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
【目的】探明贵州黑山羊(Guizhou Black Goats)干扰素-epsilon基因结构与功能,为羊传染病的防治及开发新型抗病毒药物提供理论依据。【方法】提取贵州黑山羊肝脏总RNA,通过RT-PCR扩增贵州黑山羊IFN-ε基因(GZHSY-IFN-ε)并测序,采用生...【目的】探明贵州黑山羊(Guizhou Black Goats)干扰素-epsilon基因结构与功能,为羊传染病的防治及开发新型抗病毒药物提供理论依据。【方法】提取贵州黑山羊肝脏总RNA,通过RT-PCR扩增贵州黑山羊IFN-ε基因(GZHSY-IFN-ε)并测序,采用生物信息学分析基因序列和预测蛋白结构。【结果】GZHSY-IFN-ε基因编码区长度为582 bp,编码194个氨基酸,贵州黑山羊与山羊、绵羊、羚牛、大羚羊IFN-ε的核苷酸序列同源性依次为99.7%、99.1%、99.1%、97.9%,氨基酸序列同源性依次为99.0%、97.9%、97.9%、94.8%;重组表达质粒p ET-28a-IFN-ε的双酶切结果正确;阳性菌株经诱导后,重组蛋白大小约39 ku,以可溶性蛋白形式表达,与抗His标签鼠单克隆抗体发生特异性反应;IFN-ε蛋白为不稳定亲水蛋白,有信号肽,无跨膜结构,亚细胞定位主要为胞外。IFN-ε蛋白存在16个磷酸化位点,无糖基化位点。二级结构主要为α-螺旋,与IL10RB、IFNAR^(2)、IFNAR1等蛋白存在相互作用。【结论】首次成功克隆贵州黑山羊IFN-ε基因序列,构建pET-28a-IFN-ε重组质粒并成功表达,具有良好的免疫原性。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
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 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
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
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
Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challengin...Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challenging due to its large genome size and high proportion of repetitive sequences.Allele-specific expression(ASE)plays a key role in regulating plant development and evolution,yet research on ASE in coconut is limited(Shao et al.,2019;Li et al.,2021;Zhang et al.,2021;Hu et al.,2022).Among phenotypic traits,fruit color is especially important as an indicator of maturity,guiding harvest timing and post-harvest processes(Kapoor et al.,2022).While prior studies have explored various coconut traits such as salt tolerance,fiber content,and plant height(Wang et al.,2021;Yang et al.,2021),investigations into ASE and fruit color remain scarce.展开更多
In order to investigate the correlation between the expression of the apoptotic regulatory proteins (Fas, Bcl 2) in peripheral blood lymphocytes (PBLC) and the level of IFN γ and IL 4 in serum of the patients with...In order to investigate the correlation between the expression of the apoptotic regulatory proteins (Fas, Bcl 2) in peripheral blood lymphocytes (PBLC) and the level of IFN γ and IL 4 in serum of the patients with condyloma acuminata (CA) in the immune pathogenesis of CA, indirect immunofluorescence labeling method of flow cytometer and solid sandwich ELISA method were performed for detecting the expression of Fas, Bcl 2 in PBLC and the level of IFN γ and IL 4 in serum of 60 cases of CA. The results showed the expression level of Fas in PBLC of CA was significantly higher than in the normal control group, but the expression level of Bcl 2 was significantly lower (both P< 0.01). The level of IFN γ in serum of CA was significantly lower than in the normal control group ( P< 0.01), but IL 4 was significantly lower (both P< 0.01). The expression of Fas in PBLC had a negative correlation with the level of IFN γ in serum of patients with CA, but had a positive correlation with the level of IL 4; The expression of Bcl 2 had a positive correlation with the level of IFN γ, but had a negative correlation with the level of IL 4. All the correlation coefficients had significant differerce by t test ( P< 0.01). It was suggested abnormal apoptosis in PBLC, the suppressed secretion of the THl associated cytokines (eg: IFN γ) and the increased secretion of the TH2 asssociated cytokines (eg: IL 4) existed in the patients with CA and might play an important role in the immune pathogenesis of CA.展开更多
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 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.
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.
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.
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 Central Public-interest Scientific Institution Basal Research Fund(CATAS-Nos.1630152023007,1630152023011,1630152023012,1630152023013)the National Natural Science Foundation of China(Grant No.32071805).
文摘Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challenging due to its large genome size and high proportion of repetitive sequences.Allele-specific expression(ASE)plays a key role in regulating plant development and evolution,yet research on ASE in coconut is limited(Shao et al.,2019;Li et al.,2021;Zhang et al.,2021;Hu et al.,2022).Among phenotypic traits,fruit color is especially important as an indicator of maturity,guiding harvest timing and post-harvest processes(Kapoor et al.,2022).While prior studies have explored various coconut traits such as salt tolerance,fiber content,and plant height(Wang et al.,2021;Yang et al.,2021),investigations into ASE and fruit color remain scarce.
文摘In order to investigate the correlation between the expression of the apoptotic regulatory proteins (Fas, Bcl 2) in peripheral blood lymphocytes (PBLC) and the level of IFN γ and IL 4 in serum of the patients with condyloma acuminata (CA) in the immune pathogenesis of CA, indirect immunofluorescence labeling method of flow cytometer and solid sandwich ELISA method were performed for detecting the expression of Fas, Bcl 2 in PBLC and the level of IFN γ and IL 4 in serum of 60 cases of CA. The results showed the expression level of Fas in PBLC of CA was significantly higher than in the normal control group, but the expression level of Bcl 2 was significantly lower (both P< 0.01). The level of IFN γ in serum of CA was significantly lower than in the normal control group ( P< 0.01), but IL 4 was significantly lower (both P< 0.01). The expression of Fas in PBLC had a negative correlation with the level of IFN γ in serum of patients with CA, but had a positive correlation with the level of IL 4; The expression of Bcl 2 had a positive correlation with the level of IFN γ, but had a negative correlation with the level of IL 4. All the correlation coefficients had significant differerce by t test ( P< 0.01). It was suggested abnormal apoptosis in PBLC, the suppressed secretion of the THl associated cytokines (eg: IFN γ) and the increased secretion of the TH2 asssociated cytokines (eg: IL 4) existed in the patients with CA and might play an important role in the immune pathogenesis of CA.
