)。
文摘Mytilus contain abundant antimicrobial peptides(AMPs)that play a key role in the innate immunity.However,heterologous production of these AMPs remains challenging due to their short sequences,multiple disulfide bonds,and high content of cationic amino acids,which hinder functional expression in prokaryotic systems such as Escherichia coli.To establish a eukaryotic recombinant expression system for the AMPs of mussel and obtain recombinant mussel AMPs for subsequent studies,we reported the successful recombinant expression of myticofensin B1,a novel defensin-like AMP identified previously in Mytiluscoruscus,using the eukaryotic host Pichia pastoris.The codon-optimized gene encoding the mature myticofensin-B1(composed of 65 amino acid residues,including 6 conserved cysteine residues)was cloned into a pPICZαA vector and expressed in P.pastoris GS115.Structural fidelity of the recombinant peptide was confirmed by liquid chromatography-tandem mass spectrometry(LC-MS/MS),showing a molecular weight of 8849.9 Da,which was consistent with the theoretical prediction.Functional assays demonstrated a broad-spectrum antimicrobial activity of the recombinant myticofensin-B1,with stronger inhibition against Gram-negative bacteria.Scanning electron microscopy revealed different effects of the recombinant myticofensin-B1 against different bacteria.In addition,the recombinant myticofensin-B1 exhibited a very low hemolytic activity against sheep red blood cells and weak cytotoxicity against human A549 lung cancer cells.This study establishes P.pastoris as a powerful platform to produce functional mussel AMP and highlights the potential of the recombinant myticofensin-B1 as a therapeutic agent for aquaculture pathogens and infections.
基金supported by grants from the Biological Breeding-National Science and Technology Major Project(2024ZD04077)the Invigorate the Seed Industry of Guangdong Province(2024-NPY-00-044)+3 种基金the National Natural Science Foundation of China(32272120)the Guangxi Science and Technology Major Project(GKAA24206023)the National Key Research and Development Program of China(2024YFF1000800)the Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops Major Project(FCBRCE-202502,FCBRCE-202504).
文摘Betalain,an economically valuable water-soluble natural plant pigment,is prized for its strong antioxidant activity,making it popular as a dietary supplement and a visual marker for plant transformation.However,market demand significantly outstrips current production capacity.This study reports the development of an efficient push-and-pull multigene strategy based on polycistronic expression and metabolic flux regulation to enhance betalain biosynthesis in transgenic maize(Zea mays L.)endosperm.We engineered a novel enhanced RUBY(eRUBY)system derived from the original polycistronic RUBY construct(CYP76AD1P2ADODA1P2ADOPA5GT unit,abbreviated CDG)by introducing arogenate dehydrogenase(ADHα)to increase the L-tyrosine substrate supply.All the genes were driven by the endosperm-specific promoter.Fusion of ADHαinto a single polycistronic eRUBY construct(CDGA)produced significantly higher betanin(6.88 mg g−1 dry weight)and isobetanin(1.81 mg g−1 dry weight)levels than in CDG+A,which stacked the ADHαcassette independently with CDG.The high betalain accumulation in CDGA lines(which also exhibited higher transgene copy number)resulted in a 2.85–7.58-fold improvement in endosperm antioxidant capacity compared to WT(versus 2.48–2.80-fold in CDG+A).Importantly,transgenic plants maintained a normal phenotype.Transcriptome and metabolome analyses further indicated that metabolism of phenylalanine,alanine,aspartate,and glutamate contributes to betalain production.Hybridization with sweet corn successfully created a high-sugar eRUBY maize variety.Collectively,these results demonstrate the successful development of a novel maize germplasm with significantly enhanced nutritional value through high betalain accumulation.
文摘Quantitative real-time PCR(qPCR)is widely used for gene expression analysis,but its accuracy critically depends on stable internal reference genes for normalization.In marine invertebrates,especially non-model taxa such as cephalopods,systematic evaluation of reference genes is limited,leading to potential bias.The cuttlefish Sepiella japonica is ecologically and economically important in China,yet previous molecular studies have often relied on single unvalidated reference genes,which may compromise data reliability.This study aimed to systematically evaluate the stability of five commonly used reference genes(18S,ef-1α,ef-1γ,gapdh,andβ-actin)across multiple tissues and sexes of S.japonica,and to identify the most suitable reference genes and optimal number for qPCR normalization.Fifteen to sixteen tissue types were collected from ten healthy adults(five males and five females).Total RNA was extracted,reverse-transcribed,and analyzed by qPCR.Gene stability was assessed using four algorithms(geNorm,NormFinder,BestKeeper,andΔCt)integrated with RefFinder,and the optimal gene number was determined using geNorm pairwise variation(V_(n/n+1)<0.15).Four transcriptome-derived genes(creld2,cd109,acy1,and miox)were used for validation.The C_(t)values of the five genes ranged from 15.47 to 20.83.β-actin and gapdh showed pronounced variability in expression stability among tissues and sexes,indicating their limited suitability for normalization.18S exhibited the highest expression(mean C_(t):15.47-16.29)and lowest variability but displayed sex-biased expression,whereas ef-1αand ef-1γremained consistently stable across most tissues in both sexes,with ef-1αbeing the most robust and showing no sex-related bias.Although specific rankings varied among tissues and sexes,the comprehensive results indicated that ef-1αand ef-1γpossessed the highest overall stability,followed by 18S,whileβ-actin and gapdh were the least stable.The final comprehensive rankings were ef-1γ>ef-1α>18S>gapdh>β-actin(male)and ef-1α>ef-1γ>18S>gapdh>β-actin(female).geNorm analysis(V2/3<0.15)indicated that two genes,mainly ef-1αand ef-1γ,were generally sufficient for reliable normalization in most tissues.Validation confirmed that normalization using the stable ef-1αand ef-1γaccurately reflected the expression differences among tissues,whereasβ-actin and gapdh can bias or confound statistical analyses.ef-1αand ef-1γare identified as the most reliable reference gene combination for qPCR analysis in S.japonica,while 18S can serve as an auxiliary gene for within-sex comparisons.The use ofβ-actin or gapdh alone is not recommended.This study establishes a systematic framework for selecting reliable reference genes in S.japonica,thereby facilitating robust qPCR normalization and providing a foundation for future gene expression research in S.japonica and other cephalopods.
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.
基金supported by the Xi'an Key Research and Development Program(Grant No.24NYGG0057)the National Natural Science Foundation of China(Grant No.U22A20491)the Shaanxi Key Research and Development Program(Grant No.2024NC-YBXM-024).
文摘Although both abscisic acid(ABA)and methyl jasmonate(MeJA)play significant roles in regulating the development and quality of grape(Vitis vinifera L.)berries,the regulatory effects and mechanisms of the combined application of ABA and MeJA remain unclear.To further explore the optimal combination of these hormones for regulating the development of grape quality,combined ABA and MeJA treatments were carried out in this study,with‘Jumeigui’grape used as the material.The results indicated that the combined treatment of high-ABA and low-MeJA(HA+LM)increased the sugar-acid ratio,promoted the accumulation of phenolic substances in grape skins,and resulted in anthocyanin content 168.9%higher than that of the control,significantly enhancing coloration.Additionally,the combined treatment of low-ABA and low-MeJA(LA+LM)was more conducive to the accumulation of phenols in grape,especially phenolic acid and resveratrol,as the total phenolic content increased by 38.96%relative to that of the control.Moreover,the expressions of aroma-related genes were upregulated by the combined high-MeJA treatments.The combined treatment of high-ABA and high-MeJA(HA+HM)markedly increased terpene biosynthesis,followed by the LA+HM treatment,increasing the intensity of the rose flavor characteristics of the‘Jumeigui’grape.Therefore,the combination of MeJA and ABA at different concentrations had distinct effects on fruit quality and appropriate combinations can be selected according to the specific needs for the targeted metabolites.
基金Supported by the Science and Technology Program of Guizhou Provence(Qiankehejichu-ZK[2023]Yiban 271).
文摘[Objectives]To investigate the structure and function of the lipoxygenase(LOX)gene family in Physcomitrella patens.[Methods]This study employed bioinformatics methods to identify and predict LOX gene family members.Quantitative real-time PCR(qRT-PCR)was utilized to analyze the expression patterns of LOX genes at different stages of Botrytis cinerea infection.[Results]The P.patens LOX gene family comprises eight putative proteins,including two 12-LOX-type members and six 13-LOX-type members.Among the eight LOX proteins,PpLOX7 exhibited the lowest molecular weight and shortest amino acid sequence.PpLOX7 was identified as a basic protein with an isoelectric point(pI)of 8.54,while all other members were acidic.Subcellular localization analysis indicated that PpLOX7 was localized to the chloroplast,whereas the remaining members were distributed in the cytoplasm.Secondary structure prediction showed that all eight proteins were predominantly composed of random coils andα-helixes.Chromosomal mapping revealed that the LOX genes were distributed across 7 of the 27 chromosomes in P.patens,with PpLOX1 and PpLOX2 tandemly arranged on chromosome 15.The qRT-PCR analysis demonstrated distinct expression patterns among the eight PpLOX genes following B.cinerea infection.PpLOX1-3 and PpLOX7 were upregulated to varying degrees,suggesting their potential involvement in the early defense response of P.patens against B.cinerea.Notably,PpLOX2 exhibited highly significant differential expression,making it a key candidate for further investigation.[Conclusions]This study provides foundational insights into the functional roles of the LOX gene family in P.patens during biotic stress responses.
基金funded by the Regional Ministry of Health of the Junta de Andalucıa(PI-0395-2016)the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement(No.101027215)+1 种基金supported by the PLACENTRAINING project,funded through the FEDER-UGR23 funding call(European Regional Development Fund University of Granada programGrant No.C-EXP-336UGR23)。
文摘Background:The mechanisms underlying the beneficial effects of exercise on the human placenta are poorly understood.The objective of the current study was to ascertain the influence of a supervised concurrent exercise intervention from gestational Week 17 until birth on key cytokines involved in placental development and function.Secondary aims were to explore:(a)the moderating effects of fetal sex and maternal weight status;and(b)whether gestational weight gain,lifestyle behaviors(diet,sleep patterns,and physical activity),and physical fitness(strength and cardiorespiratory fitness)mediated the effects of exercise on placental cytokines.Methods:Seventy-six pregnant women(33±4 years,mean±SD),divided into exercise(n=40)and control(n=36)groups,participated in this study.The exercise group followed a 60-min,3 days/week(aerobic+resistance)training program of moderate-to-vigorous intensity.Placental cytokines—including granulocyte-macrophage colony-stimulating factor(GM-CSF),granulocyte colony-stimulating factor(G-CSF),plateletderived growth factor AA(PDGF-AA),epidermal growth factor(EGF),monocyte chemoattractant protein-1(MCP-1),fractalkine,interleukin(IL)-8,IL-6,IL-1β,interleukin 1-receptor antagonist(IL-1ra),IL-10,tumor necrosis factor alpha(TNF-a),and interferon gamma(IFN-γ)were analyzed using Luminex multi-analyte profiling(x MAP)technology.Results:The exercise group presented higher placental levels of G-CSF and lower concentrations of EGF and IL-1ra than the control group(p<0.05).Significant effects of exercise on placental G-CSF and TNF-a(p<0.05)and a trend toward lower IL-6(p=0.08)were observed only in female placentas.Additionally,a reduction in weight gain partially mediated the effects of exercise on G-CSF(p<0.05).Conclusion:Maternal exercise during pregnancy is related to increased placental levels of G-CSF and lower EGF and IL-1ra levels.Some exercise-induced effects are observed exclusively in female placentas,including increased G-CSF and lower TNF-a and IL-6 concentrations.Notably,the increased levels of G-CSF observed with exercise might be due to a more adequate gestational weight gain.
基金General Program of National Natural Science Foundation of China(82474390)Construction Project of Pudong New Area Famous TCM Studios(National Pilot Zone for TCM Development,Shanghai)(PDZY-2025-0716)Shanghai Municipal Science and Technology Program Project Shanghai Key Laboratory of Health Identification and Assessment(21DZ2271000).
文摘Objective To develop a depression recognition model by integrating the spirit-expression diagnostic framework of traditional Chinese medicine(TCM)with machine learning algorithms.The proposed model seeks to establish a TCM-informed tool for early depression screening,thereby bridging traditional diagnostic principles with modern computational approaches.Methods The study included patients with depression who visited the Shanghai Pudong New Area Mental Health Center from October 1,2022 to October 1,2023,as well as students and teachers from Shanghai University of Traditional Chinese Medicine during the same period as the healthy control group.Videos of 3–10 s were captured using a Xiaomi Pad 5,and the TCM spirit and expressions were determined by TCM experts(at least 3 out of 5 experts agreed to determine the category of TCM spirit and expressions).Basic information,facial images,and interview information were collected through a portable TCM intelligent analysis and diagnosis device,and facial diagnosis features were extracted using the Open CV computer vision library technology.Statistical analysis methods such as parametric and non-parametric tests were used to analyze the baseline data,TCM spirit and expression features,and facial diagnosis feature parameters of the two groups,to compare the differences in TCM spirit and expression and facial features.Five machine learning algorithms,including extreme gradient boosting(XGBoost),decision tree(DT),Bernoulli naive Bayes(BernoulliNB),support vector machine(SVM),and k-nearest neighbor(KNN)classification,were used to construct a depression recognition model based on the fusion of TCM spirit and expression features.The performance of the model was evaluated using metrics such as accuracy,precision,and the area under the receiver operating characteristic(ROC)curve(AUC).The model results were explained using the Shapley Additive exPlanations(SHAP).Results A total of 93 depression patients and 87 healthy individuals were ultimately included in this study.There was no statistically significant difference in the baseline characteristics between the two groups(P>0.05).The differences in the characteristics of the spirit and expressions in TCM and facial features between the two groups were shown as follows.(i)Quantispirit facial analysis revealed that depression patients exhibited significantly reduced facial spirit and luminance compared with healthy controls(P<0.05),with characteristic features such as sad expressions,facial erythema,and changes in the lip color ranging from erythematous to cyanotic.(ii)Depressed patients exhibited significantly lower values in facial complexion L,lip L,and a values,and gloss index,but higher values in facial complexion a and b,lip b,low gloss index,and matte index(all P<0.05).(iii)The results of multiple models show that the XGBoost-based depression recognition model,integrating the TCM“spirit-expression”diagnostic framework,achieved an accuracy of 98.61%and significantly outperformed four benchmark algorithms—DT,BernoulliNB,SVM,and KNN(P<0.01).(iv)The SHAP visualization results show that in the recognition model constructed by the XGBoost algorithm,the complexion b value,categories of facial spirit,high gloss index,low gloss index,categories of facial expression and texture features have significant contribution to the model.Conclusion This study demonstrates that integrating TCM spirit-expression diagnostic features with machine learning enables the construction of a high-precision depression detection model,offering a novel paradigm for objective depression diagnosis.
文摘The fertile soil of the countryside is also rich in artistic inspiration.“If farmers pick up a brush,they can become artists.If one devotes oneself wholeheartedly to something,a stroke of genius will follow,”said Miao Huixin,a cultural envoy to Shengfeng Village in Youchegang Town,Xiuzhou District,Jiaxing City,Zhejiang Province.
基金supported by the National Key R&D Program of China(2023YFD1300040 and 2022YFF1000100)the Sichuan Science and Technology Program,China(2022NSFSC0132,2021YFYZ0009 and 2022JDJQ0054)the National Natural Science Foundation of China(32225046)。
文摘The development of skeletal muscle are complicated processes involving genes responsible for proper muscle morphology,contractility,cell proliferation,differentiation,interactions,migration,and death.The three-dimensional chromatin architecture of skeletal muscle development has not been studied intensively although dynamic transcriptional regulation during differentiation of muscle cells is one of the most deeply studied processes.The RNA-seq was used to analyze the transcriptome pattern during chicken muscle development across 12 stages.Hi-C was used to build chromatin architectures during four representative stages.Ch IP-seq was conducted to identify enhancers and promoters in these four stages,which are occupied by histone H3K27ac and H3K4me3 peaks.Results show that large-scale genome architecture changes are mostly unidirectional,and coupled by complex on/off dynamic patterns of gene expression.Specifically,we observed 258.30 Mb of the genome undergoing A/B compartment switching.Notable alterations(316.57 Mb)of interaction frequencies within TADs were observed.Substantial aging-associated genes exhibited ascending connectivity with the compartment transition from repressive to active status during muscle development.Some muscle-related gene promoters that interacted with active enhancers during development,and some myopathy/aging-associated genes that were activated in aging muscle were founded.These results provide key insights into skeletal muscle development in vivo,and offer a valuable resource that allows in-depth functional characterization of candidate genes.
基金financially supported by grants from the National Key Research and Development Program of China (No.2024YFE0102000)the National Natural Science Foundation of China (Nos.81925037,82321004,U22A20371,U24A20782,32170060,22177037,22207039,22307045)+6 种基金the Guangdong Major Project of Basic and Applied Basic Research (No.2023B0303000026)the Guangdong Natural Science Funds for Distinguished Young Scholars (No.2022B1515020028,China)the Guangdong International Science and Technology Cooperation Base (No.2021A0505020015,China)the Guangdong Basic and Applied Basic Research Foundation (Nos.2023B1515040016,2023A1515110388)the Innovative and Research Teams Project of Guangdong Higher Education Institution (No.2021KCXTD001,China)the Guangzhou Science and Technology Project (Nos.202206010020,2024A04J6241,2023A04J0080,China)the Fundamental Research Funds for the Central Universities (Nos.21623105,21624210)。
文摘Mangicol-type sesterterpenoids possess potent anti-inflammatory activity,characterized by a 5-5-6-5tetracyclic carbon skeleton formed by mangicdiene synthase Fg MS.Two proposed mechanisms for mangicdiene formation involve either C6-C10 cyclization(path a) or C2-C10 cyclization(path b) after the C10carbocation formation,but neither has been experimentally validated.Here,we have identified a second mangicdiene synthase Man D,which is derived from Fusarium sp.JNU-XJ070152-01 and shares high amino acid sequence identity with Fg MS.Through heterologous expression of man D in Aspergillus oryzae NSAR1,we observed production not only of mangicdiene(1) and variecoltetraene(2),previously identified by expression of Fg MS in Escherichia coli,but also two novel sesterterpene skeletons fusadiene(3)and fusatriene(4).The identification of fusadiene and fusatriene supports the occurrence of two key carbocation intermediates in path b,thus experimentally confirming that mangicdiene is built via path b for the first time,consistent with previous density functional theory(DFT) calculation results.
基金Supported by General Project of Yunnan Provincial Agricultural Basic Research Joint Special Project(202301BD070001-229)Yunnan Provincial Key R&D Program(202403AK140075)+1 种基金Modern Sericulture Industry Technology System of Yunan Province(KJTX-07)Honghe Comprehensive Test Station of National Sericulture Industry Technology System(CARS-18).
文摘[Objectives]The present study was conducted to investigate the change rule ofβ-fructofuranosidase gene expression and its enzyme activity in the midgut of 5 th instar silkworm(Bombyx mori),in order to provide a reference for illustrating the enzymatic mechanism of usingβ-fructofuranosidase to absorb sucrose nutrition from mulberry leaves.[Methods]Real-time fluorescent quantitative PCR was applied to analyze the expression of BmSuc1 and BmSuc2 in midgut of 5 th-instar silkworm larvae,meanwhile the activities ofβ-fructofuranosidase was determined.[Results]BmSuc1 was expressed in the midgut of 5 th-instar silkworm larvae at different developmental stages.Its expression was upregulated at the beginning of the 5 th instar and during the peak feeding period,whereas BmSuc2 expression remained very low throughout the entire 5 th instar.The activity ofβ-fructofuranosidase was relatively high during the peak feeding period of 5 th-instar larvae,showing a trend of increasing first and then decreasing.[Conclusions]The expression pattern of the BmSuc1 gene and the changes inβ-fructofuranosidase activity were generally consistent with the physiological process of sugar nutrient absorption and utilization from mulberry leaves in 5 th-instar silkworms.It suggests that BmSuc1,as a sucrose hydrolase gene,plays a major role in the digestion and absorption of sucrose nutrients from mulberry leaves in the midgut tissue.
基金supported by the National Key R&D Program of China(2022YFD1200400)the National Natural Science Foundation of China(32301851)。
文摘The pathogenesis-related protein PR10 plays a vital role in plant growth,development,and stress responses.This study systematically identified and analyzed PR10 genes in cultivated peanut(Arachis hypogaea L.),examining their phylogenetic relationships,conserved motifs,gene structures,and syntenic relationships.The analysis identified 54 Ah PR10 genes,which were classified into eight groups based on phylogenetic relationships,supported by gene structure and conserved motif characterization.Analysis of chromosomal distribution and synteny demonstrated that segmental duplications played a crucial role in the expansion of the Ah PR10 gene family.The identified Ah PR10 genes exhibited both constitutive and inducible expression patterns.Significantly,Ah PR10-7,Ah PR10-33,and Ah PR10-41 demonstrated potential importance in peanut resistance to Aspergillus flavus.In vitro fungistatic experiments demonstrated that recombinant Ah PR10-33 effectively inhibited A.flavus mycelial growth.These findings provide valuable insights for future investigations into Ah PR10 functions in protecting peanut from A.flavus infection.
文摘While methodology for determining the mode of evolution in coding sequences has been well established,evaluation of adaptation events in emerging types of phenotype data needs further development.Here,we propose an analysis framework(expression variance decomposition,EVaDe)for comparative single-cell expression data based on phenotypic evolution theory.After decomposing the gene expression variance into separate components,we use two strategies to identify genes exhibiting large between-taxon expression divergence and small within-cell-type expression noise in certain cell types,attributing this pattern to putative adaptive evolution.In a dataset of primate prefrontal cortex,we find that such humanspecific key genes enrich with neurodevelopment-related functions,while most other genes exhibit neutral evolution patterns.Specific neuron types are found to harbor more of these key genes than other cell types,thus likely to have experienced more extensive adaptation.Reassuringly,at the molecular sequence level,the key genes are significantly associated with the rapidly evolving conserved non-coding elements.An additional case analysis comparing the naked mole-rat(NMR)with the mouse suggests that innateimmunity-related genes and cell types have undergone putative expression adaptation in NMR.Overall,the EVaDe framework may effectively probe adaptive evolution mode in single-cell expression data.
基金supported by grants from Shanghai Agriculture Applied Technology Development Program(Grant No.2022-02-08-00-12-F01109)the National Natural Science Foundation of China(Grant No.32272721).
文摘The B-box(BBX)gene family plays a vital role in plant growth,development,and stress responses.This study aimed to characterize the SmBBX gene family in eggplant(Solanum melongena L.),addressing the lack of systematic bioinformatics and functional studies in this species.A total of 33 SmBBX genes were identified through genome-wide analysis.These genes were phylogenetically grouped into five major clades,with shared domain structures,motifs,and genomic architectures among clade members.The gene duplication analysis revealed segmental duplication as the primary mechanism underlying the expansion of SmBBX proteins in eggplant.Additionally,expression profiling across diverse tissues and abiotic stress conditions,combined with the construction of protein—protein interaction networks and luciferase complementation assay,provided valuable insights into the functional roles of SmBBX genes.SmBBX21-2 and SmBBX22 were identified as the key regulators of anthocyanin biosynthesis,activating the expression of SmCHS and SmDFR promoters.Functional validation via heterologous and homologous overexpression demonstrated that SmBBX22 promoted anthocyanin accumulation by upregulating the expression of structural genes(SmCHS,SmF3H,SmF3′5′H,SmDFR,and SmANS)and transcription factors(SmTT8 and SmHY5)important for anthocyanin biosynthesis.Furthermore,the integration of DNA affinity purification sequencing and RNA-seq data revealed the direct transcriptional targets of SmBBX22,including genes involved in secondary metabolism,hormone signaling,and developmental regulation.This highlighted the role of SmBBX22 in phenylpropanoid and flavonoid biosynthesis.This study lays the foundation for understanding the functional roles of BBX genes in eggplant and provides new directions for future research in plant metabolism and stress adaptation.
基金supported by the Natural Science Foundation of China(32272364)the Shanghai Education Committee Scientific Research Innovation Projects,China(2101070007800120)+2 种基金National Science Foundation for Distinguished Young Scholars(32025029)Shanghai Key Project in Synthetic Biology(23HC1400900)the Shanghai Engineering Research Center of 460 Food Microbiology Program(19DZ2281100).
文摘This study examined the potential response mechanisms of Ligilactobacillus salivarius AR612 to glucose stress through whole-genome and comparative transcriptome analysis.We obtained the basic genome information of L.salivarius AR612.The full genome length of L.salivarius AR612 was 1970245 bp,with a GC content of 33.01%and 1894 coding genes.Moreover,we identified many genes associated with genetic adaptations to various stress factors,including temperature,p H,osmotic pressure,bile salts,and oxidative stress.Physiological analysis revealed that the growth and morphology of AR612 changed significantly under glucose stress,with a decrease in the maximum growth and irregular cell morphology.Furthermore,a comparison of transcriptome data indicated that glucose stress induced changes in the number of differential genes.Moreover,AR612 could respond to extracellular glucose stress by changing the expression of genes related to cell morphology,carbohydrate metabolism,amino acid metabolism,fatty acid synthesis,and nucleotide metabolism.This study provides valuable theoretical insights for future research on the adaptation of L.salivarius AR612 to nutritional stress and its application in industrial processes.
基金Supported by the Natural Science Foundation of Shandong Province(No.ZR2021QD110)the National Natural Science Foundation of China(No.42106128)。
文摘Due to the unique microstructure and diverse opsin genes of the trinocular compound eye,stomatopoda possess an extraordinary ability to perceive multiple properties of light.They not only can detect natural light(NL)and linearly polarized light(LPL),but also are the only animals capable of recognizing circularly polarized light(CPL).Here,we integrated single-cell RNA sequencing,previously published Illumina data,and in-situ hybridization(ISH)to quantify and localize functional opsin genes in Oratosquilla oratoria,a common stomatopoda species in the China Sea.A total of high-quality 31777 cells were captured for the first time in the O.oratoria compound eye,which were classified into 25 cell subpopulations,and hypothesized that cluster 22 is a critical cell subpopulation responsible for light(whether NL,LPL,or CPL)response in O.oratoria.Furthermore,we propose that the long-wavelengthsensitive opsin gene(lws)gene family,retinol dehydrogenase(rdh),voltage-gated ion channel(vgic),arrestin(arr),and myosin(myo)collectively mediate the light response in O.oratoria.Considering that very few vision-related opsin genes show differential expression in right-handed CPL(RCPL)-vs.-dark(DL),which provides additional evidence that stomatopoda cannot recognize RCPL.Meanwhile,we believe that UV-stimulated scaffold protein A(uvssa)and red pigment concentrating hormone(rpch)play special contributions in the left-handed CPL(LCPL)environment response.ISH revealing that 16 lws,6 middle-wavelength-sensitive(mws),and 2 ultraviolet(uv)opsin genes were expressed in the photoreceptors of the O.oratoria compound eye.Although the inability to determine the functional types of cell subpopulations limits the resolution of opsin genes,these findings systematically elucidate the specific expression patterns of opsin genes in O.oratoria and represent a significant step toward refining the visual ecological theory of O.oratoria and other stomatopod species.
