Objective:Propionibacterium acnes(P.acnes)plays an important role in the development of acne,an inflammatory skin disease with a high-incidence.In this study,we used high-throughput RNA sequencing(RNA-seq)to reveal th...Objective:Propionibacterium acnes(P.acnes)plays an important role in the development of acne,an inflammatory skin disease with a high-incidence.In this study,we used high-throughput RNA sequencing(RNA-seq)to reveal the anti-inflammatory mechanism of baicalin on P.acnes-induced acne in rabbits.Methods:The Kligman method was used to induce acne in the ears of New Zealand rabbits.The effect of baicalin on the acne model was evaluated by the number of acne lesions and hematoxylin and eosin(H&E)staining of acne tissues.Enzyme-linked immunoabsorbent assay was used to measure the protein expression levels of tumor necrosis factor a(TNFA),interleukin-1 b(IL1B),IL6,and IL8 in the serum of rabbits.RNA-seq was performed to investigate the mechanism of anti-inflammatory activities of baicalin on acne.Immunohistochemical analysis and Western blot were used to validate the expression levels of related proteins in acne tissues.Results:Baicalin treatment significantly reduced the number of acne lesions and lesions of the ear as well as levels of serum inflammatory cytokines.RNA-seq data showed that baicalin treatment globally suppressed inflammation,especially the TNF signaling pathway and Staphylococcus aureus infection pathway,in the rabbit acne model.Conclusion: Baicalin effectively ameliorates P. acnes-induced acne in rabbits by suppressingthe inflammatory response in rabbits.展开更多
Objective:To explore the structural and functional characteristics of the fecal-associated microbiome(FAM)in a traditional Chinese medicine(TCM)qi-deficiency constitution(QDC)by comparing with balanced constitution(BC...Objective:To explore the structural and functional characteristics of the fecal-associated microbiome(FAM)in a traditional Chinese medicine(TCM)qi-deficiency constitution(QDC)by comparing with balanced constitution(BC)and screen the related biomarkers.Methods:In this cross-sectional study,the TCM constitutions of subjects were determined based on published the Classification and Determination of constitution in TCM and further confirmed by a TCM clinician.Clinical characteristics were recorded,and fecal samples were collected for 16S rDNA sequencing using the Illumina Miseq platform.The FAM structure was described using alpha-diversity indexes,beta-diversity indexes,and the relative abundances of the dominant taxa.Differences in the FAM distribution and function were analyzed with a Wilcoxon rank-sum test,MetagenomeSeq,and LEfSe analysis,after which a receiver operating characteristic curve based on the specific operational taxonomic units(OTUs)was constructed to calculate the area under the curve.Results:Our study population was composed of 22 BCs and 9 QDCs.There were no significant differences between the two groups in the distribution of clinical characteristics or alpha-diversity indexes,except for the sweets preference and blood glucose level.In principal coordinate analysis and partial least squares discriminant analysis,the bacterial communities in the BC group samples and QDC group samples clustered separately.Notably,there were 214 OTUs significantly distributed between groups in the MetagenomeSeq analysis,200 OTUs identified by the Wilcoxon rank-sum test,and 6 OTUs found by the LEfSe analysis.Predicted function analysis revealed that six metabolic pathways were distinctly distributed between the two groups.The area under the curve for the receiver operating characteristic curve based on the four specific OTUs was 0.88.Conclusion:Unique FAM structural and related functional characteristics are displayed in individuals with a QDC,and four specific OTUs could be used as QDC biomarkers to assist in clinical diagnosis.展开更多
Objective:To identify potential serum protein candidates involved in linking the traditional Chinese medicine(TCM)-defined qi deficiency constitution(QDC)to Pi-qi-deficiency syndrome(PQDS)of chronic superficial gastri...Objective:To identify potential serum protein candidates involved in linking the traditional Chinese medicine(TCM)-defined qi deficiency constitution(QDC)to Pi-qi-deficiency syndrome(PQDS)of chronic superficial gastritis(CSG).Methods:Using participants with the TCM-defined balanced constitution as a control population,labelfree quantitative proteomics was adopted to identify differentially expressed proteins(DEPs)in serum samples from two case populations:case population 1(participants with QDC)and case population 2(patients with PQDS of CSG).The DEPs discovered in both case populations were analyzed to identify common DEPs as potential candidates for proteins involved in the link between QDC and PQDS.Based on Kyoto Encyclopedia of Genes and Genomes pathway(KEGG)and Gene Ontology(GO)enrichment analysis and analysis of proteineprotein interaction networks,we evaluated the possible functions of these potential serum candidates.Results:We discovered 24 and 28 proteins that were differentially expressed in case populations 1 and 2,respectively,compared with the control population.Hierarchical clustering analysis showed that the expression profile of DEPs of individuals from the same population clustered well,while those from different populations were segregated.Furthermore,GO analysis revealed the 10 DEPs that were common to both case populations to be mainly associated with negative regulation of cellular metabolic and immune system processes while KEGG analysis indicated these proteins to be associated with complement and coagulation cascades and peroxisome proliferator-activated receptor signaling.Notably,serum levels of C4b-binding protein beta chain,glycosylphosphatidylinositol-specific phospholipase D1 and MS-F1 light chain variable region proteins were notably higher in the two case populations compared with the control,particularly in the case of CSG with PQDS.Conclusion:The results presented here provide new insights into the molecular mechanisms underlying development of PQDS of CSG from QDC,and suggest candidate serum biomarkers for future application in integrative medicine.展开更多
Objective:To screen for blood leukocyte microRNA(miRNA)biomarkers responsible for the association between the traditional Chinese medicine(TCM)qi deficiency constitution(QDC)and the Pi-qi-deficiency syndrome(PQDS)of c...Objective:To screen for blood leukocyte microRNA(miRNA)biomarkers responsible for the association between the traditional Chinese medicine(TCM)qi deficiency constitution(QDC)and the Pi-qi-deficiency syndrome(PQDS)of chronic superficial gastritis(CSG).Methods:Peripheral blood leukocytes were separated from people of two TCM constitutions(balance and qi deficiency)and from CSG patients with PQDS.Total RNA was isolated from the leukocytes and subjected to subsequent high-throughput miRNA sequencing to identify the miRNAs that are specifically and highly expressed in persons of QDC and CSG patients with PQDS.In addition,the target genes of the associated miRNAs were predicted.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway-based enrichment analyses of these target genes were performed to further evaluate the associated miRNA candidates as potential biomarkers responsible for the association between QDC and PQDS of CSG.Results:Compared with the control group with a balance constitution(P<.05,fold change>1.5 or<0.5),31 and 38 differentially expressed miRNAs were found in persons of QDC and CSG patients with PQDS,respectively.In particular,hsa-miR-145-5p and hsa-miR-146a-3p were highly expressed in both the persons of QDC and CSG patients with PQDS.GO analysis of the target genes of the two common miRNAs showed that they were mainly associated with functions related to synthesis and metabolism,such as cellular nitrogen compound metabolic processes,biosynthetic processes,cellular protein modification processes,and cellular component assembly.KEGG analysis identified the common pathways enriched among the target genes,including the Hippo signaling pathway and the transcriptional misregulation pathway.The common target genes of the two miRNAs seemed to be associated with the spliceosome pathway and the RNA degradation pathway.Conclusion:Hsa-miR-145-5p and hsa-miR-146a-3p may serve as candidate biomarkers responsible for the association between QDC and PQDS of CSG.展开更多
Understanding how gene expression is translated to phenotype is central to modern molecular biology,and the success is contingent on the intrinsic tractability of the specific traits under examination.However, an a pr...Understanding how gene expression is translated to phenotype is central to modern molecular biology,and the success is contingent on the intrinsic tractability of the specific traits under examination.However, an a priori estimate of trait tractability from the perspective of gene expression is unavailable.Motivated by the concept of entropy in a thermodynamic system, we here propose such an estimate(S_T)by gauging the number(N) of expression states that underlie the same trait abnormality, with large S_T corresponding to large N. By analyzing over 200 yeast morphological traits, we show that S_T predicts the tractability of an expression-trait relationship. We further show that S_T is ultimately determined by natural selection, which builds co-regulated gene modules to minimize possible expression states.展开更多
Objective:To clarify the structural and functional characteristics of the gut microbiota in individuals with qi stagnation constitution(QSC)and identify the potential biomarkers related to QSC.Methods:This cross-secti...Objective:To clarify the structural and functional characteristics of the gut microbiota in individuals with qi stagnation constitution(QSC)and identify the potential biomarkers related to QSC.Methods:This cross-sectional study involved individuals with QSC and balanced constitution(BC)confirmed by TCM clinicians.The clinical features were recorded,and fecal samples were collected for 16S rDNA sequencing.The structure of the fecal-associated microbiome(FAM)was described by the alpha-diversity indexes,beta-distances,and relative abundances of dominant taxa.The differences in FAM distribution were analyzed by the Wilcoxon rank-sum test,MetagenomeSeq,and LEfSe analysis.The 16S rDNA gene sequences were assigned to the KEGG dataset to predict the functional information of bacterial metabolic pathways by using PICRUSt.Differences in functional pathways between groups were assessed with the Wilcoxon rank-sum test.The ROC curve based on specific operational taxonomic units(OTUs)was constructed,and the AUC was calculated.Results:Twenty-two individuals with BC and 8 with QSC were recruited.Significant differences between the two groups were found in body mass index,health status,and low-density lipoprotein,etc.There was no significant difference in the alpha-diversity index.PCoA showed no evident clustering of bacterial communities according to constitutions.Bacteroidaceae,Lachnospiraceae,Ruminococcaceae,and Prevotellaceae were the four common bacteria with high abundances.Notably,MetagenomeSeq,LEfSe analysis,and the Wilcoxon rank-sum test identified significantly different distributions of 66,42,and 36 OTUs,respectively.Predictive function analysis showed that 13 metabolic pathways were significantly differentially distributed,including those related to fatty acid synthesis.Five specific OTUs were selected as potential biomarkers of a QSC,and the AUC was 0.94.Conclusion:Individuals with QSC have unique FAM structure and related functional characteristics.Five specific OTUs were identified to serve as potentially effective biomarkers related to QSC.展开更多
The authors regret<In the version of this article initially published,there was an unintended error that the first photo in the first row of Figure 5C was wrongly adopted.The corrected Fig.5C is shown here.We are s...The authors regret<In the version of this article initially published,there was an unintended error that the first photo in the first row of Figure 5C was wrongly adopted.The corrected Fig.5C is shown here.We are sorry for the inconvenience caused by this error.展开更多
The golden mushroom(Floccularia luteovirens),a nutritionally valuable edible fungus endemic to the Qinghai-Tibet Plateau,exhibits significant quality heterogeneity across different geographical origins.This study empl...The golden mushroom(Floccularia luteovirens),a nutritionally valuable edible fungus endemic to the Qinghai-Tibet Plateau,exhibits significant quality heterogeneity across different geographical origins.This study employed ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry(UPLC-Q/ToFMS)-based metabolomics integrated with multivariate analyses to authenticate specimens from Ganzi(Sichuan,SC),Haibei(Qinghai,QH),and Naqu(Xizang,XZ).Principal component analysis(PCA;Q^(2)>0.98,R2Y>0.99)and partial least squares discriminant analysis(PLS-DA;Q^(2)>0.98,R2Y>0.98)confirmed robust geographical discrimination,identifying 52 lipid-dominated markers as critical discriminators.Region-specific markers included triacylglycerols(TG)(54:6),phosphatidylinositols(PI)(18:2/18:2),phosphatidic acids(PA)(18:2/18:2),diacylglycerols(DG)(33:3),and bioactive compounds(e.g.,N-linoleoyl-γ-aminobutyric acid,epoxymurin A)in XZ;phosphatidylcholines(PC)(16:0/18:2),lysophosphatidylserines(LysoPS)(16:0),ergocalciferol,and hydroxylated fatty acids((9Z,12Z)-15,16-dihydroxyoctadeca-9,12-dienoic acid(dihydroxyoctadecadienoic acid,DiHODE),2-β-methoxy-1-α,25-dihydroxyvitamin D3)in QH;and cerebrosides,ceramides(Cer)(t20:0/22:0(2OH)),and saturated lipid derivatives(PA)(24:0/24:0)in SC.Nutritional profiling revealed that XZ had the highest unsaturated fatty acid content(49.94%)and hydroxyl radical scavenging capacity(18.34%/mg),whereas QH exhibited superior 2,2-diphenyl-1-picrylhydrazyl(DPPH)inhibition(87.62%/mg).Lipidomics analysis indicated that XZ’s lipid profile was enriched in polyunsaturated species(e.g.,9-hexadecenoic acid,tricosanoic acid),while QH was characterized by omega-3 fatty acids(9,12,15-octadecatrienoic acid)and SC by medium-chain fatty acids(decanoic acid).Key biochemical differences included peak crude and soluble protein levels in XZ(433.5 mg/g and 83.96 mg/g,respectively),whereas QH exhibited the highest free amino acid content(37.58 mg/g).Hydrolyzed amino acid composition varied by region,with SC displaying the lowest leucine(Leu)and alanine(Ala)concentrations.In terms of polysaccharide and polyphenol contents,SC contained the highest polysaccharide levels(116.72 mg/g),whereas QH had the highest polyphenol content(3.64 mg/g).Antioxidant assays further validated origin-dependent bioactivity,with XZ exhibiting the strongest hydroxyl radical scavenging activity,while SC displayed the lowest DPPH/ABTS activities(73.91%/mg;0.2 nM trolox/mg)and FRAP values(0.31 mM FeSO4/mg).This metabolomics-driven framework establishes a reliable tool for geographical authentication,supporting quality control and the sustainable utilization of golden mushroom resources in functional food industries.展开更多
To explore whether the metabolic state reprogramming approach may be used to explore previously unknown metabolic pathways that contribute to antibiotic resistance,especially those that have been neglected in previous...To explore whether the metabolic state reprogramming approach may be used to explore previously unknown metabolic pathways that contribute to antibiotic resistance,especially those that have been neglected in previous studies,pyruvate reprogramming was performed to reverse the resistance of multidrug-resistant Edwardsiella tarda.Surprisingly,we identified a pyruvate-regulated glutathione system that occurs by boosting glycine,serine,and threonine metabolism.Moreover,cysteine and methionine metabolism played a key role in this reversal.This process involved pyruvate-depressed glutathione and pyruvate-promoted glutathione oxidation,which was attributed to the elevated glutathione peroxidase and depressed glutathione reductase that was inhibited by glycine.This regulation inhibited reactive oxygen species(ROS)degradation and thereby elevated ROS to eliminate E.tarda.Loss of metB,gpx,and gor of the metabolic pathways increased and decreased resistance,respectively,both in vitro and in vivo,thereby supporting the hypothesis of a pyruvate–cysteine–glutathione system/glycine–ROS metabolic pathway.The role of this metabolic pathway in drug resistance and reprogramming reversal was demonstrated in laboratory-evolved gentamicin-resistant E.tarda and other clinically isolated multidrug-and carbapenem-resistant pathogens.Thus,we reveal a less studied antibiotic resistance metabolic pathway along with the mechanisms involved in its reversal.展开更多
Two types of Hepialus larvae with different diets were distinguished in the Sejila Mountain,Tibetan Plateau based on the stable carbon isotope data of the host Hepialus larva of Cordyceps sinensis and its closely adja...Two types of Hepialus larvae with different diets were distinguished in the Sejila Mountain,Tibetan Plateau based on the stable carbon isotope data of the host Hepialus larva of Cordyceps sinensis and its closely adjacent tender plant roots and humus fractions.Type I is the larva chiefly fed by soil humus,and characterized by the δ 13C values of -22.6‰ to-23.4‰,and more than -23.4‰ in its heads.Type II is the larva chiefly fed by tender plant roots,and characterized by the δ 13C values of-24.6‰ to -27.6‰,and less than -24.6‰ in its heads.Our result has exceeded the traditional understanding that their food sources only come from the tender plant roots,and may provide evidence for choosing cheap and high-quality foods and further establishing artificial habitats in their large-scale reproduction.展开更多
Dear Editor, Fungal infection involves the invasion of tissues by one or more species of fungi, and this is a serious problem in both medical settings and agriculture [Brown et al., 2012]. Thus, the development of eff...Dear Editor, Fungal infection involves the invasion of tissues by one or more species of fungi, and this is a serious problem in both medical settings and agriculture [Brown et al., 2012]. Thus, the development of efficient strategies for management of these infections is urgently needed [Rodriguez-Martfn et al., 2010]. Recently, a number of antifungal proteins have been reported, including AFP from Aspergillus giganteus, PAF from Penicillium chrysogenum, NAF from Penicillium nalviogense, and AnAFP from Aspergillus niger [Marx et al., 2008; Geisen 2000]. These proteins have demonstrated antifungal activity against opportunistic plant and animal pathogens, such as Fusanum sp., Botrytis sp., and Asper- gillus sp. [Meyer, 2008]. We have previously characterized an antifungal protein （PcPAF） from the culture supernatant of the fungal strain Penicillium citrinum W1, which was isolated from sediment obtained from the Southwest Indian Ocean. PcPAF is thermostable and displays antifungal activity against various pathogenic fungi, including Trichoderma viride, Fusarium oxysporum, Alternaria Iongipes, and Pae- cilomyces variotii [Wen et al., 2014]. Therefore, large-scale production of PcPAF would enable the further drug development of this compound.展开更多
基金This work was supported by the National Natural Science Foundation of China(81430099)International S&T Cooperation Program of China(2014DFA32950).
文摘Objective:Propionibacterium acnes(P.acnes)plays an important role in the development of acne,an inflammatory skin disease with a high-incidence.In this study,we used high-throughput RNA sequencing(RNA-seq)to reveal the anti-inflammatory mechanism of baicalin on P.acnes-induced acne in rabbits.Methods:The Kligman method was used to induce acne in the ears of New Zealand rabbits.The effect of baicalin on the acne model was evaluated by the number of acne lesions and hematoxylin and eosin(H&E)staining of acne tissues.Enzyme-linked immunoabsorbent assay was used to measure the protein expression levels of tumor necrosis factor a(TNFA),interleukin-1 b(IL1B),IL6,and IL8 in the serum of rabbits.RNA-seq was performed to investigate the mechanism of anti-inflammatory activities of baicalin on acne.Immunohistochemical analysis and Western blot were used to validate the expression levels of related proteins in acne tissues.Results:Baicalin treatment significantly reduced the number of acne lesions and lesions of the ear as well as levels of serum inflammatory cytokines.RNA-seq data showed that baicalin treatment globally suppressed inflammation,especially the TNF signaling pathway and Staphylococcus aureus infection pathway,in the rabbit acne model.Conclusion: Baicalin effectively ameliorates P. acnes-induced acne in rabbits by suppressingthe inflammatory response in rabbits.
基金the National Natural Science Foundation of China(81430099 and 31500704)International Science&Technology Cooperation Program of China(2014DFA32950)Research program from Beijing University of Chinese Medicine(1000041510049,BUCM-2019-JCRC006 and 2019-JYB-TD013).
文摘Objective:To explore the structural and functional characteristics of the fecal-associated microbiome(FAM)in a traditional Chinese medicine(TCM)qi-deficiency constitution(QDC)by comparing with balanced constitution(BC)and screen the related biomarkers.Methods:In this cross-sectional study,the TCM constitutions of subjects were determined based on published the Classification and Determination of constitution in TCM and further confirmed by a TCM clinician.Clinical characteristics were recorded,and fecal samples were collected for 16S rDNA sequencing using the Illumina Miseq platform.The FAM structure was described using alpha-diversity indexes,beta-diversity indexes,and the relative abundances of the dominant taxa.Differences in the FAM distribution and function were analyzed with a Wilcoxon rank-sum test,MetagenomeSeq,and LEfSe analysis,after which a receiver operating characteristic curve based on the specific operational taxonomic units(OTUs)was constructed to calculate the area under the curve.Results:Our study population was composed of 22 BCs and 9 QDCs.There were no significant differences between the two groups in the distribution of clinical characteristics or alpha-diversity indexes,except for the sweets preference and blood glucose level.In principal coordinate analysis and partial least squares discriminant analysis,the bacterial communities in the BC group samples and QDC group samples clustered separately.Notably,there were 214 OTUs significantly distributed between groups in the MetagenomeSeq analysis,200 OTUs identified by the Wilcoxon rank-sum test,and 6 OTUs found by the LEfSe analysis.Predicted function analysis revealed that six metabolic pathways were distinctly distributed between the two groups.The area under the curve for the receiver operating characteristic curve based on the four specific OTUs was 0.88.Conclusion:Unique FAM structural and related functional characteristics are displayed in individuals with a QDC,and four specific OTUs could be used as QDC biomarkers to assist in clinical diagnosis.
基金This study was supported by the National Natural Science Foundation of China(81430099,81300016)Projects of International Cooperation and Exchanges(2014DFA32950).
文摘Objective:To identify potential serum protein candidates involved in linking the traditional Chinese medicine(TCM)-defined qi deficiency constitution(QDC)to Pi-qi-deficiency syndrome(PQDS)of chronic superficial gastritis(CSG).Methods:Using participants with the TCM-defined balanced constitution as a control population,labelfree quantitative proteomics was adopted to identify differentially expressed proteins(DEPs)in serum samples from two case populations:case population 1(participants with QDC)and case population 2(patients with PQDS of CSG).The DEPs discovered in both case populations were analyzed to identify common DEPs as potential candidates for proteins involved in the link between QDC and PQDS.Based on Kyoto Encyclopedia of Genes and Genomes pathway(KEGG)and Gene Ontology(GO)enrichment analysis and analysis of proteineprotein interaction networks,we evaluated the possible functions of these potential serum candidates.Results:We discovered 24 and 28 proteins that were differentially expressed in case populations 1 and 2,respectively,compared with the control population.Hierarchical clustering analysis showed that the expression profile of DEPs of individuals from the same population clustered well,while those from different populations were segregated.Furthermore,GO analysis revealed the 10 DEPs that were common to both case populations to be mainly associated with negative regulation of cellular metabolic and immune system processes while KEGG analysis indicated these proteins to be associated with complement and coagulation cascades and peroxisome proliferator-activated receptor signaling.Notably,serum levels of C4b-binding protein beta chain,glycosylphosphatidylinositol-specific phospholipase D1 and MS-F1 light chain variable region proteins were notably higher in the two case populations compared with the control,particularly in the case of CSG with PQDS.Conclusion:The results presented here provide new insights into the molecular mechanisms underlying development of PQDS of CSG from QDC,and suggest candidate serum biomarkers for future application in integrative medicine.
基金the National Natural Science Foundation of China(81430099,81300016&31500704)Projects of International Cooperation and Exchanges(2014DFA32950).
文摘Objective:To screen for blood leukocyte microRNA(miRNA)biomarkers responsible for the association between the traditional Chinese medicine(TCM)qi deficiency constitution(QDC)and the Pi-qi-deficiency syndrome(PQDS)of chronic superficial gastritis(CSG).Methods:Peripheral blood leukocytes were separated from people of two TCM constitutions(balance and qi deficiency)and from CSG patients with PQDS.Total RNA was isolated from the leukocytes and subjected to subsequent high-throughput miRNA sequencing to identify the miRNAs that are specifically and highly expressed in persons of QDC and CSG patients with PQDS.In addition,the target genes of the associated miRNAs were predicted.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway-based enrichment analyses of these target genes were performed to further evaluate the associated miRNA candidates as potential biomarkers responsible for the association between QDC and PQDS of CSG.Results:Compared with the control group with a balance constitution(P<.05,fold change>1.5 or<0.5),31 and 38 differentially expressed miRNAs were found in persons of QDC and CSG patients with PQDS,respectively.In particular,hsa-miR-145-5p and hsa-miR-146a-3p were highly expressed in both the persons of QDC and CSG patients with PQDS.GO analysis of the target genes of the two common miRNAs showed that they were mainly associated with functions related to synthesis and metabolism,such as cellular nitrogen compound metabolic processes,biosynthetic processes,cellular protein modification processes,and cellular component assembly.KEGG analysis identified the common pathways enriched among the target genes,including the Hippo signaling pathway and the transcriptional misregulation pathway.The common target genes of the two miRNAs seemed to be associated with the spliceosome pathway and the RNA degradation pathway.Conclusion:Hsa-miR-145-5p and hsa-miR-146a-3p may serve as candidate biomarkers responsible for the association between QDC and PQDS of CSG.
基金supported by research grants from National Natural Science Foundation of China (Nos. 31630042 and 91731302)
文摘Understanding how gene expression is translated to phenotype is central to modern molecular biology,and the success is contingent on the intrinsic tractability of the specific traits under examination.However, an a priori estimate of trait tractability from the perspective of gene expression is unavailable.Motivated by the concept of entropy in a thermodynamic system, we here propose such an estimate(S_T)by gauging the number(N) of expression states that underlie the same trait abnormality, with large S_T corresponding to large N. By analyzing over 200 yeast morphological traits, we show that S_T predicts the tractability of an expression-trait relationship. We further show that S_T is ultimately determined by natural selection, which builds co-regulated gene modules to minimize possible expression states.
基金This study was supported by the National Key Research and Development Project(Ministry of Science and Technology,China,grant ID:2019YFC1710104)National Natural Science Foundation of China(grant IDs:8200152760 and 81430099)Research Program from Beijing University of Chinese Medicine(grant IDs:1000041510049,2019-JYB-TD013 and BUCM-2019-JCRC006).
文摘Objective:To clarify the structural and functional characteristics of the gut microbiota in individuals with qi stagnation constitution(QSC)and identify the potential biomarkers related to QSC.Methods:This cross-sectional study involved individuals with QSC and balanced constitution(BC)confirmed by TCM clinicians.The clinical features were recorded,and fecal samples were collected for 16S rDNA sequencing.The structure of the fecal-associated microbiome(FAM)was described by the alpha-diversity indexes,beta-distances,and relative abundances of dominant taxa.The differences in FAM distribution were analyzed by the Wilcoxon rank-sum test,MetagenomeSeq,and LEfSe analysis.The 16S rDNA gene sequences were assigned to the KEGG dataset to predict the functional information of bacterial metabolic pathways by using PICRUSt.Differences in functional pathways between groups were assessed with the Wilcoxon rank-sum test.The ROC curve based on specific operational taxonomic units(OTUs)was constructed,and the AUC was calculated.Results:Twenty-two individuals with BC and 8 with QSC were recruited.Significant differences between the two groups were found in body mass index,health status,and low-density lipoprotein,etc.There was no significant difference in the alpha-diversity index.PCoA showed no evident clustering of bacterial communities according to constitutions.Bacteroidaceae,Lachnospiraceae,Ruminococcaceae,and Prevotellaceae were the four common bacteria with high abundances.Notably,MetagenomeSeq,LEfSe analysis,and the Wilcoxon rank-sum test identified significantly different distributions of 66,42,and 36 OTUs,respectively.Predictive function analysis showed that 13 metabolic pathways were significantly differentially distributed,including those related to fatty acid synthesis.Five specific OTUs were selected as potential biomarkers of a QSC,and the AUC was 0.94.Conclusion:Individuals with QSC have unique FAM structure and related functional characteristics.Five specific OTUs were identified to serve as potentially effective biomarkers related to QSC.
文摘The authors regret<In the version of this article initially published,there was an unintended error that the first photo in the first row of Figure 5C was wrongly adopted.The corrected Fig.5C is shown here.We are sorry for the inconvenience caused by this error.
基金supported by Young Scholar Innovation Project from Xizang Autonomous Region(QC 2015-76,QCZ 2016-83)Program for Scientific and Technological Innovation Team Construction in Universities of Xizang Autonomous Region(Xizang Vocational Technical College 2014-2017).
文摘The golden mushroom(Floccularia luteovirens),a nutritionally valuable edible fungus endemic to the Qinghai-Tibet Plateau,exhibits significant quality heterogeneity across different geographical origins.This study employed ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry(UPLC-Q/ToFMS)-based metabolomics integrated with multivariate analyses to authenticate specimens from Ganzi(Sichuan,SC),Haibei(Qinghai,QH),and Naqu(Xizang,XZ).Principal component analysis(PCA;Q^(2)>0.98,R2Y>0.99)and partial least squares discriminant analysis(PLS-DA;Q^(2)>0.98,R2Y>0.98)confirmed robust geographical discrimination,identifying 52 lipid-dominated markers as critical discriminators.Region-specific markers included triacylglycerols(TG)(54:6),phosphatidylinositols(PI)(18:2/18:2),phosphatidic acids(PA)(18:2/18:2),diacylglycerols(DG)(33:3),and bioactive compounds(e.g.,N-linoleoyl-γ-aminobutyric acid,epoxymurin A)in XZ;phosphatidylcholines(PC)(16:0/18:2),lysophosphatidylserines(LysoPS)(16:0),ergocalciferol,and hydroxylated fatty acids((9Z,12Z)-15,16-dihydroxyoctadeca-9,12-dienoic acid(dihydroxyoctadecadienoic acid,DiHODE),2-β-methoxy-1-α,25-dihydroxyvitamin D3)in QH;and cerebrosides,ceramides(Cer)(t20:0/22:0(2OH)),and saturated lipid derivatives(PA)(24:0/24:0)in SC.Nutritional profiling revealed that XZ had the highest unsaturated fatty acid content(49.94%)and hydroxyl radical scavenging capacity(18.34%/mg),whereas QH exhibited superior 2,2-diphenyl-1-picrylhydrazyl(DPPH)inhibition(87.62%/mg).Lipidomics analysis indicated that XZ’s lipid profile was enriched in polyunsaturated species(e.g.,9-hexadecenoic acid,tricosanoic acid),while QH was characterized by omega-3 fatty acids(9,12,15-octadecatrienoic acid)and SC by medium-chain fatty acids(decanoic acid).Key biochemical differences included peak crude and soluble protein levels in XZ(433.5 mg/g and 83.96 mg/g,respectively),whereas QH exhibited the highest free amino acid content(37.58 mg/g).Hydrolyzed amino acid composition varied by region,with SC displaying the lowest leucine(Leu)and alanine(Ala)concentrations.In terms of polysaccharide and polyphenol contents,SC contained the highest polysaccharide levels(116.72 mg/g),whereas QH had the highest polyphenol content(3.64 mg/g).Antioxidant assays further validated origin-dependent bioactivity,with XZ exhibiting the strongest hydroxyl radical scavenging activity,while SC displayed the lowest DPPH/ABTS activities(73.91%/mg;0.2 nM trolox/mg)and FRAP values(0.31 mM FeSO4/mg).This metabolomics-driven framework establishes a reliable tool for geographical authentication,supporting quality control and the sustainable utilization of golden mushroom resources in functional food industries.
基金supported by the National Key Research and Development Program of China(grant number 2023YFD1800104)National Natural Science Foundation of China(grant numbers 32273177 and 42276125)+2 种基金Fundamental Research Funds for the Central Universities,Sun Yat-sen University(grant number 24lgzy004)Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)(grant number 311020006)Science and Technology Planning Project of Guangdong Province(no.2023B1212060028).
文摘To explore whether the metabolic state reprogramming approach may be used to explore previously unknown metabolic pathways that contribute to antibiotic resistance,especially those that have been neglected in previous studies,pyruvate reprogramming was performed to reverse the resistance of multidrug-resistant Edwardsiella tarda.Surprisingly,we identified a pyruvate-regulated glutathione system that occurs by boosting glycine,serine,and threonine metabolism.Moreover,cysteine and methionine metabolism played a key role in this reversal.This process involved pyruvate-depressed glutathione and pyruvate-promoted glutathione oxidation,which was attributed to the elevated glutathione peroxidase and depressed glutathione reductase that was inhibited by glycine.This regulation inhibited reactive oxygen species(ROS)degradation and thereby elevated ROS to eliminate E.tarda.Loss of metB,gpx,and gor of the metabolic pathways increased and decreased resistance,respectively,both in vitro and in vivo,thereby supporting the hypothesis of a pyruvate–cysteine–glutathione system/glycine–ROS metabolic pathway.The role of this metabolic pathway in drug resistance and reprogramming reversal was demonstrated in laboratory-evolved gentamicin-resistant E.tarda and other clinically isolated multidrug-and carbapenem-resistant pathogens.Thus,we reveal a less studied antibiotic resistance metabolic pathway along with the mechanisms involved in its reversal.
基金Supported by the National Key Technology R & D Program (Grant No. 2007BAI32B05)
文摘Two types of Hepialus larvae with different diets were distinguished in the Sejila Mountain,Tibetan Plateau based on the stable carbon isotope data of the host Hepialus larva of Cordyceps sinensis and its closely adjacent tender plant roots and humus fractions.Type I is the larva chiefly fed by soil humus,and characterized by the δ 13C values of -22.6‰ to-23.4‰,and more than -23.4‰ in its heads.Type II is the larva chiefly fed by tender plant roots,and characterized by the δ 13C values of-24.6‰ to -27.6‰,and less than -24.6‰ in its heads.Our result has exceeded the traditional understanding that their food sources only come from the tender plant roots,and may provide evidence for choosing cheap and high-quality foods and further establishing artificial habitats in their large-scale reproduction.
基金the Comra fund Grant （DY125-15-T-07）, the National Natural Science Foundation of China （Grant Nos. 30972279 and 40976080）, and the National Basic Research Program （973 Program） （No. 2015CB755903）.
文摘Dear Editor, Fungal infection involves the invasion of tissues by one or more species of fungi, and this is a serious problem in both medical settings and agriculture [Brown et al., 2012]. Thus, the development of efficient strategies for management of these infections is urgently needed [Rodriguez-Martfn et al., 2010]. Recently, a number of antifungal proteins have been reported, including AFP from Aspergillus giganteus, PAF from Penicillium chrysogenum, NAF from Penicillium nalviogense, and AnAFP from Aspergillus niger [Marx et al., 2008; Geisen 2000]. These proteins have demonstrated antifungal activity against opportunistic plant and animal pathogens, such as Fusanum sp., Botrytis sp., and Asper- gillus sp. [Meyer, 2008]. We have previously characterized an antifungal protein （PcPAF） from the culture supernatant of the fungal strain Penicillium citrinum W1, which was isolated from sediment obtained from the Southwest Indian Ocean. PcPAF is thermostable and displays antifungal activity against various pathogenic fungi, including Trichoderma viride, Fusarium oxysporum, Alternaria Iongipes, and Pae- cilomyces variotii [Wen et al., 2014]. Therefore, large-scale production of PcPAF would enable the further drug development of this compound.
