The genus Thuja is ideal for investigating the genetic basis of the East Asia-North America disjunction.The biogeographical background of the genus is debatable and an adaptive strategy is lacking.Through the analysis...The genus Thuja is ideal for investigating the genetic basis of the East Asia-North America disjunction.The biogeographical background of the genus is debatable and an adaptive strategy is lacking.Through the analysis and mining of comparative transcriptomes,species differentiation and positively selected genes(PSGs)were identified to provide information for understanding the environmental adaptation strategies of the genus Thuja.De novo assembly yielded 44,397-74,252 unigenes of the five Thuja species with contig N50length ranging from 1,559 to 1,724 bp.Annotations revealed a similar distribution of functional categories among them.Based on the phylogenetic trees constructed using the transcriptome data,T.sutchuenensis was divided first,followed by T.plicata and T.occidentalis.The final differentiation of T.koraiensis and T.standishii formed a clade.Enrichment analysis indicated that the PSGs of the North American Thuja species were involved in plant hormone signal transduction and carbon fixation of photosynthetic organisms pathways.The PSGs of East Asian Thuja were related to phenolic,alkaloid,and terpenoid synthesis,important stress-resistant genes and could increase plant resistance to external environmental stresses.This study discovered numerous aroma synthetic-related PSGs including terpene synthase(TPS)genes and lipid phosphate phosphatase 2(LPP2),associated with the synthetic aroma of T.sutchuenensis.Physiological indicators,such as the contents of soluble sugars,total chlorophyll,total phenolics,and total flavonoids were determined,which are consistent with the PSGs enrichment pathways associated with adaptive strategies in the five Thuja species.The results of this study provide an important basis for future studies on conservation genetics.展开更多
Background:Tibetan chickens,a unique native breed in the Qinghai-Tibet Plateau of China,possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment.Increasing evidence sugge...Background:Tibetan chickens,a unique native breed in the Qinghai-Tibet Plateau of China,possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment.Increasing evidence suggests that long non-coding RNAs(lncRNAs)and microRNAs(miRNAs)play roles in the hypoxic adaptation of high-altitude animals,although their exact involvement remains unclear.Results:This study aimed to elucidate the global landscape of mRNAs,lncRNAs,and miRNAs using transcriptome sequencing to construct a regulatory network of competing endogenous RNAs(ceRNAs)and thus provide insights into the hypoxic adaptation of Tibetan chicken embryos.In total,354 differentially expressed genes(DE genes),389 differentially expressed lncRNAs(DE lncRNAs),and 73 differentially expressed miRNAs(DE miRNAs)were identified between Tibetan chickens(TC)and control Chahua chickens(CH).GO and KEGG enrichment analysis revealed that several important DE miRNAs and their target DE lncRNAs and DE genes are involved in angiogenesis(including blood vessel development and blood circulation)and energy metabolism(including glucose,carbohydrate,and lipid metabolism).The ceRNA network was then constructed with the predicted DE gene-DE miRNA-DE lncRNA interactions,which further revealed the regulatory roles of these differentially expressed RNAs during hypoxic adaptation of Tibetan chickens.Conclusions:Analysis of transcriptomic data revealed several key candidate ceRNAs that may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism.These results provide insights into the molecular mechanisms of hypoxic adaptation regulatory networks from the perspective of coding and non-coding RNAs.展开更多
RNA sequencing of the sensitive GH01 variety of Brassica napus L. seedling roots under 12 h of waterlogging was compared with previously published data of the ZS9 tolerant variety to unravel genetic mechanisms of wate...RNA sequencing of the sensitive GH01 variety of Brassica napus L. seedling roots under 12 h of waterlogging was compared with previously published data of the ZS9 tolerant variety to unravel genetic mechanisms of waterlogging tolerance beyond natural variation. A total of 2 977 genes with similar expression patterns and 17 genes with opposite expression patterns were identiifed in the transcription proifles of ZS9 and GH01. An additional 1 438 genes in ZS9 and 1 861 genes in GH01 showed strain speciifc regulation. Analysis of the overlapped genes between ZS9 and GH01 revealed that waterlogging tolerance is determined by ability to regulate genes with similar expression patterns. Moreover, differences in both gene expression proifles and abscisic acid (ABA) contents between the two varieties suggest that ABA may play some role in waterlogging tolerance. This study identiifes a subset of candidate genes for further functional analysis.展开更多
Tassel, the male reproductive organs in maize, its development is adversely affected by drought during tasseling. To determine drought tolerance mechanisms of tassel differentiation at transcriptome level, RNA-Seq was...Tassel, the male reproductive organs in maize, its development is adversely affected by drought during tasseling. To determine drought tolerance mechanisms of tassel differentiation at transcriptome level, RNA-Seq was performed using RNA of early developing tassel from 10 maize inbred lines under well-watered （control） and drought-stressed conditions, respectively. Results showed that the most active pathway for drought stress in maize were related to metabolic regulation at RNA level. And some genes, encoding enzymes involved in carbohydrate and lipid metabolism, were significantly down-regulated in drought-stressed plants. While, the transcription factors and genes, encoding catabolic or degradative enzymes, were over-expressed in maize early developing tassels under drought-stressed conditions, and among them, the transcripts of genes encoding exon-junction complexes involved in ＇RNA transcript＇ and ＇mRNA surveillance＇ pathways were significantly affected by drought stress. In addition, many other genes related to drought stress showed transcriptional changes at the later period of stress.展开更多
The sea cucumberApostichopus japonicus is an important economic species in China. Its dorsal body wall color is commonly tawny, whereas its ventral surface is fawn. Albino sea cucumbers are rarely observed. In order t...The sea cucumberApostichopus japonicus is an important economic species in China. Its dorsal body wall color is commonly tawny, whereas its ventral surface is fawn. Albino sea cucumbers are rarely observed. In order to profile gene expression and screen albinism-related genes, we compared the transcriptome of albino samples with a control by 454 cDNA sequencing. We found that 6 539 identified genes on the basis of sequence similarity to known genes were expressed in the albino A. japonicus. The gene ontology analysis indicated that the transcription of genes associated with the terms of biological regulation and pigmenta-tion was non-abundant in the albino library compared to the control. Based on an analysis using the Kyoto Encyclopedia of Genes and Genomics （KEGG） database, we identified 14 important genes that were in-volved in major intercellular signaling pathways related to melanin synthesis, such as tyrosine metabolism, the mitogen-activated protein kinase （MAPK） pathway, and melanogenesis. The expressions of fibroblast growth factor receptor 4 （FGFR4）, protein kinase C （PKC）, protein kinase A （PKA）, and Ras genes were sig-nificantly down-regulated in the albino transcriptome compared with the control, while the expressions of homogentisate 1, 2-dioxygenase gene （HGO）, cAMP-responsive element binding protein （CREB）, transcrip-tion factor AP-1（c-jun）, and calmodulin （CaM） were significantly up-regulated （Fisher＇s exact test,p 〈 0.05）. These differentially expressed genes could be candidate genes for revealing the mechanism of albinism and investigating regulation of melanin synthesis inA. japonicus.展开更多
Lactation in dairy cattle is coupled with increased nutrient requirements for milk synthesis. Therefore, dairy cattle metabolism has to adapt to meet lactation-associated challenges and requires major functional adjus...Lactation in dairy cattle is coupled with increased nutrient requirements for milk synthesis. Therefore, dairy cattle metabolism has to adapt to meet lactation-associated challenges and requires major functional adjustments of the rumen and whole digestive system. This report describes the use of next-generation sequencing technology for assembly and profiling of the transcriptome of cattle rumen epithelial tissues from cattle in both dry and lactation periods. Transcriptomics profiling and comparison revealed extensive changes in gene expression related to metabolism in rumen epithelial tissue due to the adaptation to lactation. Ruminal epithelial adaptation to the challenges of metabolism and high nutrient requirements during lactation is presumably the primary triggers for these alterations in gene expression. Principal component analysis (PCA) indicated that the gene expression profiles of the rumen epithelia from dry and lactating cattle fall into two very distinct clusters. Gene Ontology (GO) enrichment analysis revealed that the most GO terms were related to various metabolic processes in lactating cattle. The most significantly (false discovery rate (FDR) p-value < 0.05) enriched GO term in biological processes was “carbohydrate derivative metabolic process”, followed by “nucleoside metabolic process”. Up-stream regulators, such as PPARA (Peroxisome proliferator-activated receptor alpha) gene, and up-regulated genes of molecular transporters are the focal points of this report.展开更多
The genus Croomia(Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia(EA)-Eastern North America(ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In ad...The genus Croomia(Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia(EA)-Eastern North America(ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In addition to the presence of both actinomorphic and zygomorphic flowers within the genus, species are disjunctively distributed between EA and ENA. However, due to the limited availability of genomic resources, few studies of Croomia have examined these questions. In this study,we sequenced the floral and leaf transcriptomes of the zygomorphic flowered Croomia heterosepala and the actinomorphic flowered Croomia japonica, and used comparative genomic approaches to investigate the transcriptome evolution of the two closely related species. The sequencing and de novo assembly of transcriptomes from flowers of C. heterosepala(ChFlower), flowers of C. japonica(CjFlower), and leaves of C. japonica(CjLeaf) yielded 57,193, 62,131 and 64,448 unigenes, respectively. In addition, estimation of Ka/Ks ratios for 11,566 potential orthologous groups between ChFlower and CjFlower revealed that only six pairs had Ka/Ks ratios significantly greater than 1 and are likely under positive selection. A total of 429 single copy nuclear genes(SCNGs) and 21,460 expression sequence tags-simple sequence repeats(ESTSSRs) were identified in this study. Specifically, we identified seven CYC/TB1-like genes from Stemonaceae. Phylogenetic and molecular evolution analyses indicated that these CYC/TB1-like genes formed a monophyletic clade(SteTBL1) and were subject to strong purifying selection. The shifts of floral symmetry in Stemonaceae do not appear to be correlated with TBL copy number.展开更多
Oxidative stress induced by factors such as ammonia nitrogen has become a major issue in shrimp farming.The effects of carotenoids on the growth and antioxidant capability of Litopenaeus vannamei juveniles were invest...Oxidative stress induced by factors such as ammonia nitrogen has become a major issue in shrimp farming.The effects of carotenoids on the growth and antioxidant capability of Litopenaeus vannamei juveniles were investigated in this study using dietary archaeal carotenoids supplementation.For four weeks,shrimp were given diets containing 0 mg/kg(Ctrl)and 55.98 mg/kg(Car)archaeal carotenoids.Dietary archaeal carotenoids significantly enhanced the astaxanthin content in shrimp muscles and carapaces,as well as the superoxide dismutase(SOD)and glutathione peroxidase(GSH-Px)activity(P<0.05).The malonaldehyde(MDA)content in Car group significantly decreased(P<0.05).The transcriptome analysis was conducted to determine the molecular processes in response to archaeal carotenoids supplementation.A total of 1536 differentially expressed genes(DEGs)were detected,including 538 upregulated DEGs and 998 downregulated DEGs.GO functional enrichment analysis between Ctrl and Car indicated that 26 GO terms including extracellular region,metabolic process,and proteolysis were enriched.The KEGG pathway enrichment analysis revealed that the amino sugar and nucleotide sugar metabolism,cysteine and methionine metabolism,glycine serine and threonine metabolism,and amino acid biosynthesis were enriched.Archaeal carotenoids influenced the expression of several important genes involved in reactive oxygen species(ROS)generation,Nrf2 signaling,and antioxidant enzymes.Seven DEGs were chosen to confirm the RNA-Seq data using qRT-PCR.The genes and pathways discovered in this work assist to elucidate the molecular processes through which archaeal carotenoid enhances L.vannamei antioxidative system.展开更多
Characterization of occurrence, density and motif sequence of tandem repeats in the transcribed regions is helpful in understanding the functional significance of these repeats in the modern genomes. We analyzed tande...Characterization of occurrence, density and motif sequence of tandem repeats in the transcribed regions is helpful in understanding the functional significance of these repeats in the modern genomes. We analyzed tandem repeats present in expressed sequences of thirteen species belonging to genera Capsicum, Nicotiana, Petunia and Solanum of family Solanaceae and the genus Coffea of Rubiaceae to investigate the propagation and evolutionary sustenance of these repeats. Tandem repeat containing sequences constituted 1.58% to 7.46% of sequences analyzed. Tandem repetitions of size 2, 15, 18 and 21 bp motifs were more frequent. Repeats with unit sizes 21 and 22 bp were also abundant in genomic sequences of potato and tomato. While mutations occurring in these repeats may alter the repeat number, genomes adjust to these changes by keeping the translated products unaffected. Surprisingly, in majority of the species under study, tandem repeat motif length did not exceed 228 bp. Conserved tandem repeat motifs of sizes 180, 192 and 204 bp were also abundant in the genomic sequences. Our observations lead us to propose that these tandem repeats are actually remnants of ancestral megasatellite repeats, which have split into multiple repeats due to frequent insertions over the course of evolution.展开更多
The diversity of cell types in the brain and how these change during different developmental stages,remains largely unknown.The life cycle of insects is short and goes through 4 distinct stages including embryonic,lar...The diversity of cell types in the brain and how these change during different developmental stages,remains largely unknown.The life cycle of insects is short and goes through 4 distinct stages including embryonic,larval,pupal,and adult stages.During postembryonic life,the larval brain transforms into a mature adult version after metamorphosis.The silkworm,Bombyx mori,is a lepidopteran model insect.Here,we characterized the brain cell repertoire of larval and adult B.mori by obtaining 50708 single-cell transcriptomes.Seventeen and 12 cell clusters from larval and adult brains were assigned based on marker genes,respectively.Identified cell types include Kenyon cells,optic lobe cells,monoaminergic neurons,surface glia,and astrocyte glia.We further assessed the cell type compositions of larval and adult brains.We found that the transition from larva to adult resulted in great expansion of glial cells.The glial cell accounted for 49.8%of adult midbrain cells.Compared to flies and ants,the mushroom body kenyon cell is insufficient in B.mori,which accounts for 5.4%and 3.6%in larval and adult brains,respectively.Analysis of neuropeptide expression showed that the abundance and specificity of expression varied among individual neuropeptides.Intriguingly,we found that ion transport peptide was specifically expressed in glial cells of larval and adult brains.The cell atlas dataset provides an important resource to explore cell diversity,neural circuits and genetic profiles.展开更多
The cerebellum is critical for controlling motor and non-motor functions via cerebellar circuit that is composed of defined cell types, which approximately account for more than half of neurons in mammalsThe molecular...The cerebellum is critical for controlling motor and non-motor functions via cerebellar circuit that is composed of defined cell types, which approximately account for more than half of neurons in mammalsThe molecular mechanisms controlling developmental progression and maturation processes of various cerebellar cell types need systematic investigationHere, we analyzed transcriptome profiles of 21119 single cells of the postnatal mouse cerebellum and identified eight main cell clusters. Functional annotation of differentially expressed genes revealed trajectory hierarchies of granule cells (GCs) at various states and implied roles of mitochondrion and ATPases in the maturation of Purkinje cells (PCs), the sole output cells of the cerebellar cortexFurthermore, we analyzed gene expression patterns and co-expression networks of 28 ataxia risk genes, and found that most of them are related with biological process of mitochondrion and around half of them are enriched in PCs. Our results also suggested core transcription factors that are correlated with interneuron differentiation and characteristics for the expression of secretory proteins in glia cells, which may participate in neuronal modulationThus, this study presents a systematic landscape of cerebellar gene expression in defined cell types and a general gene expression framework for cerebellar development and dysfunction.展开更多
Elucidating the complex dynamic cellular organization in the hypothalamus is critical for understanding its role in coordinating fundamental body functions. Over the past decade, single-cell and spatial omics technolo...Elucidating the complex dynamic cellular organization in the hypothalamus is critical for understanding its role in coordinating fundamental body functions. Over the past decade, single-cell and spatial omics technologies have significantly evolved, overcoming initial technical challenges in capturing and analyzing individual cells. These high-throughput omics technologies now offer a remarkable opportunity to comprehend the complex spatiotemporal patterns of transcriptional diversity and cell-type characteristics across the entire hypothalamus. Current single-cell and single-nucleus RNA sequencing methods comprehensively quantify gene expression by exploring distinct phenotypes across various subregions of the hypothalamus. However, single-cell/single-nucleus RNA sequencing requires isolating the cell/nuclei from the tissue, potentially resulting in the loss of spatial information concerning neuronal networks. Spatial transcriptomics methods, by bypassing the cell dissociation, can elucidate the intricate spatial organization of neural networks through their imaging and sequencing technologies. In this review, we highlight the applicative value of single-cell and spatial transcriptomics in exploring the complex molecular-genetic diversity of hypothalamic cell types, driven by recent high-throughput achievements.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
We previously demonstrated that inhibiting neural stem cells necroptosis enhances functional recovery after spinal cord injury.While exosomes are recognized as playing a pivotal role in neural stem cells exocrine func...We previously demonstrated that inhibiting neural stem cells necroptosis enhances functional recovery after spinal cord injury.While exosomes are recognized as playing a pivotal role in neural stem cells exocrine function,their precise function in spinal cord injury remains unclear.To investigate the role of exosomes generated following neural stem cells necroptosis after spinal cord injury,we conducted singlecell RNA sequencing and validated that neural stem cells originate from ependymal cells and undergo necroptosis in response to spinal cord injury.Subsequently,we established an in vitro necroptosis model using neural stem cells isolated from embryonic mice aged 16-17 days and extracted exosomes.The results showed that necroptosis did not significantly impact the fundamental characteristics or number of exosomes.Transcriptome sequencing of exosomes in necroptosis group identified 108 differentially expressed messenger RNAs,104 long non-coding RNAs,720 circular RNAs,and 14 microRNAs compared with the control group.Construction of a competing endogenous RNA network identified the following hub genes:tuberous sclerosis 2(Tsc2),solute carrier family 16 member 3(Slc16a3),and forkhead box protein P1(Foxp1).Notably,a significant elevation in TSC2 expression was observed in spinal cord tissues following spinal cord injury.TSC2-positive cells were localized around SRY-box transcription factor 2-positive cells within the injury zone.Furthermore,in vitro analysis revealed increased TSC2 expression in exosomal receptor cells compared with other cells.Further assessment of cellular communication following spinal cord injury showed that Tsc2 was involved in ependymal cellular communication at 1 and 3 days post-injury through the epidermal growth factor and midkine signaling pathways.In addition,Slc16a3 participated in cellular communication in ependymal cells at 7 days post-injury via the vascular endothelial growth factor and macrophage migration inhibitory factor signaling pathways.Collectively,these findings confirm that exosomes derived from neural stem cells undergoing necroptosis play an important role in cellular communication after spinal cord injury and induce TSC2 upregulation in recipient cells.展开更多
Background:This study aims to identify distinct cellular subtypes within brain tissue using single-cell transcriptomic analysis,focusing on specific biomarkers that differentiate cell types and the effects of traditio...Background:This study aims to identify distinct cellular subtypes within brain tissue using single-cell transcriptomic analysis,focusing on specific biomarkers that differentiate cell types and the effects of traditional and exercise therapy.Methods:Four samples were analyzed:older control(OC),older exercise(OE),younger control(YC),and younger exercise(YE).Single-cell RNA sequencing was used to distinguish cellular subtypes through their biomarker profiles.Data visualization included violin and t-SNE plots to illustrate biomarker expression across cell clusters such as oligodendrocytes,microglia,and astrocytes.Additionally,BV2 cells were exposed to amyloid-beta fragments to simulate Alzheimer’s disease,assessing the impact of exercise-induced cellular responses.Results:Distinct cellular subtypes were identified:oligodendrocytes(MBP,St18),microglia(Dock8),and astrocytes(Aqp4,Gpc5).Sample OE was predominantly oligodendrocytes,while YE had more astrocytes,inhibitory neurons,and Canal-Retzius cells.YC showed a significant presence of Olfm3+ganglion neurons.ZEB1 gene knockout revealed changes in SMAD family gene expression,which regulate ferroptosis.Oxidative stress levels were also evaluated.Conclusion:This profiling enhances our understanding of brain cellular functions and interactions,potentially informing targeted therapies in neurological research.Exercise may influence brain cell immune responses and cell death pathways by regulating specific gene expressions,offering new insights for treating neuroinflammation and degeneration.展开更多
Pecan is an extremely important crop cultivated worldwide for edible nuts and nut oil.Considering the changes in precipitation and soil moisture caused by climate change and worsening global water scarcity,it is impor...Pecan is an extremely important crop cultivated worldwide for edible nuts and nut oil.Considering the changes in precipitation and soil moisture caused by climate change and worsening global water scarcity,it is important to understand the mechanism of pecan response to drought.To this end,this study investigated the response of pecan to drought stress and rehydration using physiological and transcriptomic analyses.Superoxide dismutase(SOD)enzyme activity in leaves was significantly upregulated during drought stress,suggesting that it might play an important role in drought response.Weighted gene co-expression network analysis of the transcriptome data was used to screen for a key drought-responsive gene,CiNAC2,which was overexpressed in Arabidopsis thaliana for functional validation.The analysis of stomatal apertures and the water loss rate in leaves showed that CiNAC2 might respond to drought stress via mediating stomatal aperture size.In addition,CiNAC2 could promote root growth under drought conditions.CiSOD1 was verified as a direct target gene of CiNAC2 by yeast one-hybrid assay dual-luciferase reporter assay.Yeast one-hybrid analysis confirmed that CiNAC2 bound to the promoters of CiSOD1.Transient expression in Nicotiana benthamiana epidermis showed that CiNAC2 upregulated the expression of CiSOD1.These results demonstrated that CiNAC2 enhanced drought stress tolerance via promoting SOD activity in pecan and provided a theoretical basis for breeding drought-resistant varieties in pecan.展开更多
Ascorbic acid, also referred to as vitamin C(Vc), is an important nutrient found in fruits and vegetables that promotes produce quality and human health. Rosa roxburghii is an underutilized natural fruit that contains...Ascorbic acid, also referred to as vitamin C(Vc), is an important nutrient found in fruits and vegetables that promotes produce quality and human health. Rosa roxburghii is an underutilized natural fruit that contains very high levels of Vc. However, the Vc content of R. roxburghii varies considerably during plant development and ripening. To better understand the molecular mechanisms that underlie fluctuations in Vc content of R. roxburghii fruit at different developmental stages, we performed transcriptomic and metabolomic analyses and identified two significant gene networks/modules and 168 transcription factors directly involved in Vc synthesis. Promoter analysis of two core genes involved in Vc synthesis, RrGGP and RrGalUR, revealed the presence of a retroviral long terminal repeat(LTR) insert in the RrGalUR promoter. Using yeast one-hybrid and dual-luciferase assays, we demonstrated that the transcription factors RrHY5H and RrZIP9 bind to the promoter of RrGGP to promote its expression. RrZIP6 and RrWRKY4 bind to the LTR in the RrGalUR promoter to promote its expression. Our results reveal a molecular mechanism that controls Vc synthesis and accumulation in R. roxburghii fruit.展开更多
BACKGROUND Schizophrenia(SZ),a chronic and widespread brain disorder,presents with complex etiology and pathogenesis that remain inadequately understood.Despite the absence of a universally recognized endophenotype,pe...BACKGROUND Schizophrenia(SZ),a chronic and widespread brain disorder,presents with complex etiology and pathogenesis that remain inadequately understood.Despite the absence of a universally recognized endophenotype,peripheral blood mononuclear cells(PBMCs)serve as a robust model for investigating intracellular alterations linked to SZ.AIM To preliminarily investigate potential pathogenic mechanisms and identify novel biomarkers for SZ.METHODS PBMCs from SZ patients were subjected to integrative transcriptomic and proteomic analyses to uncover differentially expressed genes(DEGs)and differentially expressed proteins while mapping putative disease-associated signaling pathways.Key findings were validated using western blot(WB)and real-time fluorescence quantitative PCR(RT-qPCR).RNAi-lentivirus was employed to transfect rat hippocampal CA1 neurons in vitro,with subsequent verification of target gene expression via RT-qPCR.The levels of neuronal conduction proteins,including calmodulin-dependent protein kinase II(caMKII),CREB,and BDNF,were assessed through WB.Apoptosis was quantified by flow cytometry,while cell proliferation and viability were evaluated using the Cell Counting Kit-8 assay.RESULTS The integration of transcriptomic and proteomic analyses identified 6079 co-expressed genes,among which 25 DEGs were significantly altered between the SZ group and healthy controls.Notably,haptoglobin(HP),lactotransferrin(LTF),and SERPING1 exhibited marked upregulation.KEGG pathway enrichment analysis implicated neuroactive ligand-receptor interaction pathways in disease pathogenesis.Clinical sample validation demonstrated elevated protein and mRNA levels of HP,LTF,and SERPING1 in the SZ group compared to controls.WB analysis of all clinical samples further corroborated the significant upregulation of SERPING1.In hippocampal CA1 neurons transfected with lentivirus,reduced SERPING1 expression was accompanied by increased levels of CaMKII,CREB,and BDNF,enhanced cell viability,and reduced apoptosis.CONCLUSION SERPING1 may suppress neural cell proliferation in SZ patients via modulation of the CaMKII-CREB-BDNF signaling pathway.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
Tomato(Solanum lycopersicum)is an important fruit and vegetable crop in worldwide.The fertility of tomato reproductive organs can be dramatically decreased when ambient temperatures rise above 35°C,reducing tomat...Tomato(Solanum lycopersicum)is an important fruit and vegetable crop in worldwide.The fertility of tomato reproductive organs can be dramatically decreased when ambient temperatures rise above 35°C,reducing tomato fruit yield.It is necessary to identify transcription factors(TFs)and target genes involved in heat stress response(HSR)signaling cascades in tomato flower buds to improve tomato plant thermotolerance.In this study,we profiled genes expressed in three developmental stages of tomato flower buds.Red and turquoise modules for heat stress(HS)were identified through gene co-expression network analysis,and the genes within these modules were enriched in HS-related pathways.By focusing on the TFs in the two modules,we identified several novel HSR-related TFs,including SlWRKY75,SlMYB117,and SlNAM.Furthermore,homology analysis illustrated a conserved signaling cascade in tomato.Lastly,we identified and experimentally validated four HSF-regulated genes,namely SlGrpE,SlERDJ3A,SlTIL,and SlPOM1,that likely modulate thermotolerance in plants.These results provide a high-resolution atlas of gene expression during tomato flower bud development under HS conditions,which is a valuable resource for uncovering potential regulatory networks associated with the HSR in tomato.展开更多
基金supported by the National Natural Science Foundation of China(31870664)the 948 Program of National Forestry and Grassland Administration(2013-4-47)the National Key Research and Development Program of China(2022YFD2200103)。
文摘The genus Thuja is ideal for investigating the genetic basis of the East Asia-North America disjunction.The biogeographical background of the genus is debatable and an adaptive strategy is lacking.Through the analysis and mining of comparative transcriptomes,species differentiation and positively selected genes(PSGs)were identified to provide information for understanding the environmental adaptation strategies of the genus Thuja.De novo assembly yielded 44,397-74,252 unigenes of the five Thuja species with contig N50length ranging from 1,559 to 1,724 bp.Annotations revealed a similar distribution of functional categories among them.Based on the phylogenetic trees constructed using the transcriptome data,T.sutchuenensis was divided first,followed by T.plicata and T.occidentalis.The final differentiation of T.koraiensis and T.standishii formed a clade.Enrichment analysis indicated that the PSGs of the North American Thuja species were involved in plant hormone signal transduction and carbon fixation of photosynthetic organisms pathways.The PSGs of East Asian Thuja were related to phenolic,alkaloid,and terpenoid synthesis,important stress-resistant genes and could increase plant resistance to external environmental stresses.This study discovered numerous aroma synthetic-related PSGs including terpene synthase(TPS)genes and lipid phosphate phosphatase 2(LPP2),associated with the synthetic aroma of T.sutchuenensis.Physiological indicators,such as the contents of soluble sugars,total chlorophyll,total phenolics,and total flavonoids were determined,which are consistent with the PSGs enrichment pathways associated with adaptive strategies in the five Thuja species.The results of this study provide an important basis for future studies on conservation genetics.
基金supported by the National Natural Science Foundation of China(31972532)the China Agricultural Research System(CARS-40-K05)the Innovation Base Cu。
文摘Background:Tibetan chickens,a unique native breed in the Qinghai-Tibet Plateau of China,possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment.Increasing evidence suggests that long non-coding RNAs(lncRNAs)and microRNAs(miRNAs)play roles in the hypoxic adaptation of high-altitude animals,although their exact involvement remains unclear.Results:This study aimed to elucidate the global landscape of mRNAs,lncRNAs,and miRNAs using transcriptome sequencing to construct a regulatory network of competing endogenous RNAs(ceRNAs)and thus provide insights into the hypoxic adaptation of Tibetan chicken embryos.In total,354 differentially expressed genes(DE genes),389 differentially expressed lncRNAs(DE lncRNAs),and 73 differentially expressed miRNAs(DE miRNAs)were identified between Tibetan chickens(TC)and control Chahua chickens(CH).GO and KEGG enrichment analysis revealed that several important DE miRNAs and their target DE lncRNAs and DE genes are involved in angiogenesis(including blood vessel development and blood circulation)and energy metabolism(including glucose,carbohydrate,and lipid metabolism).The ceRNA network was then constructed with the predicted DE gene-DE miRNA-DE lncRNA interactions,which further revealed the regulatory roles of these differentially expressed RNAs during hypoxic adaptation of Tibetan chickens.Conclusions:Analysis of transcriptomic data revealed several key candidate ceRNAs that may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism.These results provide insights into the molecular mechanisms of hypoxic adaptation regulatory networks from the perspective of coding and non-coding RNAs.
文摘RNA sequencing of the sensitive GH01 variety of Brassica napus L. seedling roots under 12 h of waterlogging was compared with previously published data of the ZS9 tolerant variety to unravel genetic mechanisms of waterlogging tolerance beyond natural variation. A total of 2 977 genes with similar expression patterns and 17 genes with opposite expression patterns were identiifed in the transcription proifles of ZS9 and GH01. An additional 1 438 genes in ZS9 and 1 861 genes in GH01 showed strain speciifc regulation. Analysis of the overlapped genes between ZS9 and GH01 revealed that waterlogging tolerance is determined by ability to regulate genes with similar expression patterns. Moreover, differences in both gene expression proifles and abscisic acid (ABA) contents between the two varieties suggest that ABA may play some role in waterlogging tolerance. This study identiifes a subset of candidate genes for further functional analysis.
基金jointly funded by the National Natural Science Foundation of China (31661143010)the Pilot Project of Breeding of the Seven Major Crops,China (2016YFD0101803)
文摘Tassel, the male reproductive organs in maize, its development is adversely affected by drought during tasseling. To determine drought tolerance mechanisms of tassel differentiation at transcriptome level, RNA-Seq was performed using RNA of early developing tassel from 10 maize inbred lines under well-watered （control） and drought-stressed conditions, respectively. Results showed that the most active pathway for drought stress in maize were related to metabolic regulation at RNA level. And some genes, encoding enzymes involved in carbohydrate and lipid metabolism, were significantly down-regulated in drought-stressed plants. While, the transcription factors and genes, encoding catabolic or degradative enzymes, were over-expressed in maize early developing tassels under drought-stressed conditions, and among them, the transcripts of genes encoding exon-junction complexes involved in ＇RNA transcript＇ and ＇mRNA surveillance＇ pathways were significantly affected by drought stress. In addition, many other genes related to drought stress showed transcriptional changes at the later period of stress.
基金The National Natural Science Foundation of China under contract No.40976089the State Science&Technology Support Program in the 12th Five Year Plan of China under contract No.2011BAD13B05the National High-tech R&D Program of China(863 Program) under contract No.2012AA10A412
文摘The sea cucumberApostichopus japonicus is an important economic species in China. Its dorsal body wall color is commonly tawny, whereas its ventral surface is fawn. Albino sea cucumbers are rarely observed. In order to profile gene expression and screen albinism-related genes, we compared the transcriptome of albino samples with a control by 454 cDNA sequencing. We found that 6 539 identified genes on the basis of sequence similarity to known genes were expressed in the albino A. japonicus. The gene ontology analysis indicated that the transcription of genes associated with the terms of biological regulation and pigmenta-tion was non-abundant in the albino library compared to the control. Based on an analysis using the Kyoto Encyclopedia of Genes and Genomics （KEGG） database, we identified 14 important genes that were in-volved in major intercellular signaling pathways related to melanin synthesis, such as tyrosine metabolism, the mitogen-activated protein kinase （MAPK） pathway, and melanogenesis. The expressions of fibroblast growth factor receptor 4 （FGFR4）, protein kinase C （PKC）, protein kinase A （PKA）, and Ras genes were sig-nificantly down-regulated in the albino transcriptome compared with the control, while the expressions of homogentisate 1, 2-dioxygenase gene （HGO）, cAMP-responsive element binding protein （CREB）, transcrip-tion factor AP-1（c-jun）, and calmodulin （CaM） were significantly up-regulated （Fisher＇s exact test,p 〈 0.05）. These differentially expressed genes could be candidate genes for revealing the mechanism of albinism and investigating regulation of melanin synthesis inA. japonicus.
文摘Lactation in dairy cattle is coupled with increased nutrient requirements for milk synthesis. Therefore, dairy cattle metabolism has to adapt to meet lactation-associated challenges and requires major functional adjustments of the rumen and whole digestive system. This report describes the use of next-generation sequencing technology for assembly and profiling of the transcriptome of cattle rumen epithelial tissues from cattle in both dry and lactation periods. Transcriptomics profiling and comparison revealed extensive changes in gene expression related to metabolism in rumen epithelial tissue due to the adaptation to lactation. Ruminal epithelial adaptation to the challenges of metabolism and high nutrient requirements during lactation is presumably the primary triggers for these alterations in gene expression. Principal component analysis (PCA) indicated that the gene expression profiles of the rumen epithelia from dry and lactating cattle fall into two very distinct clusters. Gene Ontology (GO) enrichment analysis revealed that the most GO terms were related to various metabolic processes in lactating cattle. The most significantly (false discovery rate (FDR) p-value < 0.05) enriched GO term in biological processes was “carbohydrate derivative metabolic process”, followed by “nucleoside metabolic process”. Up-stream regulators, such as PPARA (Peroxisome proliferator-activated receptor alpha) gene, and up-regulated genes of molecular transporters are the focal points of this report.
基金supported by the National Natural Science Foundation of China (Grant Nos. 31370241, 31570214)the International Cooperation and Exchange of the National Natural Science Foundation of China (Grant Nos. 31511140095, 31561143015)National Science Foundation of China (grant no. 30960027)
文摘The genus Croomia(Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia(EA)-Eastern North America(ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In addition to the presence of both actinomorphic and zygomorphic flowers within the genus, species are disjunctively distributed between EA and ENA. However, due to the limited availability of genomic resources, few studies of Croomia have examined these questions. In this study,we sequenced the floral and leaf transcriptomes of the zygomorphic flowered Croomia heterosepala and the actinomorphic flowered Croomia japonica, and used comparative genomic approaches to investigate the transcriptome evolution of the two closely related species. The sequencing and de novo assembly of transcriptomes from flowers of C. heterosepala(ChFlower), flowers of C. japonica(CjFlower), and leaves of C. japonica(CjLeaf) yielded 57,193, 62,131 and 64,448 unigenes, respectively. In addition, estimation of Ka/Ks ratios for 11,566 potential orthologous groups between ChFlower and CjFlower revealed that only six pairs had Ka/Ks ratios significantly greater than 1 and are likely under positive selection. A total of 429 single copy nuclear genes(SCNGs) and 21,460 expression sequence tags-simple sequence repeats(ESTSSRs) were identified in this study. Specifically, we identified seven CYC/TB1-like genes from Stemonaceae. Phylogenetic and molecular evolution analyses indicated that these CYC/TB1-like genes formed a monophyletic clade(SteTBL1) and were subject to strong purifying selection. The shifts of floral symmetry in Stemonaceae do not appear to be correlated with TBL copy number.
基金Supported by the Project of China One-Belt-One-Road Foreign Expert Research Collaboration,Ministry of Science and Technology,China (No.DL2021002001L)the Open Project Program of State Key Laboratory of Food Nutrition and Safety,Tianjin University of Science&Technology (No.SKLFNS-KF-202205)。
文摘Oxidative stress induced by factors such as ammonia nitrogen has become a major issue in shrimp farming.The effects of carotenoids on the growth and antioxidant capability of Litopenaeus vannamei juveniles were investigated in this study using dietary archaeal carotenoids supplementation.For four weeks,shrimp were given diets containing 0 mg/kg(Ctrl)and 55.98 mg/kg(Car)archaeal carotenoids.Dietary archaeal carotenoids significantly enhanced the astaxanthin content in shrimp muscles and carapaces,as well as the superoxide dismutase(SOD)and glutathione peroxidase(GSH-Px)activity(P<0.05).The malonaldehyde(MDA)content in Car group significantly decreased(P<0.05).The transcriptome analysis was conducted to determine the molecular processes in response to archaeal carotenoids supplementation.A total of 1536 differentially expressed genes(DEGs)were detected,including 538 upregulated DEGs and 998 downregulated DEGs.GO functional enrichment analysis between Ctrl and Car indicated that 26 GO terms including extracellular region,metabolic process,and proteolysis were enriched.The KEGG pathway enrichment analysis revealed that the amino sugar and nucleotide sugar metabolism,cysteine and methionine metabolism,glycine serine and threonine metabolism,and amino acid biosynthesis were enriched.Archaeal carotenoids influenced the expression of several important genes involved in reactive oxygen species(ROS)generation,Nrf2 signaling,and antioxidant enzymes.Seven DEGs were chosen to confirm the RNA-Seq data using qRT-PCR.The genes and pathways discovered in this work assist to elucidate the molecular processes through which archaeal carotenoid enhances L.vannamei antioxidative system.
文摘Characterization of occurrence, density and motif sequence of tandem repeats in the transcribed regions is helpful in understanding the functional significance of these repeats in the modern genomes. We analyzed tandem repeats present in expressed sequences of thirteen species belonging to genera Capsicum, Nicotiana, Petunia and Solanum of family Solanaceae and the genus Coffea of Rubiaceae to investigate the propagation and evolutionary sustenance of these repeats. Tandem repeat containing sequences constituted 1.58% to 7.46% of sequences analyzed. Tandem repetitions of size 2, 15, 18 and 21 bp motifs were more frequent. Repeats with unit sizes 21 and 22 bp were also abundant in genomic sequences of potato and tomato. While mutations occurring in these repeats may alter the repeat number, genomes adjust to these changes by keeping the translated products unaffected. Surprisingly, in majority of the species under study, tandem repeat motif length did not exceed 228 bp. Conserved tandem repeat motifs of sizes 180, 192 and 204 bp were also abundant in the genomic sequences. Our observations lead us to propose that these tandem repeats are actually remnants of ancestral megasatellite repeats, which have split into multiple repeats due to frequent insertions over the course of evolution.
基金supported by the National Science Foundation of China(32000339,32000336 and 31925007)the Natural Science Foundation of Jiangsu Province(BK20231249,BK20221292 and BK20210880)。
文摘The diversity of cell types in the brain and how these change during different developmental stages,remains largely unknown.The life cycle of insects is short and goes through 4 distinct stages including embryonic,larval,pupal,and adult stages.During postembryonic life,the larval brain transforms into a mature adult version after metamorphosis.The silkworm,Bombyx mori,is a lepidopteran model insect.Here,we characterized the brain cell repertoire of larval and adult B.mori by obtaining 50708 single-cell transcriptomes.Seventeen and 12 cell clusters from larval and adult brains were assigned based on marker genes,respectively.Identified cell types include Kenyon cells,optic lobe cells,monoaminergic neurons,surface glia,and astrocyte glia.We further assessed the cell type compositions of larval and adult brains.We found that the transition from larva to adult resulted in great expansion of glial cells.The glial cell accounted for 49.8%of adult midbrain cells.Compared to flies and ants,the mushroom body kenyon cell is insufficient in B.mori,which accounts for 5.4%and 3.6%in larval and adult brains,respectively.Analysis of neuropeptide expression showed that the abundance and specificity of expression varied among individual neuropeptides.Intriguingly,we found that ion transport peptide was specifically expressed in glial cells of larval and adult brains.The cell atlas dataset provides an important resource to explore cell diversity,neural circuits and genetic profiles.
基金This study was partially supported by grants from the National Natural Science Foundation of China (31490591,31330032,and 61327902)the National Key R&D Program of China (2017YFA 0700500)+1 种基金the Frontier Key Project of the Chinese Academy of Sciences (QYZDJ-SSW-SMCO25)Shanghai Municipal Science and Technology Major Project (2018SHZDZX05).
文摘The cerebellum is critical for controlling motor and non-motor functions via cerebellar circuit that is composed of defined cell types, which approximately account for more than half of neurons in mammalsThe molecular mechanisms controlling developmental progression and maturation processes of various cerebellar cell types need systematic investigationHere, we analyzed transcriptome profiles of 21119 single cells of the postnatal mouse cerebellum and identified eight main cell clusters. Functional annotation of differentially expressed genes revealed trajectory hierarchies of granule cells (GCs) at various states and implied roles of mitochondrion and ATPases in the maturation of Purkinje cells (PCs), the sole output cells of the cerebellar cortexFurthermore, we analyzed gene expression patterns and co-expression networks of 28 ataxia risk genes, and found that most of them are related with biological process of mitochondrion and around half of them are enriched in PCs. Our results also suggested core transcription factors that are correlated with interneuron differentiation and characteristics for the expression of secretory proteins in glia cells, which may participate in neuronal modulationThus, this study presents a systematic landscape of cerebellar gene expression in defined cell types and a general gene expression framework for cerebellar development and dysfunction.
基金supported by the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI)the Ministry of Health&Welfare,Republic of Korea (HR22C1734)+2 种基金the National Research Foundation (NRF) of Korea (2020R1A6A1A03043539,2020M3A9D8037604,2022R1C1C1004756)(to SBL)the NRF of Korea (2022R1C1C1005741 and RS-2023-00217595)the new faculty research fund of Ajou University School of Medicine (to EJL)。
文摘Elucidating the complex dynamic cellular organization in the hypothalamus is critical for understanding its role in coordinating fundamental body functions. Over the past decade, single-cell and spatial omics technologies have significantly evolved, overcoming initial technical challenges in capturing and analyzing individual cells. These high-throughput omics technologies now offer a remarkable opportunity to comprehend the complex spatiotemporal patterns of transcriptional diversity and cell-type characteristics across the entire hypothalamus. Current single-cell and single-nucleus RNA sequencing methods comprehensively quantify gene expression by exploring distinct phenotypes across various subregions of the hypothalamus. However, single-cell/single-nucleus RNA sequencing requires isolating the cell/nuclei from the tissue, potentially resulting in the loss of spatial information concerning neuronal networks. Spatial transcriptomics methods, by bypassing the cell dissociation, can elucidate the intricate spatial organization of neural networks through their imaging and sequencing technologies. In this review, we highlight the applicative value of single-cell and spatial transcriptomics in exploring the complex molecular-genetic diversity of hypothalamic cell types, driven by recent high-throughput achievements.
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,No.81801907(to NC)Shenzhen Key Laboratory of Bone Tissue Repair and Translational Research,No.ZDSYS20230626091402006(to NC)+2 种基金Sanming Project of Medicine in Shenzhen,No.SZSM201911002(to SL)Foundation of Shenzhen Committee for Science and Technology Innovation,Nos.JCYJ20230807110310021(to NC),JCYJ20230807110259002(to JL)Science and Technology Program of Guangzhou,No.2024A04J4716(to TL)。
文摘We previously demonstrated that inhibiting neural stem cells necroptosis enhances functional recovery after spinal cord injury.While exosomes are recognized as playing a pivotal role in neural stem cells exocrine function,their precise function in spinal cord injury remains unclear.To investigate the role of exosomes generated following neural stem cells necroptosis after spinal cord injury,we conducted singlecell RNA sequencing and validated that neural stem cells originate from ependymal cells and undergo necroptosis in response to spinal cord injury.Subsequently,we established an in vitro necroptosis model using neural stem cells isolated from embryonic mice aged 16-17 days and extracted exosomes.The results showed that necroptosis did not significantly impact the fundamental characteristics or number of exosomes.Transcriptome sequencing of exosomes in necroptosis group identified 108 differentially expressed messenger RNAs,104 long non-coding RNAs,720 circular RNAs,and 14 microRNAs compared with the control group.Construction of a competing endogenous RNA network identified the following hub genes:tuberous sclerosis 2(Tsc2),solute carrier family 16 member 3(Slc16a3),and forkhead box protein P1(Foxp1).Notably,a significant elevation in TSC2 expression was observed in spinal cord tissues following spinal cord injury.TSC2-positive cells were localized around SRY-box transcription factor 2-positive cells within the injury zone.Furthermore,in vitro analysis revealed increased TSC2 expression in exosomal receptor cells compared with other cells.Further assessment of cellular communication following spinal cord injury showed that Tsc2 was involved in ependymal cellular communication at 1 and 3 days post-injury through the epidermal growth factor and midkine signaling pathways.In addition,Slc16a3 participated in cellular communication in ependymal cells at 7 days post-injury via the vascular endothelial growth factor and macrophage migration inhibitory factor signaling pathways.Collectively,these findings confirm that exosomes derived from neural stem cells undergoing necroptosis play an important role in cellular communication after spinal cord injury and induce TSC2 upregulation in recipient cells.
文摘Background:This study aims to identify distinct cellular subtypes within brain tissue using single-cell transcriptomic analysis,focusing on specific biomarkers that differentiate cell types and the effects of traditional and exercise therapy.Methods:Four samples were analyzed:older control(OC),older exercise(OE),younger control(YC),and younger exercise(YE).Single-cell RNA sequencing was used to distinguish cellular subtypes through their biomarker profiles.Data visualization included violin and t-SNE plots to illustrate biomarker expression across cell clusters such as oligodendrocytes,microglia,and astrocytes.Additionally,BV2 cells were exposed to amyloid-beta fragments to simulate Alzheimer’s disease,assessing the impact of exercise-induced cellular responses.Results:Distinct cellular subtypes were identified:oligodendrocytes(MBP,St18),microglia(Dock8),and astrocytes(Aqp4,Gpc5).Sample OE was predominantly oligodendrocytes,while YE had more astrocytes,inhibitory neurons,and Canal-Retzius cells.YC showed a significant presence of Olfm3+ganglion neurons.ZEB1 gene knockout revealed changes in SMAD family gene expression,which regulate ferroptosis.Oxidative stress levels were also evaluated.Conclusion:This profiling enhances our understanding of brain cellular functions and interactions,potentially informing targeted therapies in neurological research.Exercise may influence brain cell immune responses and cell death pathways by regulating specific gene expressions,offering new insights for treating neuroinflammation and degeneration.
基金supported by the National Key R&D Program of China(Grant No.2022YFD220040203)Jiangxi Forestry Bureau forestry Science and technology innovation special project“Introduction test and Screening of pecan clones”innovation special project[Grant No.(2020)04]。
文摘Pecan is an extremely important crop cultivated worldwide for edible nuts and nut oil.Considering the changes in precipitation and soil moisture caused by climate change and worsening global water scarcity,it is important to understand the mechanism of pecan response to drought.To this end,this study investigated the response of pecan to drought stress and rehydration using physiological and transcriptomic analyses.Superoxide dismutase(SOD)enzyme activity in leaves was significantly upregulated during drought stress,suggesting that it might play an important role in drought response.Weighted gene co-expression network analysis of the transcriptome data was used to screen for a key drought-responsive gene,CiNAC2,which was overexpressed in Arabidopsis thaliana for functional validation.The analysis of stomatal apertures and the water loss rate in leaves showed that CiNAC2 might respond to drought stress via mediating stomatal aperture size.In addition,CiNAC2 could promote root growth under drought conditions.CiSOD1 was verified as a direct target gene of CiNAC2 by yeast one-hybrid assay dual-luciferase reporter assay.Yeast one-hybrid analysis confirmed that CiNAC2 bound to the promoters of CiSOD1.Transient expression in Nicotiana benthamiana epidermis showed that CiNAC2 upregulated the expression of CiSOD1.These results demonstrated that CiNAC2 enhanced drought stress tolerance via promoting SOD activity in pecan and provided a theoretical basis for breeding drought-resistant varieties in pecan.
基金supported in part by the Priority Academic Program Development of Jiangsu Higher Education Institutions and the State Key Laboratory of Crop Genetics and Germplasm Enhancement (Grant No. ZW201813)supported by the high-performance computing platform at the Bioinformatics Center of Nanjing Agricultural University。
文摘Ascorbic acid, also referred to as vitamin C(Vc), is an important nutrient found in fruits and vegetables that promotes produce quality and human health. Rosa roxburghii is an underutilized natural fruit that contains very high levels of Vc. However, the Vc content of R. roxburghii varies considerably during plant development and ripening. To better understand the molecular mechanisms that underlie fluctuations in Vc content of R. roxburghii fruit at different developmental stages, we performed transcriptomic and metabolomic analyses and identified two significant gene networks/modules and 168 transcription factors directly involved in Vc synthesis. Promoter analysis of two core genes involved in Vc synthesis, RrGGP and RrGalUR, revealed the presence of a retroviral long terminal repeat(LTR) insert in the RrGalUR promoter. Using yeast one-hybrid and dual-luciferase assays, we demonstrated that the transcription factors RrHY5H and RrZIP9 bind to the promoter of RrGGP to promote its expression. RrZIP6 and RrWRKY4 bind to the LTR in the RrGalUR promoter to promote its expression. Our results reveal a molecular mechanism that controls Vc synthesis and accumulation in R. roxburghii fruit.
基金Supported by the Key R&D Projects of Hainan Province,No.ZDYF2022SHFZ295.
文摘BACKGROUND Schizophrenia(SZ),a chronic and widespread brain disorder,presents with complex etiology and pathogenesis that remain inadequately understood.Despite the absence of a universally recognized endophenotype,peripheral blood mononuclear cells(PBMCs)serve as a robust model for investigating intracellular alterations linked to SZ.AIM To preliminarily investigate potential pathogenic mechanisms and identify novel biomarkers for SZ.METHODS PBMCs from SZ patients were subjected to integrative transcriptomic and proteomic analyses to uncover differentially expressed genes(DEGs)and differentially expressed proteins while mapping putative disease-associated signaling pathways.Key findings were validated using western blot(WB)and real-time fluorescence quantitative PCR(RT-qPCR).RNAi-lentivirus was employed to transfect rat hippocampal CA1 neurons in vitro,with subsequent verification of target gene expression via RT-qPCR.The levels of neuronal conduction proteins,including calmodulin-dependent protein kinase II(caMKII),CREB,and BDNF,were assessed through WB.Apoptosis was quantified by flow cytometry,while cell proliferation and viability were evaluated using the Cell Counting Kit-8 assay.RESULTS The integration of transcriptomic and proteomic analyses identified 6079 co-expressed genes,among which 25 DEGs were significantly altered between the SZ group and healthy controls.Notably,haptoglobin(HP),lactotransferrin(LTF),and SERPING1 exhibited marked upregulation.KEGG pathway enrichment analysis implicated neuroactive ligand-receptor interaction pathways in disease pathogenesis.Clinical sample validation demonstrated elevated protein and mRNA levels of HP,LTF,and SERPING1 in the SZ group compared to controls.WB analysis of all clinical samples further corroborated the significant upregulation of SERPING1.In hippocampal CA1 neurons transfected with lentivirus,reduced SERPING1 expression was accompanied by increased levels of CaMKII,CREB,and BDNF,enhanced cell viability,and reduced apoptosis.CONCLUSION SERPING1 may suppress neural cell proliferation in SZ patients via modulation of the CaMKII-CREB-BDNF signaling pathway.
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 grants from the National Natural Science Foundation of China(Grant No.32072571)the 111 Project(Grant No.B17043)the Construction of Beijing Science,and Technology Innovation and Service Capacity in Top Subjects(Grant No.CEFF-PXM2019_014207_000032)。
文摘Tomato(Solanum lycopersicum)is an important fruit and vegetable crop in worldwide.The fertility of tomato reproductive organs can be dramatically decreased when ambient temperatures rise above 35°C,reducing tomato fruit yield.It is necessary to identify transcription factors(TFs)and target genes involved in heat stress response(HSR)signaling cascades in tomato flower buds to improve tomato plant thermotolerance.In this study,we profiled genes expressed in three developmental stages of tomato flower buds.Red and turquoise modules for heat stress(HS)were identified through gene co-expression network analysis,and the genes within these modules were enriched in HS-related pathways.By focusing on the TFs in the two modules,we identified several novel HSR-related TFs,including SlWRKY75,SlMYB117,and SlNAM.Furthermore,homology analysis illustrated a conserved signaling cascade in tomato.Lastly,we identified and experimentally validated four HSF-regulated genes,namely SlGrpE,SlERDJ3A,SlTIL,and SlPOM1,that likely modulate thermotolerance in plants.These results provide a high-resolution atlas of gene expression during tomato flower bud development under HS conditions,which is a valuable resource for uncovering potential regulatory networks associated with the HSR in tomato.
