Background Methamphetamine(METH)addiction causes a huge burden on society.The prefrontal cortex(PFC),associated with emotion and cognitive behaviours,is also involved in addiction neurocircuitry.Although bulk RNA sequ...Background Methamphetamine(METH)addiction causes a huge burden on society.The prefrontal cortex(PFC),associated with emotion and cognitive behaviours,is also involved in addiction neurocircuitry.Although bulk RNA sequencing has shown METH-induced gene alterations in the mouse PFC,the impact on different cell types remains unknown.Aims To clarify the effects of METH treatment on different cell types of the PFC and the potential pathways involved in METH-related disorders.Methods We performed single-nucleus RNA sequencing(snRNA-seq)to examine the transcriptomes of 20465 nuclei isolated from the PFC of chronic METH-treated and control mice.Main cell types and differentially expressed genes(DEGs)were identified and confirmed by RNA fluorescence in situ hybridization(FISH).Results Six main cell types were identified depending on the single-cell nucleus sequencing;of particular interest were the mature oligodendrocytes in the PFC.The DEGs of mature oligodendrocytes were enriched in the myelin sheath,adenosine triphosphate(ATP)metabolic process,mitochondrial function and components,and so on.The messenger RNA levels of Aldoc and Atp5l(FISH)and the protein level of the mitochondrial membrane pore subunit TOM40(immunofluorescence)decreased in the mature oligodendrocytes.Fast blue staining and transmission electron microscopy image indicated myelin damage,and the myelin thickness decreased in METH brains.Conclusions snRNA-seq reveals altered transcriptomes of different cell types in mouse PFC induced by chronic METH treatment,underscoring potential relationships with psychiatric disorders.展开更多
Pigs are important agricultural animals and valuable biomedical models.The intestinal tract is a crucial digestive organ and the largest immune organ.However,the function of pig intestines at single-cell resolution re...Pigs are important agricultural animals and valuable biomedical models.The intestinal tract is a crucial digestive organ and the largest immune organ.However,the function of pig intestines at single-cell resolution remains poorly understood.Here,we created single-nucleus transcriptomic maps of the ileum and cecum for wild boars,Bama Xiang pigs,and Large White pigs,aged 30,42,150,and 730 d.Our atlas revealed 19 major cell types and 58 cellular subtypes,including several previously uncharacterized cellular subtypes,such as EBF1+fibroblasts,TMEM163+macrophages,and neuron subtypes expressing FCAMR.We discovered and confirmed that ileum neurons,rather than cecum neurons,can regulate inflammatory responses,highlighting interactions of neurons with dendritic cells(DCs)and lymphatic endothelial cells(LECs)through the NAMPT-INSR ligand-receptor pair in the ileum.Microbial-derived short-chain fatty acids,such as propionic acid and acetic acid,enhanced plasma cell differentiation and humoral immune responses by upregulating XBP1 and SDC1 expression,thereby endowing wild boars with a stronger immune response than domestic pigs.We identified and validated the enterocyteenriched transcription factors FOXO1 and NR1H4 in wild boars,which contributed to the superior nutrient absorption of wild boars relative to domestic pigs.Furthermore,we comprehensively characterized the postnatal development of wild boar intestinal cells and revealed that plasma cells presented the most pronounced developmental changes.We identified highly conserved cell types and features between pig and human intestines.Overall,our work provides a foundation for improving pig feed conversion and health while also providing a reference for research on human intestinal diseases.展开更多
Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocyt...Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocytes,microglia,and oligodendrocytes in the central nervous system,and satellite glial cells and Schwann cells in the peripheral nervous system.Despite the greater understanding of glial cell types and functional heterogeneity achieved through single-cell and single-nucleus RNA sequencing in animal models,few studies have investigated the transcriptomic profiles of glial cells in the human spinal cord.Here,we used high-throughput single-nucleus RNA sequencing and spatial transcriptomics to map the cellular and molecular heterogeneity of astrocytes,microglia,and oligodendrocytes in the human spinal cord.To explore the conservation and divergence across species,we compared these findings with those from mice.In the human spinal cord,astrocytes,microglia,and oligodendrocytes were each divided into six distinct transcriptomic subclusters.In the mouse spinal cord,astrocytes,microglia,and oligodendrocytes were divided into five,four,and five distinct transcriptomic subclusters,respectively.The comparative results revealed substantial heterogeneity in all glial cell types between humans and mice.Additionally,we detected sex differences in gene expression in human spinal cord glial cells.Specifically,in all astrocyte subtypes,the levels of NEAT1 and CHI3L1 were higher in males than in females,whereas the levels of CST3 were lower in males than in females.In all microglial subtypes,all differentially expressed genes were located on the sex chromosomes.In addition to sex-specific gene differences,the levels of MT-ND4,MT2A,MT-ATP6,MT-CO3,MT-ND2,MT-ND3,and MT-CO_(2) in all spinal cord oligodendrocyte subtypes were higher in females than in males.Collectively,the present dataset extensively characterizes glial cell heterogeneity and offers a valuable resource for exploring the cellular basis of spinal cordrelated illnesses,including chronic pain,amyotrophic lateral sclerosis,and multiple sclerosis.展开更多
For red pear,the anthocyanin content is a crucial factor determining the fruit skin color,which affects consumer preferences.Low overnight temperatures promote anthocyanin accumulation,but the molecular mechanism resp...For red pear,the anthocyanin content is a crucial factor determining the fruit skin color,which affects consumer preferences.Low overnight temperatures promote anthocyanin accumulation,but the molecular mechanism responsible is unclear.In this study,‘Hongzaosu’pear(Pyrus pyrifolia×Pyrus communis)fruit were treated with a low nighttime temperature(LNT,16℃)or a warm nighttime temperature(WNT,26℃),with sampling conducted within two diurnal cycles.The results showed that LNT promoted anthocyanin accumulation in the fruit skin.The structural anthocyanin biosynthetic genes PpCHS,PpF3H,and PpUFGT exhibited a rhythmic increase in expression at night under LNT.To examine the underlying mechanism,RNA sequencing was conducted using pear calli exposed to LNT and WNT for different durations(24,48,72,or 96 h).Transcriptome analysis revealed 285 differentially expressed genes(DEGs)common to all pairwise comparisons of LNT-and WNT-treated calli of‘Clapp's Favorite’(P.communis)at the sampling time points.KEGG pathway and gene ontology enrichment analyses indicated that the common DEGs were enriched in secondary metabolic processes and phenylpropanoid metabolic processes,which are associated with anthocyanin biosynthesis.The transcription factor PpCDF5,which was responsive to LNT,was selected for further study.Dual-luciferase assays showed that PpCDF5 activated the transcription of anthocyanin biosynthetic genes PpMYB10,PpCHS,PpF3H,PpDFR,PpANS,and PpUFGT.The yeast one-hybrid and EMSA assays demonstrated that PpCDF5 directly binds to the PpF3H promoter,which contains an AAAG motif.Overexpression of PpCDF5 in pear calli and transient overexpression in pear fruit both increased anthocyanin accumulation.The results indicate that PpCDF5 is involved in LNT-induced anthocyanin biosynthesis in pear fruit and provide insights into the molecular regulation of commercial fruit coloration.展开更多
Atmospheric carbon dioxide(CO_(2))levels are escalating at an unprecedented rate,leading to the phenomenon of ocean acidification(OA).Parental exposure to acidification has the potential to enhance offspring resilienc...Atmospheric carbon dioxide(CO_(2))levels are escalating at an unprecedented rate,leading to the phenomenon of ocean acidification(OA).Parental exposure to acidification has the potential to enhance offspring resilience through cross-generation plasticity.In this study,we analyzed larval growth and transcriptomic profiles in the Pacific oyster,Crassostrea gigas,a species of significant ecological relevance,under both control and elevated CO_(2)conditions experienced by their parental generation.Our findings indicate that the oyster populations exposed to OA exhibited a higher incidence of abnormalities during the D-shaped larval stage,followed by accelerated growth at the eyed stage.Through a comparative transcriptomic investigation of eyed larvae(25 d after fertilization),we observed that parental exposure to OA substantially influenced the gene expression in the offspring.Genes associated with lipid catabolism and shell formation were notably upregulated in oysters with parental OA exposure,potentially playing a role in cross-generational conditioning and conferring resilience to OA stressors.These results underscore the profound impact of OA on oyster larval development via cross-generational mechanisms and shed light on the molecular underpinnings of cross-generation plasticity.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
Peanut seedlings develop from seeds by hypocotyl elongation and differentiation.However,the intricate gene regulatory networks and molecular crosstalk underlying hypocotyl growth in peanuts remain largely unknown.In t...Peanut seedlings develop from seeds by hypocotyl elongation and differentiation.However,the intricate gene regulatory networks and molecular crosstalk underlying hypocotyl growth in peanuts remain largely unknown.In this study,a single-nucleus gene expression landscape in peanut seedlings was initially developed from diverse tissues,including stems,roots,leaves,and hypocotyls.Core transcription factor interaction networks driving developmental trajectories were identified to decipher hypocotyl cell heterogeneity.Jasmonic acid and cytokinin regulate peanut hypocotyl expansion and differentiation based on the number and size of cortex cells and hormone levels between the hypocotyl at 3 and 7 d after germination.We further demonstrated that AhBHLH143 potentially represses hypocotyl elongation by promoting the JA pathway and inhibiting the cytokinin pathway.The single-nucleus transcriptomic atlas of peanut seedlings reveals new insights into hypocotyl development and provides a valuable resource for future investigations of seedling development.展开更多
BACKGROUND Hemorrhoids,a prevalent chronic condition globally,significantly impact patients'quality of life.While various surgical interventions,such as external stripping and internal ligation,procedure for prola...BACKGROUND Hemorrhoids,a prevalent chronic condition globally,significantly impact patients'quality of life.While various surgical interventions,such as external stripping and internal ligation,procedure for prolapse and hemorrhoids,and tissue selecting technique,are employed for treatment,they are often associated with postoperative complications,including unsatisfactory defecation,bleeding,and anal stenosis.In contrast,Xiaozhiling injection,a traditional Chinese medicine-based therapy,has emerged as a minimally invasive and effective alternative for internal hemorrhoids.This treatment offers distinct advantages,such as reduced dietary restrictions,broad applicability,and minimal induction of systemic inflammatory responses.Additionally,Xiaozhiling injection effectively eliminates hemorrhoid nuclei,prevents local tissue necrosis,preserves anal cushion integrity,and mitigates postoperative complications,including bleeding and prolapse.Despite its clinical efficacy,the molecular mechanisms underlying its therapeutic effects remain poorly understood,warranting further investigation.AIM To investigate the molecular mechanism underlying the therapeutic effect of Xiaozhiling injection in the treatment of internal hemorrhoids.METHODS An internal hemorrhoid model was established in rats,and the rats were randomly divided into a modeling group[control group(CK group)]and a treatment group.One week after injection,Stereo-seq and electron microscopy were used to study the changes in gene expression and subcellular structures in fibroblasts.RESULTS Single-cell sequencing revealed differences in the expression and transcript levels of the genes collagen 3 alpha 1,decorin,and actin alpha 2 in fibroblasts between the CK group and the treatment group.Spatial transcriptome analysis revealed that genes of the sphingosine kinase 1(Sphk1)/sphingosine-1-phosphate(S1P)pathway spatially overlapped with key genes of the transforming growth factor beta 1 pathway,namely,Sphk1,S1P receptor,and transforming growth factor beta 1,in the treatment group.The proportion of fibroblasts was lower in the treatment group than in the CK group,and Xiaozhiling treatment had a significant effect on the proportion of fibroblasts in hemorrhoidal tissue.Immunohistochemistry revealed a significant increase in the expression of a fibroblast marker.Electron microscopy showed that the endoplasmic reticulum of fibroblasts contained a large amount of glycogen,indicating cell activation.Fibroblast activation and the expression of key genes of the Sphk1-S1P pathway could be observed at the injection site,suggesting that after Xiaozhiling intervention,the Sphk1-S1P pathway could be activated to promote fibrosis.CONCLUSION Xiaozhiling injection exerts its therapeutic effects on internal hemorrhoids by promoting collagen synthesis and secretion in fibroblasts.After Xiaozhiling intervention,the Sphk1-S1P pathway can be activated to promote fibrosis.展开更多
Litchi chinensis Sonn.is an important economic fruit tree in tropical and subtropical regions.Regrettably,the efficiency of plant regeneration via somatic embryogenesis in litchi is typically low due to the poor conve...Litchi chinensis Sonn.is an important economic fruit tree in tropical and subtropical regions.Regrettably,the efficiency of plant regeneration via somatic embryogenesis in litchi is typically low due to the poor conversion of embryos to plants.The purpose of this study was to establish a regeneration system via somatic embryogenesis from immature embryos explants in‘Heiye'cultivar of litchi.Our results demonstrated that MS medium supplemented with 2.0 mg L^(-1)2,4-D was optimal for callus induction.For somatic embryo(SE)induction,MS medium containing0.5 g L^(-1) activated charcoal(AC)was the most effective,while the use of zeatin(ZT)and thidiazuron(TDZ)resulted in abnormal somatic embryos.The rooting and regeneration rate of 2.15%and 17.5%,respectively,were achieved using MS medium supplemented with 0.5 g L^(-1) AC.Furthermore,transcriptome analysis was performed on embryogenic callus(EC),globular embryo(GE),and heart embryo(HE)to explore the molecular mechanisms of early somatic embryogenesis.2,587 common differentially expressed genes(DEGs)between EC_vs_GE and EC_vs_HE were identified,and the expression patterns of these common DEGs were separated into twelve major clusters.GO annotation and KEGG pathway analysis revealed that these common DEGs were implicated in plant hormone signal transduction,auxin-activated signaling pathway,and other biological processes.Additionally,differentially expressed transcription factors were identified,and the function of LcBBM2 which is specifically highly expressed during early somatic embryogenesis was verified.Overexpression of LcBBM2 in tomato promotes callus and shoot formation.Therefore,this study can provide a theoretical basis and technical support for genetic breeding improvement of litchi.展开更多
Infection with severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) causes diverse clinical manifestations and tissue injuries in multiple organs.However, cellular and molecular understanding of SARS-CoV-2 infe...Infection with severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) causes diverse clinical manifestations and tissue injuries in multiple organs.However, cellular and molecular understanding of SARS-CoV-2 infection-associated pathology and immune defense features in different organs remains incomplete. Here, we profiled approximately 77 000single-nucleus transcriptomes of the lung, liver,kidney, and cerebral cortex in rhesus macaques(Macaca mulatta) infected with SARS-CoV-2 and healthy controls. Integrated analysis of the multiorgan dataset suggested that the liver harbored the strongest global transcriptional alterations. We observed prominent impairment in lung epithelial cells, especially in AT2 and ciliated cells, and evident signs of fibrosis in fibroblasts. These lung injury characteristics are similar to those reported in patients with coronavirus disease 2019(COVID-19).Furthermore, we found suppressed MHC class I/II molecular activity in the lung, inflammatory response in the liver, and activation of the kynurenine pathway,which induced the development of an immunosuppressive microenvironment. Analysis of the kidney dataset highlighted tropism of tubule cells to SARS-CoV-2, and we found membranous nephropathy(an autoimmune disease) caused by podocyte dysregulation. In addition, we identified the pathological states of astrocytes and oligodendrocytes in the cerebral cortex, providing molecular insights into COVID-19-related neurological implications. Overall, our multi-organ single-nucleus transcriptomic survey of SARS-CoV-2-infected rhesus macaques broadens our understanding of disease features and antiviral immune defects caused by SARS-CoV-2 infection,which may facilitate the development of therapeutic interventions for COVID-19.展开更多
Bamboo was one of the first plants to be cultivated in China and is widely used in industry and daily life.The study of gene function has become an important part of bamboo breeding,whereas quantitative real-time PCR(...Bamboo was one of the first plants to be cultivated in China and is widely used in industry and daily life.The study of gene function has become an important part of bamboo breeding,whereas quantitative real-time PCR(qRT-PCR)is a powerful tool for gene expression analysis.The accuracy of qRT-PCR results largely depends on suitable reference genes.In this study,a transcriptome-wide identification of reference genes was conducted based on 447 transcriptome datasets,comprising 200 tissue samples,107 treated samples,and 140 samples from various moso bamboo(Phyllostachys edulis)forms.A total of 3444,1013,and 3962 stably expressed genes were identified from these three groups,respectively.Functional enrichment analysis revealed significant enrichment of these genes in pathways,including the spliceosome,proteasome,and oxidative phosphorylation.Eight candidate genes(ADPRE,GAPDH,TRX,TUBA,NRP,MBF,UNK,and CAM1),were selected for qRT-PCR validation using 112 samples.To assess their stability,five statistical methods(geNorm,NormFinder,BestKeeper,Delta-Ct,and RefFinder)were employed.The most suitable reference genes were ADPRE and GAPDH for different tissues,GAPDH and CAM1 for different treatments,and GAPDH and TRX for various moso bamboo forms.Overall,ADPRE and GAPDH were the most stable reference genes across all conditions,while TUBA and TRX were the least stable reference genes.In addition,a significant negative correlation was found between the Ct values of RT-qPCR and the log2TPM values from the transcriptome data(Ct=-1.534x+37.221),providing a potential method for estimating gene expression levels.The identified reference genes,particularly ADPRE and GAPDH,provide a robust set of references for gene expression studies in moso bamboo.展开更多
Tomato is an important economic crop all over the world.Volatile flavors in tomato fruit are key factors influencing consumer liking and commercial quality.However,the regulatory mechanism controlling the volatile fla...Tomato is an important economic crop all over the world.Volatile flavors in tomato fruit are key factors influencing consumer liking and commercial quality.However,the regulatory mechanism controlling the volatile flavors of tomatoes is still not clear.Here,we integrated the metabolome and transcriptome of the volatile flavors in tomato fruit to explore the regulatory mechanism of volatile flavor formation,using wild and cultivated tomatoes with significant differences in flavors.A total of 35 volatile flavor compounds were identified,based on the solid phase microextraction-gas chromatography-mass spectrometry(SPME-GC-MS).The content of the volatiles,affecting fruit flavor,significantly increased in the transition from breaker to red ripe fruit stage.Moreover,the total content of the volatiles in wild tomatoes was much higher than that in the cultivated tomatoes.The content variations of all volatile flavors were clustered into 10 groups by hierarchical cluster and Pearson coefficient correlation(PCC)analysis.The fruit transcriptome was also patterned into 10 groups,with significant variations both from the mature green to breaker fruit stage and from the breaker to red ripe fruit stage.Combining the metabolome and the transcriptome of the same developmental stage of fruits by co-expression analysis,we found that the expression level of 1182 genes was highly correlated with the content of volatile flavor compounds,thereby constructing two regulatory pathways of important volatile flavors.One pathway is tetrahydrothiazolidine N-hydroxylase(SlTNH1)-dependent,which is regulated by two transcription factors(TFs)from the bHLH and AP2/ERF families,controlling the synthesis of 2-isobutylthiazole in amino acid metabolism.The other is lipoxygenase(Sl LOX)-dependent,which is regulated by one TF from the HD-Zip family,controlling the synthesis of hexanal and(Z)-2-heptenal in fatty acid metabolism.Dual-luciferase assay confirmed the binding of b HLH and AP2/ERF to their structural genes.The findings of this study provide new insights into volatile flavor formation in tomato fruit,which can be useful for tomato flavor improvement.展开更多
Southern corn rust(SCR)is an airborne fungal disease caused by Puccinia polysora Underw.(P.polysora)that adversely impacts maize quality and yields worldwide.Screening for new elite SCR-resistant maize loci or genes h...Southern corn rust(SCR)is an airborne fungal disease caused by Puccinia polysora Underw.(P.polysora)that adversely impacts maize quality and yields worldwide.Screening for new elite SCR-resistant maize loci or genes has the potential to enhance overall resistance to this pathogen.Using phenotypic SCR resistance-related data collected over two years and three geographical environments,a genome-wide association study was carried out in this work,which eventually identified 91 loci that were substantially correlated with SCR susceptibility.These included 13 loci that were significant in at least three environments and overlapped with 74 candidate genes(B73_RefGen_v4).Comparative transcriptomic analyses were then performed to identify the genes related to SCR infection,with 2,586 and 797 differentially expressed genes(DEGs)ultimately being identified in the resistant Qi319and susceptible 8112 inbred lines following P.polysora infection,respectively,including 306 genes common to both lines.Subsequent integrative multi-omics investigations identified four potential candidate SCR response-related genes.One of these genes is ZmHCT9,which encodes the protein hydroxycinnamoyl transferase 9.This gene was up-regulated in susceptible inbred lines and linked to greater P.polysora resistance as confirmed through cucumber mosaic virus(CMV)-based virus induced-gene silencing(VIGS)system-mediated gene silencing.These data provide important insights into the genetic basis of the maize SCR response.They will be useful for for future research on potential genes related to SCR resistance in maize.展开更多
Nicotine is widely recognized as the primary contributor to tobacco dependence.Previous studies have indicated that molecular and behavioral responses to nicotine are primarily mediated by ventral tegmental area(VTA)n...Nicotine is widely recognized as the primary contributor to tobacco dependence.Previous studies have indicated that molecular and behavioral responses to nicotine are primarily mediated by ventral tegmental area(VTA)neurons,and accumulating evidence suggests that glia play prominent roles in nicotine addiction.However,VTA neurons and glia have yet to be characterized at the transcriptional level during the progression of nicotine self-administration.Here,a male mouse model of nicotine self-administration is established and the timing of three critical phases(pre-addiction,addicting,and post-addiction phase)is characterized.Single-nucleus RNA sequencing in the VTA at each phase is performed to comprehensively classify specific cell subtypes.Adaptive changes occurred during the addicting and post-addiction phases,with the addicting phase displaying highly dynamic neuroplasticity that profoundly impacts the transcription in each cell subtype.Furthermore,significant transcriptional changes in energy metabolism-related genes are observed,accompanied by notable structural alterations in neuronal mitochondria during the progression of nicotine self-administration.The results provide insights into mechanisms underlying the progression of nicotine addiction,serving as an important resource for identifying potential molecular targets for nicotine cessation.展开更多
Microplastics(MPs)pollution has become a worldwide environmental problem.The study about the effects of microplastics on fish,especially on the fish immune system is limited.In the present study,the transcriptome of s...Microplastics(MPs)pollution has become a worldwide environmental problem.The study about the effects of microplastics on fish,especially on the fish immune system is limited.In the present study,the transcriptome of soiny mullet(Liza haematocheila)larvae at 7 d and 14 d post 0.5μm MPs exposure were analyzed by DNBSEQ platform.A total number of 96585 unigenes were obtained with average length of 1925 bp.Approximately 72.48%(70004),76.80%(74176),and 62.94%(60787)unigenes were matched with the annotated sequences for non-redundant(NR),NCBI nucleotide(NT)and Swissprot database,respectively.Compared with control group,1336 differently expressed genes(DEGs)were identified at 7 d post MPs exposure.As the MPs exposure time extended to 14 d,the number of DEGs in the MPs exposure group reached to 3561.Further,KEGG enrichment analysis revealed that several immune-related pathways,such as interleukin(IL)-17 signaling pathway,tumor necrosis factor(TNF)signaling pathway,were affected by MPs exposure.In addition,apoptosis signaling pathway was also enriched under MPs exposure.These results demonstrated that MPs can alter the expressions of immune-related genes,providing basis for understanding the immune toxicity of MPs on fish and other vertebrates.展开更多
Perchlorate(ClO_(4)^(−))is a type of novel persistent inorganic pollutant that has gained increasing attention because of its high solubility,poor degradability,and widespread distribution.However,the impacts of perch...Perchlorate(ClO_(4)^(−))is a type of novel persistent inorganic pollutant that has gained increasing attention because of its high solubility,poor degradability,and widespread distribution.However,the impacts of perchlorate on aquatic autotrophs such cyanobacterium are still unclear.Herein,Synechocystis sp.PCC6803(Synechocystis)was used to investigate the response mechanisms of perchlorate on cyanobacterium by integrating physiological and transcriptome analyses.Physiological results showed that perchlorate mainly damaged the photosystem of Synechocystis,and the inhibition degree of photosystem II(PSII)was severer than that of photosystem I(PSI).When the exposed cells were moved to a clean medium,the photosynthetic activities were slightly repaired but still lower than in the control group,indicating irreversible damage.Furthermore,perchlorate also destroyed the cellular ultrastructure and induced oxidative stress in Synechocystis.The antioxidant glutathione(GSH)content and the superoxide dismutase(SOD)enzyme activity were enhanced to scavenge harmful reactive oxygen(ROS)in Synechocystis.Transcriptome analysis revealed that the genes associated with“photosynthesis”and“electron transport”were significantly regulated.For instance,most genes related to PSI(e.g.,psaf,psaJ)and the“electron transport chain”were upregulated,whereas most genes related to PSII(e.g.,psbA3,psbD1,psbB,and psbC)were downregulated.Additionally,perchlorate also induced the expression of genes related to the antioxidant system(sod2,gpx,gst,katG,and gshB)to reduce oxidative damage.Overall,this study is the first to investigate the impacts andmechanisms of cyanobacterium under perchlorate stress,which is conducive to assessing the risk of perchlorate in aquatic environments.展开更多
Background:Macrophages are the primary innate immune cells encountered by the invading coronaviruses,and their abilities to initiate inflammatory reactions,to main-tain the immunity homeostasis by differential polariz...Background:Macrophages are the primary innate immune cells encountered by the invading coronaviruses,and their abilities to initiate inflammatory reactions,to main-tain the immunity homeostasis by differential polarization,to train the innate immune system by epigenic modification have been reported in laboratory animal research.Methods:In the current in vitro research,murine macrophage RAW 264.7 cell were infected by mouse hepatitis virus,a coronavirus existed in mouse.At 3-,6-,12-,24-,and 48-h post infection(hpi.),the attached cells were washed with PBS and harvested in Trizol reagent.Then The harvest is subjected to transcriptome sequencing.Results:The transcriptome analysis showed the immediate(3 hpi.)up regulation of DEGs related to inflammation,like Il1b and Il6.DEGs related to M2 differential po-larization,like Irf4 showed up regulation at 24 hpi.,the late term after viral infection.In addition,DEGs related to metabolism and histone modification,like Ezh2 were de-tected,which might correlate with the trained immunity of macrophages.Conclusions:The current in vitro viral infection study showed the key innated im-munity character of macrophages,which suggested the replacement value of viral infection cells model,to reduce the animal usage in preclinical research.展开更多
Mandarin fish(Siniperca scherzeri) has high market prices and significant market potential in China because of its highquality meat and high nutritional value. However, due to the limited scale of aquaculture, meeting...Mandarin fish(Siniperca scherzeri) has high market prices and significant market potential in China because of its highquality meat and high nutritional value. However, due to the limited scale of aquaculture, meeting the market demand is difficult, making the effective development of the aquaculture potential of mandarin fish an important challenge for the industry. In this study, a 30-d breeding experiment was conducted on mandarin fish larvae under three photoperiod conditions: G1 8 h light:16 h dark(8L:16D), G2 12 h light:12 h dark(12L:12D), and G3 16 h light:8 h dark(16L:8D). The results showed that the G2 group exhibited the best growth performance and development status, with final body weights, weight gain rates, and specific growth rates all higher than those of the other two groups(P < 0.05). Observations of sections from each group revealed that the intestinal villi length and muscle thickness of the G2 group were significantly greater than those of the other two groups(P < 0.05). The G2 group inhibited the transcriptional activation of key circadian rhythm genes, including nr1d2a, nr1d1 and per1, while upregulating the expression of BMAL1 in S. scherzeri.The activation of both the insulin signalling pathway and the Fox O signalling pathway enhanced the efficient secretion of insulin, which subsequently played a critical role in regulating fatty acid metabolism. This active fatty acid metabolism provided an optimal energy supply, ensuring that other nutrients were fully utilized during the growth and development process while minimizing unnecessary nutrient loss. Consequently, this mechanism effectively promoted the overall growth and development of S. scherzeri. This study was the first to elucidate the transcriptomic expression patterns of S. scherzeri under varying photoperiod conditions. In response to the cyclic alternation of day and night, S. scherzeri regulated their metabolic levels and the transcriptional activation of downstream target genes via insulin signalling.展开更多
Nitrogen(N)is a limiting factor that determines the yield and quality of chrysanthemum.Genetic variation in N use efficiency(NUE)has been reported among chrysanthemum genotypes.We performed a transcriptome analysis of...Nitrogen(N)is a limiting factor that determines the yield and quality of chrysanthemum.Genetic variation in N use efficiency(NUE)has been reported among chrysanthemum genotypes.We performed a transcriptome analysis of two chrysanthemum genotypes,'Nannonglihuang'(LH,N-efficient genotype)and'Nannongxuefeng"(XF,N-inefficient genotype),under low N(0.4 mmol L^(-1)N)and normal N(8 mmol L^(-1)N)treatments for 15 d and an N recovery treatment for 12 h(low N treatment for 15 d and then normal N treatment for 12 h)to understand the genetic factors impacting NUE in chrysanthemum.The two genotypes exhibited contrasting responses to the different N treatments.The N-efficient genotype LH had significant superiority in agronomic traits,N accumulation and glutamine synthase activity under both normal N and low N treatments.Low N treatment promoted root growth in LH,but inhibited root growth in XF.Transcriptome analysis revealed that the low N treatment increased the expression of some N metabolism genes,genes related to auxin and abscisic acid signal transduction in the roots of both genotypes,as well as genes related to gibberellin signal transduction in roots of LH.The N recovery treatment just increased the expression of genes related to cytokinin signal transduction in roots of LH.The expression levels of the NRT2.1,AMT1.1,and Gln1 genes related to gibberellin and cytokinin signal transduction were higher in roots of LH than in XF under different N treatments,suggesting that the genes related to N metabolism and hormone(auxin,abscisic acid,gibberellin,and cytokinin)signal transduction in roots of LH are more sensitive to different N treatments than those of XF.Co-expression network analysis(WGCNA)also identified hub genes like bZIP43,bHLH93,NPF6.3,IBR10,MYB62,PP2C,PP2C06 and NLP7,which may be the key regulators of N-mediated responses in chrysanthemum and play crucial roles in enhancing NUE and resistance to low N stress in the N-efficient chrysanthemum genotype.These results revealed the key factors involved in regulating NUE in chrysanthemum at the genetic level,which provides new insights into the complex mechanism of efficient nitrogen utilization in chrysanthemum,and can be useful for the improvement and breeding of high NUE chrysanthemum genotypes.展开更多
Evaluating plant stress tolerance and screening key regulatory genes under the combined stresses of high temperature and drought are important for studying plant stress tolerance mechanisms. In this study, the drought...Evaluating plant stress tolerance and screening key regulatory genes under the combined stresses of high temperature and drought are important for studying plant stress tolerance mechanisms. In this study, the drought tolerance of five grape varieties was evaluated under high-temperature conditions to screen key genes for further exploration of resistance mechanisms. By comparing and analysing the morphological characteristics and physiological indicators associated with the response of grapevines to drought stress and integrating them with the membership function to assess the strength of their drought tolerance, the order of drought tolerance was found to be as follows: 420A>110R>Cabernet Sauvignon(CS)>Fercal>188-08. To further analyse the mechanism of differences in drought tolerance, transcriptomic sequencing was performed on the drought-tolerant cultivar 420A, the drought-sensitive cultivar 188-08 and the control cultivar CS. The functional analysis of differential metabolic pathways indicated that the differentially expressed genes were enriched mainly in biological process category, that 420A had higher antioxidant activity. Furthermore, differentially expressed transcription factors were analyzed in five grape varieties. Genes like Vv AGL15, Vv LBD41, and Vv MYB86 showed close associations with drought tolerance,indicating their potential role in regulating drought tolerance and research significance.展开更多
基金supported by grants from the National Natural Science Foundation of China(31929002,31771114 and 92049107)grant from Innovative Research Groups of the National Natural Science Foundation of China(81721005)the Academic Frontier Youth Team Project(to XW)from Huazhong University of Science and Technology.
文摘Background Methamphetamine(METH)addiction causes a huge burden on society.The prefrontal cortex(PFC),associated with emotion and cognitive behaviours,is also involved in addiction neurocircuitry.Although bulk RNA sequencing has shown METH-induced gene alterations in the mouse PFC,the impact on different cell types remains unknown.Aims To clarify the effects of METH treatment on different cell types of the PFC and the potential pathways involved in METH-related disorders.Methods We performed single-nucleus RNA sequencing(snRNA-seq)to examine the transcriptomes of 20465 nuclei isolated from the PFC of chronic METH-treated and control mice.Main cell types and differentially expressed genes(DEGs)were identified and confirmed by RNA fluorescence in situ hybridization(FISH).Results Six main cell types were identified depending on the single-cell nucleus sequencing;of particular interest were the mature oligodendrocytes in the PFC.The DEGs of mature oligodendrocytes were enriched in the myelin sheath,adenosine triphosphate(ATP)metabolic process,mitochondrial function and components,and so on.The messenger RNA levels of Aldoc and Atp5l(FISH)and the protein level of the mitochondrial membrane pore subunit TOM40(immunofluorescence)decreased in the mature oligodendrocytes.Fast blue staining and transmission electron microscopy image indicated myelin damage,and the myelin thickness decreased in METH brains.Conclusions snRNA-seq reveals altered transcriptomes of different cell types in mouse PFC induced by chronic METH treatment,underscoring potential relationships with psychiatric disorders.
基金supported by the National Natural Science Foundation of China(31790410)。
文摘Pigs are important agricultural animals and valuable biomedical models.The intestinal tract is a crucial digestive organ and the largest immune organ.However,the function of pig intestines at single-cell resolution remains poorly understood.Here,we created single-nucleus transcriptomic maps of the ileum and cecum for wild boars,Bama Xiang pigs,and Large White pigs,aged 30,42,150,and 730 d.Our atlas revealed 19 major cell types and 58 cellular subtypes,including several previously uncharacterized cellular subtypes,such as EBF1+fibroblasts,TMEM163+macrophages,and neuron subtypes expressing FCAMR.We discovered and confirmed that ileum neurons,rather than cecum neurons,can regulate inflammatory responses,highlighting interactions of neurons with dendritic cells(DCs)and lymphatic endothelial cells(LECs)through the NAMPT-INSR ligand-receptor pair in the ileum.Microbial-derived short-chain fatty acids,such as propionic acid and acetic acid,enhanced plasma cell differentiation and humoral immune responses by upregulating XBP1 and SDC1 expression,thereby endowing wild boars with a stronger immune response than domestic pigs.We identified and validated the enterocyteenriched transcription factors FOXO1 and NR1H4 in wild boars,which contributed to the superior nutrient absorption of wild boars relative to domestic pigs.Furthermore,we comprehensively characterized the postnatal development of wild boar intestinal cells and revealed that plasma cells presented the most pronounced developmental changes.We identified highly conserved cell types and features between pig and human intestines.Overall,our work provides a foundation for improving pig feed conversion and health while also providing a reference for research on human intestinal diseases.
基金supported by the National Natural Science Foundation of China,No.82301403(to DZ)。
文摘Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocytes,microglia,and oligodendrocytes in the central nervous system,and satellite glial cells and Schwann cells in the peripheral nervous system.Despite the greater understanding of glial cell types and functional heterogeneity achieved through single-cell and single-nucleus RNA sequencing in animal models,few studies have investigated the transcriptomic profiles of glial cells in the human spinal cord.Here,we used high-throughput single-nucleus RNA sequencing and spatial transcriptomics to map the cellular and molecular heterogeneity of astrocytes,microglia,and oligodendrocytes in the human spinal cord.To explore the conservation and divergence across species,we compared these findings with those from mice.In the human spinal cord,astrocytes,microglia,and oligodendrocytes were each divided into six distinct transcriptomic subclusters.In the mouse spinal cord,astrocytes,microglia,and oligodendrocytes were divided into five,four,and five distinct transcriptomic subclusters,respectively.The comparative results revealed substantial heterogeneity in all glial cell types between humans and mice.Additionally,we detected sex differences in gene expression in human spinal cord glial cells.Specifically,in all astrocyte subtypes,the levels of NEAT1 and CHI3L1 were higher in males than in females,whereas the levels of CST3 were lower in males than in females.In all microglial subtypes,all differentially expressed genes were located on the sex chromosomes.In addition to sex-specific gene differences,the levels of MT-ND4,MT2A,MT-ATP6,MT-CO3,MT-ND2,MT-ND3,and MT-CO_(2) in all spinal cord oligodendrocyte subtypes were higher in females than in males.Collectively,the present dataset extensively characterizes glial cell heterogeneity and offers a valuable resource for exploring the cellular basis of spinal cordrelated illnesses,including chronic pain,amyotrophic lateral sclerosis,and multiple sclerosis.
基金supported by the National Natural Science Foundation of China(Grant Nos.32072545,32272639 and 32260745)Zhejiang Provincial Natural Science Foundation of China(Grant Nos.LTGN23C150009 and LY22C150003)Zhejiang University Experimental Technology Research Project(Grant No.SYBJS202217).
文摘For red pear,the anthocyanin content is a crucial factor determining the fruit skin color,which affects consumer preferences.Low overnight temperatures promote anthocyanin accumulation,but the molecular mechanism responsible is unclear.In this study,‘Hongzaosu’pear(Pyrus pyrifolia×Pyrus communis)fruit were treated with a low nighttime temperature(LNT,16℃)or a warm nighttime temperature(WNT,26℃),with sampling conducted within two diurnal cycles.The results showed that LNT promoted anthocyanin accumulation in the fruit skin.The structural anthocyanin biosynthetic genes PpCHS,PpF3H,and PpUFGT exhibited a rhythmic increase in expression at night under LNT.To examine the underlying mechanism,RNA sequencing was conducted using pear calli exposed to LNT and WNT for different durations(24,48,72,or 96 h).Transcriptome analysis revealed 285 differentially expressed genes(DEGs)common to all pairwise comparisons of LNT-and WNT-treated calli of‘Clapp's Favorite’(P.communis)at the sampling time points.KEGG pathway and gene ontology enrichment analyses indicated that the common DEGs were enriched in secondary metabolic processes and phenylpropanoid metabolic processes,which are associated with anthocyanin biosynthesis.The transcription factor PpCDF5,which was responsive to LNT,was selected for further study.Dual-luciferase assays showed that PpCDF5 activated the transcription of anthocyanin biosynthetic genes PpMYB10,PpCHS,PpF3H,PpDFR,PpANS,and PpUFGT.The yeast one-hybrid and EMSA assays demonstrated that PpCDF5 directly binds to the PpF3H promoter,which contains an AAAG motif.Overexpression of PpCDF5 in pear calli and transient overexpression in pear fruit both increased anthocyanin accumulation.The results indicate that PpCDF5 is involved in LNT-induced anthocyanin biosynthesis in pear fruit and provide insights into the molecular regulation of commercial fruit coloration.
基金Supported by the Key Research and Development Program of Shandong(No.2022LZGC015)the National Key R&D Program of China(No.2022YFD2401400)+1 种基金the Taishan Scholars Program,the National Key R&D Program of China(No.2022YFD2400304)the Agricultural Seed Project of Shandong Key R&D Program(No.2024LZGCQY003)。
文摘Atmospheric carbon dioxide(CO_(2))levels are escalating at an unprecedented rate,leading to the phenomenon of ocean acidification(OA).Parental exposure to acidification has the potential to enhance offspring resilience through cross-generation plasticity.In this study,we analyzed larval growth and transcriptomic profiles in the Pacific oyster,Crassostrea gigas,a species of significant ecological relevance,under both control and elevated CO_(2)conditions experienced by their parental generation.Our findings indicate that the oyster populations exposed to OA exhibited a higher incidence of abnormalities during the D-shaped larval stage,followed by accelerated growth at the eyed stage.Through a comparative transcriptomic investigation of eyed larvae(25 d after fertilization),we observed that parental exposure to OA substantially influenced the gene expression in the offspring.Genes associated with lipid catabolism and shell formation were notably upregulated in oysters with parental OA exposure,potentially playing a role in cross-generational conditioning and conferring resilience to OA stressors.These results underscore the profound impact of OA on oyster larval development via cross-generational mechanisms and shed light on the molecular underpinnings of cross-generation plasticity.
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 Guangdong Provincial Key Research and Development Program-Modern Seed Industry(2022B0202060004)National Key Research and Development Project(2023YFD1202800)+9 种基金National Natural Science Foundation of China(32272121,32172051,32301869,32000471)Guangdong Science and Technology Plan Project(2023B1212060038)Guangdong Basic and Applied Basic Research Foundation(2021A1515010811,2023A1515010098,2023A1515010569)China Agriculture Research System of MOF and MARA(CARS-13)Guangzhou Basic and Applied Basic Research Foundation(2023A04J0776)Special Fund for Scientific Innovation Strategy-Construction of High Level Academy of Agriculture Science(R2020PY-JX004,R2020PY-JG005,R2021PY-QY003,R2022YJYB3025)the Foundation of the Director of Crop Research Institute of Guangdong Academy of Agriculture Sciences(202201,202306)Special Funds for the Revitalization of Agriculture through Seed Industry under the Provincial Rural Revitalization Strategy(2022-NPY-00-022)the Project of Collaborative Innovation Center of GDAAS(XTXM202203)Science and Technology Planning Project of Heyuan City(Heyuan She Nong Da Zhuan Xiang 2022002).
文摘Peanut seedlings develop from seeds by hypocotyl elongation and differentiation.However,the intricate gene regulatory networks and molecular crosstalk underlying hypocotyl growth in peanuts remain largely unknown.In this study,a single-nucleus gene expression landscape in peanut seedlings was initially developed from diverse tissues,including stems,roots,leaves,and hypocotyls.Core transcription factor interaction networks driving developmental trajectories were identified to decipher hypocotyl cell heterogeneity.Jasmonic acid and cytokinin regulate peanut hypocotyl expansion and differentiation based on the number and size of cortex cells and hormone levels between the hypocotyl at 3 and 7 d after germination.We further demonstrated that AhBHLH143 potentially represses hypocotyl elongation by promoting the JA pathway and inhibiting the cytokinin pathway.The single-nucleus transcriptomic atlas of peanut seedlings reveals new insights into hypocotyl development and provides a valuable resource for future investigations of seedling development.
基金Supported by the National Natural Science Foundation of China,No.81774118the Foreign Cooperation Project of Science and Technology Department of Fujian Province,No.2023I0021the Medical Innovation Project of Fujian Province,No.2024CXB013.
文摘BACKGROUND Hemorrhoids,a prevalent chronic condition globally,significantly impact patients'quality of life.While various surgical interventions,such as external stripping and internal ligation,procedure for prolapse and hemorrhoids,and tissue selecting technique,are employed for treatment,they are often associated with postoperative complications,including unsatisfactory defecation,bleeding,and anal stenosis.In contrast,Xiaozhiling injection,a traditional Chinese medicine-based therapy,has emerged as a minimally invasive and effective alternative for internal hemorrhoids.This treatment offers distinct advantages,such as reduced dietary restrictions,broad applicability,and minimal induction of systemic inflammatory responses.Additionally,Xiaozhiling injection effectively eliminates hemorrhoid nuclei,prevents local tissue necrosis,preserves anal cushion integrity,and mitigates postoperative complications,including bleeding and prolapse.Despite its clinical efficacy,the molecular mechanisms underlying its therapeutic effects remain poorly understood,warranting further investigation.AIM To investigate the molecular mechanism underlying the therapeutic effect of Xiaozhiling injection in the treatment of internal hemorrhoids.METHODS An internal hemorrhoid model was established in rats,and the rats were randomly divided into a modeling group[control group(CK group)]and a treatment group.One week after injection,Stereo-seq and electron microscopy were used to study the changes in gene expression and subcellular structures in fibroblasts.RESULTS Single-cell sequencing revealed differences in the expression and transcript levels of the genes collagen 3 alpha 1,decorin,and actin alpha 2 in fibroblasts between the CK group and the treatment group.Spatial transcriptome analysis revealed that genes of the sphingosine kinase 1(Sphk1)/sphingosine-1-phosphate(S1P)pathway spatially overlapped with key genes of the transforming growth factor beta 1 pathway,namely,Sphk1,S1P receptor,and transforming growth factor beta 1,in the treatment group.The proportion of fibroblasts was lower in the treatment group than in the CK group,and Xiaozhiling treatment had a significant effect on the proportion of fibroblasts in hemorrhoidal tissue.Immunohistochemistry revealed a significant increase in the expression of a fibroblast marker.Electron microscopy showed that the endoplasmic reticulum of fibroblasts contained a large amount of glycogen,indicating cell activation.Fibroblast activation and the expression of key genes of the Sphk1-S1P pathway could be observed at the injection site,suggesting that after Xiaozhiling intervention,the Sphk1-S1P pathway could be activated to promote fibrosis.CONCLUSION Xiaozhiling injection exerts its therapeutic effects on internal hemorrhoids by promoting collagen synthesis and secretion in fibroblasts.After Xiaozhiling intervention,the Sphk1-S1P pathway can be activated to promote fibrosis.
基金supported by the National Natural Science Fund of China(Grant Nos.31872066 and 32272663)the Science and Technology Planning Project of Guangzhou(Grant No.2023B01J2002)+1 种基金the Key Research and Development Program of Hainan(Grant No.ZDYF2023XDNY052)the Seed Industry Engineering Project of Ministry of Agriculture and Rural Affairs of Guangdong(Grant Nos.2022-NPY-00-004 and 2022-NBH-00-001)。
文摘Litchi chinensis Sonn.is an important economic fruit tree in tropical and subtropical regions.Regrettably,the efficiency of plant regeneration via somatic embryogenesis in litchi is typically low due to the poor conversion of embryos to plants.The purpose of this study was to establish a regeneration system via somatic embryogenesis from immature embryos explants in‘Heiye'cultivar of litchi.Our results demonstrated that MS medium supplemented with 2.0 mg L^(-1)2,4-D was optimal for callus induction.For somatic embryo(SE)induction,MS medium containing0.5 g L^(-1) activated charcoal(AC)was the most effective,while the use of zeatin(ZT)and thidiazuron(TDZ)resulted in abnormal somatic embryos.The rooting and regeneration rate of 2.15%and 17.5%,respectively,were achieved using MS medium supplemented with 0.5 g L^(-1) AC.Furthermore,transcriptome analysis was performed on embryogenic callus(EC),globular embryo(GE),and heart embryo(HE)to explore the molecular mechanisms of early somatic embryogenesis.2,587 common differentially expressed genes(DEGs)between EC_vs_GE and EC_vs_HE were identified,and the expression patterns of these common DEGs were separated into twelve major clusters.GO annotation and KEGG pathway analysis revealed that these common DEGs were implicated in plant hormone signal transduction,auxin-activated signaling pathway,and other biological processes.Additionally,differentially expressed transcription factors were identified,and the function of LcBBM2 which is specifically highly expressed during early somatic embryogenesis was verified.Overexpression of LcBBM2 in tomato promotes callus and shoot formation.Therefore,this study can provide a theoretical basis and technical support for genetic breeding improvement of litchi.
基金supported by the National Basic Research Program of China(2020YFA0804000,2020YFC0842000,2020YFA0112200,2021YFC2301703)Strategic Priority Research Program of the Chinese Academy of Sciences(XDB32010100)+6 种基金Special Associate Research Program of the Chinese Academy of Sciences(E1290601)National Natural Science Foundation of China(32122037,81891001,32192411,32100512,U1902215)Collaborative Research Fund of the Chinese Institute for Brain Research,Beijing(2020-NKX-PT-03)CAS Project for Young Scientists in Basic Research(YSBR-013)Young Elite Scientist Sponsorship Program by the China Association for Science and Technology(2020QNRC001)National Resource Center for Non-Human Primates。
文摘Infection with severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) causes diverse clinical manifestations and tissue injuries in multiple organs.However, cellular and molecular understanding of SARS-CoV-2 infection-associated pathology and immune defense features in different organs remains incomplete. Here, we profiled approximately 77 000single-nucleus transcriptomes of the lung, liver,kidney, and cerebral cortex in rhesus macaques(Macaca mulatta) infected with SARS-CoV-2 and healthy controls. Integrated analysis of the multiorgan dataset suggested that the liver harbored the strongest global transcriptional alterations. We observed prominent impairment in lung epithelial cells, especially in AT2 and ciliated cells, and evident signs of fibrosis in fibroblasts. These lung injury characteristics are similar to those reported in patients with coronavirus disease 2019(COVID-19).Furthermore, we found suppressed MHC class I/II molecular activity in the lung, inflammatory response in the liver, and activation of the kynurenine pathway,which induced the development of an immunosuppressive microenvironment. Analysis of the kidney dataset highlighted tropism of tubule cells to SARS-CoV-2, and we found membranous nephropathy(an autoimmune disease) caused by podocyte dysregulation. In addition, we identified the pathological states of astrocytes and oligodendrocytes in the cerebral cortex, providing molecular insights into COVID-19-related neurological implications. Overall, our multi-organ single-nucleus transcriptomic survey of SARS-CoV-2-infected rhesus macaques broadens our understanding of disease features and antiviral immune defects caused by SARS-CoV-2 infection,which may facilitate the development of therapeutic interventions for COVID-19.
基金supported by the National Key Research and Development Program of China(Grant No.2021YFD2200502)the National Natural Science Foundation of China(Grant No.31971736).
文摘Bamboo was one of the first plants to be cultivated in China and is widely used in industry and daily life.The study of gene function has become an important part of bamboo breeding,whereas quantitative real-time PCR(qRT-PCR)is a powerful tool for gene expression analysis.The accuracy of qRT-PCR results largely depends on suitable reference genes.In this study,a transcriptome-wide identification of reference genes was conducted based on 447 transcriptome datasets,comprising 200 tissue samples,107 treated samples,and 140 samples from various moso bamboo(Phyllostachys edulis)forms.A total of 3444,1013,and 3962 stably expressed genes were identified from these three groups,respectively.Functional enrichment analysis revealed significant enrichment of these genes in pathways,including the spliceosome,proteasome,and oxidative phosphorylation.Eight candidate genes(ADPRE,GAPDH,TRX,TUBA,NRP,MBF,UNK,and CAM1),were selected for qRT-PCR validation using 112 samples.To assess their stability,five statistical methods(geNorm,NormFinder,BestKeeper,Delta-Ct,and RefFinder)were employed.The most suitable reference genes were ADPRE and GAPDH for different tissues,GAPDH and CAM1 for different treatments,and GAPDH and TRX for various moso bamboo forms.Overall,ADPRE and GAPDH were the most stable reference genes across all conditions,while TUBA and TRX were the least stable reference genes.In addition,a significant negative correlation was found between the Ct values of RT-qPCR and the log2TPM values from the transcriptome data(Ct=-1.534x+37.221),providing a potential method for estimating gene expression levels.The identified reference genes,particularly ADPRE and GAPDH,provide a robust set of references for gene expression studies in moso bamboo.
基金supported by the National Natural Science Foundation of China(Grant Nos.32120103010,32002050)Beijing Joint Research Program for Germplasm Innovation and New Variety Breeding(Grant No.G20220628003-03)the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences。
文摘Tomato is an important economic crop all over the world.Volatile flavors in tomato fruit are key factors influencing consumer liking and commercial quality.However,the regulatory mechanism controlling the volatile flavors of tomatoes is still not clear.Here,we integrated the metabolome and transcriptome of the volatile flavors in tomato fruit to explore the regulatory mechanism of volatile flavor formation,using wild and cultivated tomatoes with significant differences in flavors.A total of 35 volatile flavor compounds were identified,based on the solid phase microextraction-gas chromatography-mass spectrometry(SPME-GC-MS).The content of the volatiles,affecting fruit flavor,significantly increased in the transition from breaker to red ripe fruit stage.Moreover,the total content of the volatiles in wild tomatoes was much higher than that in the cultivated tomatoes.The content variations of all volatile flavors were clustered into 10 groups by hierarchical cluster and Pearson coefficient correlation(PCC)analysis.The fruit transcriptome was also patterned into 10 groups,with significant variations both from the mature green to breaker fruit stage and from the breaker to red ripe fruit stage.Combining the metabolome and the transcriptome of the same developmental stage of fruits by co-expression analysis,we found that the expression level of 1182 genes was highly correlated with the content of volatile flavor compounds,thereby constructing two regulatory pathways of important volatile flavors.One pathway is tetrahydrothiazolidine N-hydroxylase(SlTNH1)-dependent,which is regulated by two transcription factors(TFs)from the bHLH and AP2/ERF families,controlling the synthesis of 2-isobutylthiazole in amino acid metabolism.The other is lipoxygenase(Sl LOX)-dependent,which is regulated by one TF from the HD-Zip family,controlling the synthesis of hexanal and(Z)-2-heptenal in fatty acid metabolism.Dual-luciferase assay confirmed the binding of b HLH and AP2/ERF to their structural genes.The findings of this study provide new insights into volatile flavor formation in tomato fruit,which can be useful for tomato flavor improvement.
基金supported by the National Key R&D Program of China(2022YFD1201802)the Shandong Key R&D Program,China(2022CXGC010607)+2 种基金the Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences(CAAS-ZDRW202109)the Agricultural Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences(CAAS-ASTIP2017-ICS)the Subproject of the Major Project of Science and Technology in Shanxi Province,China(202201140601025-1-02)。
文摘Southern corn rust(SCR)is an airborne fungal disease caused by Puccinia polysora Underw.(P.polysora)that adversely impacts maize quality and yields worldwide.Screening for new elite SCR-resistant maize loci or genes has the potential to enhance overall resistance to this pathogen.Using phenotypic SCR resistance-related data collected over two years and three geographical environments,a genome-wide association study was carried out in this work,which eventually identified 91 loci that were substantially correlated with SCR susceptibility.These included 13 loci that were significant in at least three environments and overlapped with 74 candidate genes(B73_RefGen_v4).Comparative transcriptomic analyses were then performed to identify the genes related to SCR infection,with 2,586 and 797 differentially expressed genes(DEGs)ultimately being identified in the resistant Qi319and susceptible 8112 inbred lines following P.polysora infection,respectively,including 306 genes common to both lines.Subsequent integrative multi-omics investigations identified four potential candidate SCR response-related genes.One of these genes is ZmHCT9,which encodes the protein hydroxycinnamoyl transferase 9.This gene was up-regulated in susceptible inbred lines and linked to greater P.polysora resistance as confirmed through cucumber mosaic virus(CMV)-based virus induced-gene silencing(VIGS)system-mediated gene silencing.These data provide important insights into the genetic basis of the maize SCR response.They will be useful for for future research on potential genes related to SCR resistance in maize.
基金supported by the Major Project of Tobacco Biological Effects(552022AK0070,110202102014)。
文摘Nicotine is widely recognized as the primary contributor to tobacco dependence.Previous studies have indicated that molecular and behavioral responses to nicotine are primarily mediated by ventral tegmental area(VTA)neurons,and accumulating evidence suggests that glia play prominent roles in nicotine addiction.However,VTA neurons and glia have yet to be characterized at the transcriptional level during the progression of nicotine self-administration.Here,a male mouse model of nicotine self-administration is established and the timing of three critical phases(pre-addiction,addicting,and post-addiction phase)is characterized.Single-nucleus RNA sequencing in the VTA at each phase is performed to comprehensively classify specific cell subtypes.Adaptive changes occurred during the addicting and post-addiction phases,with the addicting phase displaying highly dynamic neuroplasticity that profoundly impacts the transcription in each cell subtype.Furthermore,significant transcriptional changes in energy metabolism-related genes are observed,accompanied by notable structural alterations in neuronal mitochondria during the progression of nicotine self-administration.The results provide insights into mechanisms underlying the progression of nicotine addiction,serving as an important resource for identifying potential molecular targets for nicotine cessation.
基金supported by the Major Projects of Natural Science Research for University and Colleges in Jiangsu Province(No.21KJA240001)the Key Research and Development Program of Jiangsu Province(No.BE2018348)+2 种基金partially by the Jiangsu Agricultural Science and Technology Innovation Fund(No.CX(22)3199)the Projects for the High-Quality Development of Fishery Industry of Yancheng City(No.YCSCYJ20210014)supported financially by the projects for‘Six Talents’of Jiangsu Province(No.NY115)。
文摘Microplastics(MPs)pollution has become a worldwide environmental problem.The study about the effects of microplastics on fish,especially on the fish immune system is limited.In the present study,the transcriptome of soiny mullet(Liza haematocheila)larvae at 7 d and 14 d post 0.5μm MPs exposure were analyzed by DNBSEQ platform.A total number of 96585 unigenes were obtained with average length of 1925 bp.Approximately 72.48%(70004),76.80%(74176),and 62.94%(60787)unigenes were matched with the annotated sequences for non-redundant(NR),NCBI nucleotide(NT)and Swissprot database,respectively.Compared with control group,1336 differently expressed genes(DEGs)were identified at 7 d post MPs exposure.As the MPs exposure time extended to 14 d,the number of DEGs in the MPs exposure group reached to 3561.Further,KEGG enrichment analysis revealed that several immune-related pathways,such as interleukin(IL)-17 signaling pathway,tumor necrosis factor(TNF)signaling pathway,were affected by MPs exposure.In addition,apoptosis signaling pathway was also enriched under MPs exposure.These results demonstrated that MPs can alter the expressions of immune-related genes,providing basis for understanding the immune toxicity of MPs on fish and other vertebrates.
基金supported by the Project of Chinese Manned Spaceflight(No.YYWT-0801-EXP-09)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDA17010502)Jiangsu Province Ecological Environment Scientific Research Project(No.2022008).
文摘Perchlorate(ClO_(4)^(−))is a type of novel persistent inorganic pollutant that has gained increasing attention because of its high solubility,poor degradability,and widespread distribution.However,the impacts of perchlorate on aquatic autotrophs such cyanobacterium are still unclear.Herein,Synechocystis sp.PCC6803(Synechocystis)was used to investigate the response mechanisms of perchlorate on cyanobacterium by integrating physiological and transcriptome analyses.Physiological results showed that perchlorate mainly damaged the photosystem of Synechocystis,and the inhibition degree of photosystem II(PSII)was severer than that of photosystem I(PSI).When the exposed cells were moved to a clean medium,the photosynthetic activities were slightly repaired but still lower than in the control group,indicating irreversible damage.Furthermore,perchlorate also destroyed the cellular ultrastructure and induced oxidative stress in Synechocystis.The antioxidant glutathione(GSH)content and the superoxide dismutase(SOD)enzyme activity were enhanced to scavenge harmful reactive oxygen(ROS)in Synechocystis.Transcriptome analysis revealed that the genes associated with“photosynthesis”and“electron transport”were significantly regulated.For instance,most genes related to PSI(e.g.,psaf,psaJ)and the“electron transport chain”were upregulated,whereas most genes related to PSII(e.g.,psbA3,psbD1,psbB,and psbC)were downregulated.Additionally,perchlorate also induced the expression of genes related to the antioxidant system(sod2,gpx,gst,katG,and gshB)to reduce oxidative damage.Overall,this study is the first to investigate the impacts andmechanisms of cyanobacterium under perchlorate stress,which is conducive to assessing the risk of perchlorate in aquatic environments.
基金CAMs innovation Fund for Medical Sciences,Grant/Award Number:2022-12M-CoV19-005National Key Projects,Grant/Award Number:2023YFF0724900 and 2021YFF0702802。
文摘Background:Macrophages are the primary innate immune cells encountered by the invading coronaviruses,and their abilities to initiate inflammatory reactions,to main-tain the immunity homeostasis by differential polarization,to train the innate immune system by epigenic modification have been reported in laboratory animal research.Methods:In the current in vitro research,murine macrophage RAW 264.7 cell were infected by mouse hepatitis virus,a coronavirus existed in mouse.At 3-,6-,12-,24-,and 48-h post infection(hpi.),the attached cells were washed with PBS and harvested in Trizol reagent.Then The harvest is subjected to transcriptome sequencing.Results:The transcriptome analysis showed the immediate(3 hpi.)up regulation of DEGs related to inflammation,like Il1b and Il6.DEGs related to M2 differential po-larization,like Irf4 showed up regulation at 24 hpi.,the late term after viral infection.In addition,DEGs related to metabolism and histone modification,like Ezh2 were de-tected,which might correlate with the trained immunity of macrophages.Conclusions:The current in vitro viral infection study showed the key innated im-munity character of macrophages,which suggested the replacement value of viral infection cells model,to reduce the animal usage in preclinical research.
基金The Science and Technology Plan of Dalian under contract Nos 2023RO058 and 2022RQ060the Liaoning Province Natural Science Planning Fund Project under contract No. 2022-BS-273+1 种基金the Liaoning Provincial Department of Education Basic Research Project under contract No. LJKQZ20222357the Discipline Construction Funding for Marine Science Subject of Dalian Ocean University。
文摘Mandarin fish(Siniperca scherzeri) has high market prices and significant market potential in China because of its highquality meat and high nutritional value. However, due to the limited scale of aquaculture, meeting the market demand is difficult, making the effective development of the aquaculture potential of mandarin fish an important challenge for the industry. In this study, a 30-d breeding experiment was conducted on mandarin fish larvae under three photoperiod conditions: G1 8 h light:16 h dark(8L:16D), G2 12 h light:12 h dark(12L:12D), and G3 16 h light:8 h dark(16L:8D). The results showed that the G2 group exhibited the best growth performance and development status, with final body weights, weight gain rates, and specific growth rates all higher than those of the other two groups(P < 0.05). Observations of sections from each group revealed that the intestinal villi length and muscle thickness of the G2 group were significantly greater than those of the other two groups(P < 0.05). The G2 group inhibited the transcriptional activation of key circadian rhythm genes, including nr1d2a, nr1d1 and per1, while upregulating the expression of BMAL1 in S. scherzeri.The activation of both the insulin signalling pathway and the Fox O signalling pathway enhanced the efficient secretion of insulin, which subsequently played a critical role in regulating fatty acid metabolism. This active fatty acid metabolism provided an optimal energy supply, ensuring that other nutrients were fully utilized during the growth and development process while minimizing unnecessary nutrient loss. Consequently, this mechanism effectively promoted the overall growth and development of S. scherzeri. This study was the first to elucidate the transcriptomic expression patterns of S. scherzeri under varying photoperiod conditions. In response to the cyclic alternation of day and night, S. scherzeri regulated their metabolic levels and the transcriptional activation of downstream target genes via insulin signalling.
基金supported by the National Key R&D Programof China(2020YFD1000400)the National Natural Science Foundation of China(32072603)+1 种基金the Jiangsu Agriculture Science and Technology Innovation Fund,China(CX(21)2004)the JBGS Project of Seed Industry Revitalization in Jiangsu Province,China(JBGS[2021]020).
文摘Nitrogen(N)is a limiting factor that determines the yield and quality of chrysanthemum.Genetic variation in N use efficiency(NUE)has been reported among chrysanthemum genotypes.We performed a transcriptome analysis of two chrysanthemum genotypes,'Nannonglihuang'(LH,N-efficient genotype)and'Nannongxuefeng"(XF,N-inefficient genotype),under low N(0.4 mmol L^(-1)N)and normal N(8 mmol L^(-1)N)treatments for 15 d and an N recovery treatment for 12 h(low N treatment for 15 d and then normal N treatment for 12 h)to understand the genetic factors impacting NUE in chrysanthemum.The two genotypes exhibited contrasting responses to the different N treatments.The N-efficient genotype LH had significant superiority in agronomic traits,N accumulation and glutamine synthase activity under both normal N and low N treatments.Low N treatment promoted root growth in LH,but inhibited root growth in XF.Transcriptome analysis revealed that the low N treatment increased the expression of some N metabolism genes,genes related to auxin and abscisic acid signal transduction in the roots of both genotypes,as well as genes related to gibberellin signal transduction in roots of LH.The N recovery treatment just increased the expression of genes related to cytokinin signal transduction in roots of LH.The expression levels of the NRT2.1,AMT1.1,and Gln1 genes related to gibberellin and cytokinin signal transduction were higher in roots of LH than in XF under different N treatments,suggesting that the genes related to N metabolism and hormone(auxin,abscisic acid,gibberellin,and cytokinin)signal transduction in roots of LH are more sensitive to different N treatments than those of XF.Co-expression network analysis(WGCNA)also identified hub genes like bZIP43,bHLH93,NPF6.3,IBR10,MYB62,PP2C,PP2C06 and NLP7,which may be the key regulators of N-mediated responses in chrysanthemum and play crucial roles in enhancing NUE and resistance to low N stress in the N-efficient chrysanthemum genotype.These results revealed the key factors involved in regulating NUE in chrysanthemum at the genetic level,which provides new insights into the complex mechanism of efficient nitrogen utilization in chrysanthemum,and can be useful for the improvement and breeding of high NUE chrysanthemum genotypes.
基金supported by the Major Innovation Project of Shandong Province, China (2022CXGC010605)the National Natural Science Foundation of China (32172518 and 32002023)+1 种基金the National Key R&D Program of China (2023YFD2301103)the Key R&D Projects in Ningxia Hui Autonomous Region, China (2022BBF02014)。
文摘Evaluating plant stress tolerance and screening key regulatory genes under the combined stresses of high temperature and drought are important for studying plant stress tolerance mechanisms. In this study, the drought tolerance of five grape varieties was evaluated under high-temperature conditions to screen key genes for further exploration of resistance mechanisms. By comparing and analysing the morphological characteristics and physiological indicators associated with the response of grapevines to drought stress and integrating them with the membership function to assess the strength of their drought tolerance, the order of drought tolerance was found to be as follows: 420A>110R>Cabernet Sauvignon(CS)>Fercal>188-08. To further analyse the mechanism of differences in drought tolerance, transcriptomic sequencing was performed on the drought-tolerant cultivar 420A, the drought-sensitive cultivar 188-08 and the control cultivar CS. The functional analysis of differential metabolic pathways indicated that the differentially expressed genes were enriched mainly in biological process category, that 420A had higher antioxidant activity. Furthermore, differentially expressed transcription factors were analyzed in five grape varieties. Genes like Vv AGL15, Vv LBD41, and Vv MYB86 showed close associations with drought tolerance,indicating their potential role in regulating drought tolerance and research significance.
