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
We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using t...We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using this measure transcriptomes from different species were evaluated by mapping them to gene families and integrating the mapping results with expression data. Statistical tests were applied to the transcriptome evaluation results to identify differentially expressed families. A Perl program named Pro-Diff was compiled to im- plement this method. To evaluate the method and provide an example of its use, two liver EST transcriptomes from two closely related fish that live in different temperature zones were compared. One EST library was from a recent sequencing project of Dissosticus maw- soni, a fish that lives in cold Antarctic sea waters, while the other was newly sequenced data （available at： http：//www.fishgenome.org/ polarbank/） from Notothenia angustata, a species that lives in temperate near-shore water of southern New Zealand. Results from the com- parison were consistent with results inferred from phenotype differences and also with our previously published Gene Ontology-based method. The Pro-Diffprogram and operation manual can be downloaded from： http：//www.fishgenome.org/download/Prodiff.rar.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
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
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
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 pmel17 gene plays a crucial role in melanin pigmentation.Our previous studies showed that in Mozambique tilapia,a transposon inserted into the 3'untranslated region(3'UTR)of pmel17 resulted in the silencin...The pmel17 gene plays a crucial role in melanin pigmentation.Our previous studies showed that in Mozambique tilapia,a transposon inserted into the 3'untranslated region(3'UTR)of pmel17 resulted in the silencing of pmel17 and led to the loss of melanin pigments(golden mutant phenotype).Additionally,the transposon insertion caused reduced growth performance and increased locomotion.In this study,to investigate the mechanisms underlying these phenotypic changes,we sequenced transcriptomes of the skin and muscle samples collected from wildtype and mutant tilapias.A total of 51 and 141 differentially expressed genes(DEGs)were identified in the skin and muscle transcriptomes,respectively.DEGs in the skin were primarily down-regulated in golden genotypes and associated with neural crest development and melanin pigmentation pathways.Besides these DEGs involved in the classic melanin pigmentation pathway of vertebrates,14 DEGs were also observed to be related to melanogenesis.In muscle transcriptomes,there was an enrichment of GO terms associated with growth factors and cellular lipid catabolic processes.Specifically,DEGs related to growth factor binding exhibited a down-regulation,while those related to lipid metabolism showed an up-regulation in mutant genotypes.These findings agree with observed phenotypic changes.Furthermore,several DEGs associated with muscle function and mobility were up-regulated.Our study sheds light on how a single mutation in a gene can modulate multiple phenotypes by rewiring gene regulation networks.The research also provides valuable insights into the complex genetic mechanisms underlying the regulation of diverse phenotypic traits by a single gene.展开更多
The Mexican fruit fly,Anastrepha ludens,is a polyphagous pest that is a constant threat to US agriculture because of its proximity to citrus production in border region of the United States and Mexico.Sterile Insect T...The Mexican fruit fly,Anastrepha ludens,is a polyphagous pest that is a constant threat to US agriculture because of its proximity to citrus production in border region of the United States and Mexico.Sterile Insect Technique has been used to manage and eradicate of the Mexican Fruit Fly.SIT,however,requires millions of sterile male flies to be released each week from mass-rearing facilities.The mass-reared colonies must deal with microbial infections that reduce survivorship,fecundity and male-male competition.Meta-transcriptomics joins culturing and next generation DNA sequencing techniques to understand these changing microbial communities.This study uses advances in microbial meta-transcriptome sequencing to analyze the microbial communities from the four major developmental stages of A.ludens.The composition of the microbial communities was analyzed and revealed the large transcriptional presence of the phyla Microsporidia,a known animal pathogen.Clustering and ordination analyses revealed groupings based on developmental phase for egg,larvae and pupa.Adult samples had little clustering;a not unexpected result given the known turn-over in microbial community that occurs in the first 5 d after pupation.The transcriptional activity of three known pathogens of A.ludens between developmental phases were investigated.Two of the three pathogens had significant transcriptional differences between the phases with the larvae phase having the most activity.This increase in transcriptional activity agrees with culture-based surveillance and current mitigation strategies employed in the mass-rearing facility.This result reinforces the utility of transcriptomics in combating microbial threats.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
Alzheimer’s disease(AD)is the most common form of dementia.In addition to the lack of effective treatments,there are limitations in diagnostic capabilities.The complexity of AD itself,together with a variety of other...Alzheimer’s disease(AD)is the most common form of dementia.In addition to the lack of effective treatments,there are limitations in diagnostic capabilities.The complexity of AD itself,together with a variety of other diseases often observed in a patient’s history in addition to their AD diagnosis,make deciphering the molecular mechanisms that underlie AD,even more important.Large datasets of single-cell RNA sequencing,single-nucleus RNA-sequencing(snRNA-seq),and spatial transcriptomics(ST)have become essential in guiding and supporting new investigations into the cellular and regional susceptibility of AD.However,with unique technology,software,and larger databases emerging;a lack of integration of these data can contribute to ineffective use of valuable knowledge.Importantly,there was no specialized database that concentrates on ST in AD that offers comprehensive differential analyses under various conditions,such as sex-specific,region-specific,and comparisons between AD and control groups until the new Single-cell and Spatial RNA-seq databasE for Alzheimer’s Disease(ssREAD)database(Wang et al.,2024)was introduced to meet the scientific community’s growing demand for comprehensive,integrated,and accessible data analysis.展开更多
Neuroserpin,a secreted protein that belongs to the serpin superfamily of serine protease inhibitors,is highly expressed in the central nervous system and plays multiple roles in brain development and pathology.As a na...Neuroserpin,a secreted protein that belongs to the serpin superfamily of serine protease inhibitors,is highly expressed in the central nervous system and plays multiple roles in brain development and pathology.As a natural inhibitor of recombinant tissue plasminogen activator,neuroserpin inhibits the increased activity of tissue plasminogen activator in ischemic conditions and extends the therapeutic windows of tissue plasminogen activator for brain ischemia.However,the neuroprotective mechanism of neuroserpin against ischemic stroke remains unclear.In this study,we used a mouse model of middle cerebral artery occlusion and oxygen-glucose deprivation/reperfusion-injured cortical neurons as in vivo and in vitro ischemia-reperfusion models,respectively.The models were used to investigate the neuroprotective effects of neuroserpin.Our findings revealed that endoplasmic reticulum stress was promptly triggered following ischemia,initially manifesting as the acute activation of endoplasmic reticulum stress transmembrane sensors and the suppression of protein synthesis,which was followed by a later apoptotic response.Notably,ischemic stroke markedly downregulated the expression of neuroserpin in cortical neurons.Exogenous neuroserpin reversed the activation of multiple endoplasmic reticulum stress signaling molecules,the reduction in protein synthesis,and the upregulation of apoptotic transcription factors.This led to a reduction in neuronal death induced by oxygen/glucose deprivation and reperfusion,as well as decreased cerebral infarction and neurological dysfunction in mice with middle cerebral artery occlusion.However,the neuroprotective effects of neuroserpin were markedly inhibited by endoplasmic reticulum stress activators thapsigargin and tunicamycin.Our findings demonstrate that neuroserpin exerts neuroprotective effects on ischemic stroke by suppressing endoplasmic reticulum stress.展开更多
Unlike mammals,zebrafish possess a remarkable ability to regenerate their spinal cord after injury,making them an ideal vertebrate model for studying regeneration.While previous research has identified key cell types ...Unlike mammals,zebrafish possess a remarkable ability to regenerate their spinal cord after injury,making them an ideal vertebrate model for studying regeneration.While previous research has identified key cell types involved in this process,the underlying molecular and cellular mechanisms remain largely unexplored.In this study,we used single-cell RNA sequencing to profile distinct cell populations at different stages of spinal cord injury in zebrafish.Our analysis revealed that multiple subpopulations of neurons showed persistent activation of genes associated with axonal regeneration post injury,while molecular signals promoting growth cone collapse were inhibited.Radial glial cells exhibited significant proliferation and differentiation potential post injury,indicating their intrinsic roles in promoting neurogenesis and axonal regeneration,respectively.Additionally,we found that inflammatory factors rapidly decreased in the early stages following spinal cord injury,creating a microenvironment permissive for tissue repair and regeneration.Furthermore,oligodendrocytes lost maturity markers while exhibiting increased proliferation following injury.These findings demonstrated that the rapid and orderly regulation of inflammation,as well as the efficient proliferation and redifferentiation of new neurons and glial cells,enabled zebrafish to reconstruct the spinal cord.This research provides new insights into the cellular transitions and molecular programs that drive spinal cord regeneration,offering promising avenues for future research and therapeutic strategies.展开更多
Retinal ganglion cells,a crucial component of the central nervous system,are often affected by irreversible visual impairment due to various conditions,including trauma,tumors,ischemia,and glaucoma.Studies have shown ...Retinal ganglion cells,a crucial component of the central nervous system,are often affected by irreversible visual impairment due to various conditions,including trauma,tumors,ischemia,and glaucoma.Studies have shown that the optic nerve crush model and glaucoma model are commonly used to study retinal ganglion cell injury.While these models differ in their mechanisms,both ultimately result in retinal ganglion cell injury.With advancements in high-throughput technologies,techniques such as microarray analysis,RNA sequencing,and single-cell RNA sequencing have been widely applied to characterize the transcriptomic profiles of retinal ganglion cell injury,revealing underlying molecular mechanisms.This review focuses on optic nerve crush and glaucoma models,elucidating the mechanisms of optic nerve injury and neuron degeneration induced by glaucoma through single-cell transcriptomics,transcriptome analysis,and chip analysis.Research using the optic nerve crush model has shown that different retinal ganglion cell subtypes exhibit varying survival and regenerative capacities following injury.Single-cell RNA sequencing has identified multiple genes associated with retinal ganglion cell protection and regeneration,such as Gal,Ucn,and Anxa2.In glaucoma models,high-throughput sequencing has revealed transcriptomic changes in retinal ganglion cells under elevated intraocular pressure,identifying genes related to immune response,oxidative stress,and apoptosis.These genes are significantly upregulated early after optic nerve injury and may play key roles in neuroprotection and axon regeneration.Additionally,CRISPR-Cas9 screening and ATAC-seq analysis have identified key transcription factors that regulate retinal ganglion cell survival and axon regeneration,offering new potential targets for neurorepair strategies in glaucoma.In summary,single-cell transcriptomic technologies provide unprecedented insights into the molecular mechanisms underlying optic nerve injury,aiding in the identification of novel therapeutic targets.Future researchers should integrate advanced single-cell sequencing with multi-omics approaches to investigate cell-specific responses in retinal ganglion cell injury and regeneration.Furthermore,computational models and systems biology methods could help predict molecular pathways interactions,providing valuable guidance for clinical research on optic nerve regeneration and repair.展开更多
Drug development for Alzheimer’s disease is extremely challenging,as demonstrated by the repeated failures of amyloid-β-targeted therapeutics and the controversies surrounding the amyloid-βcascade hypothesis.More r...Drug development for Alzheimer’s disease is extremely challenging,as demonstrated by the repeated failures of amyloid-β-targeted therapeutics and the controversies surrounding the amyloid-βcascade hypothesis.More recently,advances in the development of Lecanemab,an anti-amyloid-βmonoclonal antibody,have shown positive results in reducing brain A burden and slowing cognitive decline in patients with early-stage Alzheimer’s disease in the Phase Ⅲ clinical trial(Clarity Alzheimer’s disease).Despite these promising results,side effects such as amyloid-related imaging abnormalities(ARIA)may limit its usage.ARIA can manifest as ARIA-E(cerebral edema or effusions)and ARIA-H(microhemorrhages or superficial siderosis)and is thought to be caused by increased vascular permeability due to inflammatory responses,leading to leakages of blood products and protein-rich fluid into brain parenchyma.Endothelial dysfunction is an early pathological feature of Alzheimer’s disease,and the blood-brain barrier becomes increasingly leaky as the disease progresses.In addition,APOE4,the strongest genetic risk factor for Alzheimer’s disease,is associated with higher vascular amyloid burden,increased ARIA incidence,and accelerated blood-brain barrier disruptions.These interconnected vascular abnormalities highlight the importance of vascular contributions to the pathophysiology of Alzheimer’s disease.Here,we will closely examine recent research evaluating the heterogeneity of brain endothelial cells in the microvasculature of different brain regions and their relationships with Alzheimer’s disease progression.展开更多
Subcutaneous fat(SCF)and intramuscular fat(IMF)deposition is relevant to health in humans,as well as meat production and quality in pigs.In this study,we generated RNA sequence data for 122 SCF,120 IMF,and 87 longissi...Subcutaneous fat(SCF)and intramuscular fat(IMF)deposition is relevant to health in humans,as well as meat production and quality in pigs.In this study,we generated RNA sequence data for 122 SCF,120 IMF,and 87 longissimus dorsi muscle(LDM)samples using 155 F6 pigs from a specially designed heterogeneous population generated by intercrossing four highly selected European commercial breeds and four indigenous Chinese pig breeds.The phenotypes including waist back fat thickness and intramuscular fat content were also measured in the 155 F6 pigs.We found that the genes in SCF and IMF differed largely in both expression levels and network connectivity,and highlighted network modules that exhibited strongest gain of connectivity in SCF and IMF,containing genes that were associated with the immune process and DNA double-strand repair,respectively.We identified 215 SCF genes related to kinase inhibitor activity,mitochondrial fission,and angiogenesis,and 90 IMF genes related to lipolysis and fat cell differentiation,displayed a tissue-specific association with back fat thickness and IMF content,respectively.We found that cis-expression QTL for trait-associated genes in the two adipose tissues tended to have tissuedependent predictability for the two adipose traits.Alternative splicing of genes was also found to be associated with SCF or IMF deposition,but the association was much less extensive than that based on expression levels.This study provides a better understanding of SCF and IMF gene transcription and network organization and identified critical genes and network modules that displayed tissue-specific associations with subcutaneous and intramuscular fat deposition.These features are helpful for designing breeding programs to genetically improve the two adipose traits in a balanced way.展开更多
Panax ginseng C. A. Meyer is an important traditional herb in eastern Asia. It contains ginsenosides, which are primary bioactive compounds with medicinal properties. Although ginseng has been cultivated since at leas...Panax ginseng C. A. Meyer is an important traditional herb in eastern Asia. It contains ginsenosides, which are primary bioactive compounds with medicinal properties. Although ginseng has been cultivated since at least the Ming dynasty to increase production, cultivated ginseng has lower quantities of ginsenosides and lower disease resistance than ginseng grown under natural conditions. We extracted root RNA from six varieties of fifth-year P. ginseng cultivars representing four different growth conditions, and performed Illumina paired-end sequencing. In total, 163,165,706 raw reads were obtained and used to generate a de novo transcriptome that consisted of 151,763 contigs(76,336 unigenes), of which 100,648 contigs(66.3%) were successfully annotated. Differential expression analysis revealed that most differentially expressed genes(DEGs) were upregulated(246 out of 258, 95.3%) in ginseng grown under natural conditions compared with that grown under artificial conditions. These DEGs were enriched in gene ontology(GO) terms including response to stimuli and localization. In particular, some key ginsenoside biosynthesis-related genes, including HMG-Co A synthase(HMGS), mevalonate kinase(MVK), and squalene epoxidase(SE), were upregulated in wild-grown ginseng. Moreover, a high proportion of disease resistance-related genes were upregulated in wild-grown ginseng. This study is the first transcriptome analysis to compare wild-grown and cultivated ginseng, and identifies genes that may produce higher ginsenoside content and better disease resistance in the wild; these genes may have the potential to improve cultivated ginseng grown in artificial environments.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.
基金supported by the grants from the Ministry of Science and Technology of China (No.2006AA02Z331 and 2004CB117404)the Key Project of Chinese Academy of Sciences (No.KSCX2-YW-N-020) to Liangbiao ChenNSF OPP 0636696 to C-H CC
文摘We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using this measure transcriptomes from different species were evaluated by mapping them to gene families and integrating the mapping results with expression data. Statistical tests were applied to the transcriptome evaluation results to identify differentially expressed families. A Perl program named Pro-Diff was compiled to im- plement this method. To evaluate the method and provide an example of its use, two liver EST transcriptomes from two closely related fish that live in different temperature zones were compared. One EST library was from a recent sequencing project of Dissosticus maw- soni, a fish that lives in cold Antarctic sea waters, while the other was newly sequenced data （available at： http：//www.fishgenome.org/ polarbank/） from Notothenia angustata, a species that lives in temperate near-shore water of southern New Zealand. Results from the com- parison were consistent with results inferred from phenotype differences and also with our previously published Gene Ontology-based method. The Pro-Diffprogram and operation manual can be downloaded from： http：//www.fishgenome.org/download/Prodiff.rar.
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 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.
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.
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 internal fund(5020)of the Temasek Life Sciences Laboratory,Singapore。
文摘The pmel17 gene plays a crucial role in melanin pigmentation.Our previous studies showed that in Mozambique tilapia,a transposon inserted into the 3'untranslated region(3'UTR)of pmel17 resulted in the silencing of pmel17 and led to the loss of melanin pigments(golden mutant phenotype).Additionally,the transposon insertion caused reduced growth performance and increased locomotion.In this study,to investigate the mechanisms underlying these phenotypic changes,we sequenced transcriptomes of the skin and muscle samples collected from wildtype and mutant tilapias.A total of 51 and 141 differentially expressed genes(DEGs)were identified in the skin and muscle transcriptomes,respectively.DEGs in the skin were primarily down-regulated in golden genotypes and associated with neural crest development and melanin pigmentation pathways.Besides these DEGs involved in the classic melanin pigmentation pathway of vertebrates,14 DEGs were also observed to be related to melanogenesis.In muscle transcriptomes,there was an enrichment of GO terms associated with growth factors and cellular lipid catabolic processes.Specifically,DEGs related to growth factor binding exhibited a down-regulation,while those related to lipid metabolism showed an up-regulation in mutant genotypes.These findings agree with observed phenotypic changes.Furthermore,several DEGs associated with muscle function and mobility were up-regulated.Our study sheds light on how a single mutation in a gene can modulate multiple phenotypes by rewiring gene regulation networks.The research also provides valuable insights into the complex genetic mechanisms underlying the regulation of diverse phenotypic traits by a single gene.
基金supported by AP21PPQS&T00C108 from USDA-APHIS to ELS。
文摘The Mexican fruit fly,Anastrepha ludens,is a polyphagous pest that is a constant threat to US agriculture because of its proximity to citrus production in border region of the United States and Mexico.Sterile Insect Technique has been used to manage and eradicate of the Mexican Fruit Fly.SIT,however,requires millions of sterile male flies to be released each week from mass-rearing facilities.The mass-reared colonies must deal with microbial infections that reduce survivorship,fecundity and male-male competition.Meta-transcriptomics joins culturing and next generation DNA sequencing techniques to understand these changing microbial communities.This study uses advances in microbial meta-transcriptome sequencing to analyze the microbial communities from the four major developmental stages of A.ludens.The composition of the microbial communities was analyzed and revealed the large transcriptional presence of the phyla Microsporidia,a known animal pathogen.Clustering and ordination analyses revealed groupings based on developmental phase for egg,larvae and pupa.Adult samples had little clustering;a not unexpected result given the known turn-over in microbial community that occurs in the first 5 d after pupation.The transcriptional activity of three known pathogens of A.ludens between developmental phases were investigated.Two of the three pathogens had significant transcriptional differences between the phases with the larvae phase having the most activity.This increase in transcriptional activity agrees with culture-based surveillance and current mitigation strategies employed in the mass-rearing facility.This result reinforces the utility of transcriptomics in combating microbial threats.
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.
文摘Alzheimer’s disease(AD)is the most common form of dementia.In addition to the lack of effective treatments,there are limitations in diagnostic capabilities.The complexity of AD itself,together with a variety of other diseases often observed in a patient’s history in addition to their AD diagnosis,make deciphering the molecular mechanisms that underlie AD,even more important.Large datasets of single-cell RNA sequencing,single-nucleus RNA-sequencing(snRNA-seq),and spatial transcriptomics(ST)have become essential in guiding and supporting new investigations into the cellular and regional susceptibility of AD.However,with unique technology,software,and larger databases emerging;a lack of integration of these data can contribute to ineffective use of valuable knowledge.Importantly,there was no specialized database that concentrates on ST in AD that offers comprehensive differential analyses under various conditions,such as sex-specific,region-specific,and comparisons between AD and control groups until the new Single-cell and Spatial RNA-seq databasE for Alzheimer’s Disease(ssREAD)database(Wang et al.,2024)was introduced to meet the scientific community’s growing demand for comprehensive,integrated,and accessible data analysis.
基金supported in part by the National Key Research&Development Program of China,No.2022YFA1104900(to LS)the National Natural Science Foundation of China,Nos.82371175,82071535(both to LS),82101614(to YP)+5 种基金the International Science and Technology Cooperation Projects of Guangdong Province,No.2023A0505050121(to LS)Guangdong Basic and Applied Basic Research Foundation,Nos.2022B1515130007(to LS),2023A1515030012(to SZ),2022A1515010666(to WL)the Science and Technology Program of Guangzhou,Nos.202102070001(to LS),202201010041(to YP)Shenzhen Basic Research Grant,Nos.JCYJ20200109140414636,JCYJ20230807145103007(both to WL)awarded a Royal Society Newton Advanced Fellowship,No.AOMS-NAF0051003in collaboration with Zoltán Molnár,Department of Physiology,Anatomy and Genetics,University of Oxford(2017–2021)。
文摘Neuroserpin,a secreted protein that belongs to the serpin superfamily of serine protease inhibitors,is highly expressed in the central nervous system and plays multiple roles in brain development and pathology.As a natural inhibitor of recombinant tissue plasminogen activator,neuroserpin inhibits the increased activity of tissue plasminogen activator in ischemic conditions and extends the therapeutic windows of tissue plasminogen activator for brain ischemia.However,the neuroprotective mechanism of neuroserpin against ischemic stroke remains unclear.In this study,we used a mouse model of middle cerebral artery occlusion and oxygen-glucose deprivation/reperfusion-injured cortical neurons as in vivo and in vitro ischemia-reperfusion models,respectively.The models were used to investigate the neuroprotective effects of neuroserpin.Our findings revealed that endoplasmic reticulum stress was promptly triggered following ischemia,initially manifesting as the acute activation of endoplasmic reticulum stress transmembrane sensors and the suppression of protein synthesis,which was followed by a later apoptotic response.Notably,ischemic stroke markedly downregulated the expression of neuroserpin in cortical neurons.Exogenous neuroserpin reversed the activation of multiple endoplasmic reticulum stress signaling molecules,the reduction in protein synthesis,and the upregulation of apoptotic transcription factors.This led to a reduction in neuronal death induced by oxygen/glucose deprivation and reperfusion,as well as decreased cerebral infarction and neurological dysfunction in mice with middle cerebral artery occlusion.However,the neuroprotective effects of neuroserpin were markedly inhibited by endoplasmic reticulum stress activators thapsigargin and tunicamycin.Our findings demonstrate that neuroserpin exerts neuroprotective effects on ischemic stroke by suppressing endoplasmic reticulum stress.
基金supported by the Jiangsu Province Traditional Chinese Medicine Technology Development Plan Project,Nos.MS2023113(to JC),MS2022090Young and Middle-aged Academic Leaders of Jiangsu Qing-Lan Project(to GL).
文摘Unlike mammals,zebrafish possess a remarkable ability to regenerate their spinal cord after injury,making them an ideal vertebrate model for studying regeneration.While previous research has identified key cell types involved in this process,the underlying molecular and cellular mechanisms remain largely unexplored.In this study,we used single-cell RNA sequencing to profile distinct cell populations at different stages of spinal cord injury in zebrafish.Our analysis revealed that multiple subpopulations of neurons showed persistent activation of genes associated with axonal regeneration post injury,while molecular signals promoting growth cone collapse were inhibited.Radial glial cells exhibited significant proliferation and differentiation potential post injury,indicating their intrinsic roles in promoting neurogenesis and axonal regeneration,respectively.Additionally,we found that inflammatory factors rapidly decreased in the early stages following spinal cord injury,creating a microenvironment permissive for tissue repair and regeneration.Furthermore,oligodendrocytes lost maturity markers while exhibiting increased proliferation following injury.These findings demonstrated that the rapid and orderly regulation of inflammation,as well as the efficient proliferation and redifferentiation of new neurons and glial cells,enabled zebrafish to reconstruct the spinal cord.This research provides new insights into the cellular transitions and molecular programs that drive spinal cord regeneration,offering promising avenues for future research and therapeutic strategies.
基金supported by the National Natural Science Foundation of China,Nos.82471123,82171053the Jilin Province Special Project for Talent in Medical and Health Sciences,No.2024WSXK-E01the Natural Science Foundation of Jilin Province,YDZJ202501ZYTS318(all to GL).
文摘Retinal ganglion cells,a crucial component of the central nervous system,are often affected by irreversible visual impairment due to various conditions,including trauma,tumors,ischemia,and glaucoma.Studies have shown that the optic nerve crush model and glaucoma model are commonly used to study retinal ganglion cell injury.While these models differ in their mechanisms,both ultimately result in retinal ganglion cell injury.With advancements in high-throughput technologies,techniques such as microarray analysis,RNA sequencing,and single-cell RNA sequencing have been widely applied to characterize the transcriptomic profiles of retinal ganglion cell injury,revealing underlying molecular mechanisms.This review focuses on optic nerve crush and glaucoma models,elucidating the mechanisms of optic nerve injury and neuron degeneration induced by glaucoma through single-cell transcriptomics,transcriptome analysis,and chip analysis.Research using the optic nerve crush model has shown that different retinal ganglion cell subtypes exhibit varying survival and regenerative capacities following injury.Single-cell RNA sequencing has identified multiple genes associated with retinal ganglion cell protection and regeneration,such as Gal,Ucn,and Anxa2.In glaucoma models,high-throughput sequencing has revealed transcriptomic changes in retinal ganglion cells under elevated intraocular pressure,identifying genes related to immune response,oxidative stress,and apoptosis.These genes are significantly upregulated early after optic nerve injury and may play key roles in neuroprotection and axon regeneration.Additionally,CRISPR-Cas9 screening and ATAC-seq analysis have identified key transcription factors that regulate retinal ganglion cell survival and axon regeneration,offering new potential targets for neurorepair strategies in glaucoma.In summary,single-cell transcriptomic technologies provide unprecedented insights into the molecular mechanisms underlying optic nerve injury,aiding in the identification of novel therapeutic targets.Future researchers should integrate advanced single-cell sequencing with multi-omics approaches to investigate cell-specific responses in retinal ganglion cell injury and regeneration.Furthermore,computational models and systems biology methods could help predict molecular pathways interactions,providing valuable guidance for clinical research on optic nerve regeneration and repair.
基金supported by the National Natural Science Foundation of China,Nos.82404892(to QY),82061160374(to ZZ)the Science and Technology Development Fund,Macao Special Administrative Region,China,Nos.0023/2020/AFJ,0035/2020/AGJ+2 种基金the University of Macao Research Grant,Nos.MYRG2022-00248-ICMS,MYRG-CRG2022-00010-ICMS(to MPMH)the Natural Science Foundation of Guangdong Province,No.2024A1515012818(to ZZ)the Fundamental Research Funds for the Central Universities,No.21623114(to ZZ).
文摘Drug development for Alzheimer’s disease is extremely challenging,as demonstrated by the repeated failures of amyloid-β-targeted therapeutics and the controversies surrounding the amyloid-βcascade hypothesis.More recently,advances in the development of Lecanemab,an anti-amyloid-βmonoclonal antibody,have shown positive results in reducing brain A burden and slowing cognitive decline in patients with early-stage Alzheimer’s disease in the Phase Ⅲ clinical trial(Clarity Alzheimer’s disease).Despite these promising results,side effects such as amyloid-related imaging abnormalities(ARIA)may limit its usage.ARIA can manifest as ARIA-E(cerebral edema or effusions)and ARIA-H(microhemorrhages or superficial siderosis)and is thought to be caused by increased vascular permeability due to inflammatory responses,leading to leakages of blood products and protein-rich fluid into brain parenchyma.Endothelial dysfunction is an early pathological feature of Alzheimer’s disease,and the blood-brain barrier becomes increasingly leaky as the disease progresses.In addition,APOE4,the strongest genetic risk factor for Alzheimer’s disease,is associated with higher vascular amyloid burden,increased ARIA incidence,and accelerated blood-brain barrier disruptions.These interconnected vascular abnormalities highlight the importance of vascular contributions to the pathophysiology of Alzheimer’s disease.Here,we will closely examine recent research evaluating the heterogeneity of brain endothelial cells in the microvasculature of different brain regions and their relationships with Alzheimer’s disease progression.
基金supported by funds from the National Natural Science Foundation of China.
文摘Subcutaneous fat(SCF)and intramuscular fat(IMF)deposition is relevant to health in humans,as well as meat production and quality in pigs.In this study,we generated RNA sequence data for 122 SCF,120 IMF,and 87 longissimus dorsi muscle(LDM)samples using 155 F6 pigs from a specially designed heterogeneous population generated by intercrossing four highly selected European commercial breeds and four indigenous Chinese pig breeds.The phenotypes including waist back fat thickness and intramuscular fat content were also measured in the 155 F6 pigs.We found that the genes in SCF and IMF differed largely in both expression levels and network connectivity,and highlighted network modules that exhibited strongest gain of connectivity in SCF and IMF,containing genes that were associated with the immune process and DNA double-strand repair,respectively.We identified 215 SCF genes related to kinase inhibitor activity,mitochondrial fission,and angiogenesis,and 90 IMF genes related to lipolysis and fat cell differentiation,displayed a tissue-specific association with back fat thickness and IMF content,respectively.We found that cis-expression QTL for trait-associated genes in the two adipose tissues tended to have tissuedependent predictability for the two adipose traits.Alternative splicing of genes was also found to be associated with SCF or IMF deposition,but the association was much less extensive than that based on expression levels.This study provides a better understanding of SCF and IMF gene transcription and network organization and identified critical genes and network modules that displayed tissue-specific associations with subcutaneous and intramuscular fat deposition.These features are helpful for designing breeding programs to genetically improve the two adipose traits in a balanced way.
基金supported by the International Science and Technology Cooperation of China(2011DFA32730)
文摘Panax ginseng C. A. Meyer is an important traditional herb in eastern Asia. It contains ginsenosides, which are primary bioactive compounds with medicinal properties. Although ginseng has been cultivated since at least the Ming dynasty to increase production, cultivated ginseng has lower quantities of ginsenosides and lower disease resistance than ginseng grown under natural conditions. We extracted root RNA from six varieties of fifth-year P. ginseng cultivars representing four different growth conditions, and performed Illumina paired-end sequencing. In total, 163,165,706 raw reads were obtained and used to generate a de novo transcriptome that consisted of 151,763 contigs(76,336 unigenes), of which 100,648 contigs(66.3%) were successfully annotated. Differential expression analysis revealed that most differentially expressed genes(DEGs) were upregulated(246 out of 258, 95.3%) in ginseng grown under natural conditions compared with that grown under artificial conditions. These DEGs were enriched in gene ontology(GO) terms including response to stimuli and localization. In particular, some key ginsenoside biosynthesis-related genes, including HMG-Co A synthase(HMGS), mevalonate kinase(MVK), and squalene epoxidase(SE), were upregulated in wild-grown ginseng. Moreover, a high proportion of disease resistance-related genes were upregulated in wild-grown ginseng. This study is the first transcriptome analysis to compare wild-grown and cultivated ginseng, and identifies genes that may produce higher ginsenoside content and better disease resistance in the wild; these genes may have the potential to improve cultivated ginseng grown in artificial environments.
