The plant genome possesses a large number of microRNAs （miRNAs） mainly 21-24 nucleotides in length. They play a vital role in regulation of target gene expression at various stages throughout the whole plant life cy...The plant genome possesses a large number of microRNAs （miRNAs） mainly 21-24 nucleotides in length. They play a vital role in regulation of target gene expression at various stages throughout the whole plant life cycle. Here we sequenced and analyzed ~ 10 million non-coding RNAs （ncRNAs） derived from fiber tissue of the allotetraploid cotton （Gossypium hirsutum） 7 days post-anthesis using ncRNA-seq technology. In terms of distinct reads, 24 nt ncRNA is by far the dominant species, followed by 21 nt and 23 nt ncRNAs. Using ab initio prediction, we identified and characterized a total of 562 candidate miRNA gene loci on the recently assembled D5 genome of the diploid cotton G. raimondii. Of all the 562 predicted miRNAs, 22 were previously discovered in cotton species and 187 had sequence conservation and homology to homologous miRNAs of other plant species. Nucleotide bias analysis showed that the 9th and 1st positions were significantly conserved among different types of miRNA genes. Among the 463 putative miRNA target genes, most significant up/down-regulation occurred in 10-20 days post-anthesis, indicating that miRNAs played an important role during the elongation and secondary cell wall synthesis stages of cotton fiber development. The discovery of new miRNA genes will help understand the mechanisms of miRNA generation and regulation in cotton.展开更多
Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacteri...Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft(partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.展开更多
Border-associated macrophages are located at the interface between the brain and the periphery, including the perivascular spaces, choroid plexus, and meninges. Until recently, the functions of border-associated macro...Border-associated macrophages are located at the interface between the brain and the periphery, including the perivascular spaces, choroid plexus, and meninges. Until recently, the functions of border-associated macrophages have been poorly understood and largely overlooked. However, a recent study reported that border-associated macrophages participate in stroke-induced inflammation, although many details and the underlying mechanisms remain unclear. In this study, we performed a comprehensive single-cell analysis of mouse border-associated macrophages using sequencing data obtained from the Gene Expression Omnibus(GEO) database(GSE174574 and GSE225948). Differentially expressed genes were identified, and enrichment analysis was performed to identify the transcription profile of border-associated macrophages. CellChat analysis was conducted to determine the cell communication network of border-associated macrophages. Transcription factors were predicted using the ‘pySCENIC' tool. We found that, in response to hypoxia, borderassociated macrophages underwent dynamic transcriptional changes and participated in the regulation of inflammatory-related pathways. Notably, the tumor necrosis factor pathway was activated by border-associated macrophages following ischemic stroke. The pySCENIC analysis indicated that the activity of signal transducer and activator of transcription 3(Stat3) was obviously upregulated in stroke, suggesting that Stat3 inhibition may be a promising strategy for treating border-associated macrophages-induced neuroinflammation. Finally, we constructed an animal model to investigate the effects of border-associated macrophages depletion following a stroke. Treatment with liposomes containing clodronate significantly reduced infarct volume in the animals and improved neurological scores compared with untreated animals. Taken together, our results demonstrate comprehensive changes in border-associated macrophages following a stroke, providing a theoretical basis for targeting border-associated macrophages-induced neuroinflammation in stroke treatment.展开更多
Global brain ischemia and neurological deficit are consequences of cardiac arrest that lead to high mortality.Despite advancements in resuscitation science,our limited understanding of the cellular and molecular mecha...Global brain ischemia and neurological deficit are consequences of cardiac arrest that lead to high mortality.Despite advancements in resuscitation science,our limited understanding of the cellular and molecular mechanisms underlying post-cardiac arrest brain injury have hindered the development of effective neuroprotective strategies.Previous studies primarily focused on neuronal death,potentially overlooking the contributions of non-neuronal cells and intercellular communication to the pathophysiology of cardiac arrest-induced brain injury.To address these gaps,we hypothesized that single-cell transcriptomic analysis could uncover previously unidentified cellular subpopulations,altered cell communication networks,and novel molecular mechanisms involved in post-cardiac arrest brain injury.In this study,we performed a single-cell transcriptomic analysis of the hippocampus from pigs with ventricular fibrillation-induced cardiac arrest at 6 and 24 hours following the return of spontaneous circulation,and from sham control pigs.Sequencing results revealed changes in the proportions of different cell types,suggesting post-arrest disruption in the blood-brain barrier and infiltration of neutrophils.These results were validated through western blotting,quantitative reverse transcription-polymerase chain reaction,and immunofluorescence staining.We also identified and validated a unique subcluster of activated microglia with high expression of S100A8,which increased over time following cardiac arrest.This subcluster simultaneously exhibited significant M1/M2 polarization and expressed key functional genes related to chemokines and interleukins.Additionally,we revealed the post-cardiac arrest dysfunction of oligodendrocytes and the differentiation of oligodendrocyte precursor cells into oligodendrocytes.Cell communication analysis identified enhanced post-cardiac arrest communication between neutrophils and microglia that was mediated by neutrophil-derived resistin,driving pro-inflammatory microglial polarization.Our findings provide a comprehensive single-cell map of the post-cardiac arrest hippocampus,offering potential novel targets for neuroprotection and repair following cardiac arrest.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
Ferroptosis,a type of cell death that mainly involves iron metabolism imbalance and lipid peroxidation,is strongly correlated with the phagocytic response caused by bleeding after spinal cord injury.Thus,in this study...Ferroptosis,a type of cell death that mainly involves iron metabolism imbalance and lipid peroxidation,is strongly correlated with the phagocytic response caused by bleeding after spinal cord injury.Thus,in this study,bulk RNA sequencing data(GSE47681 and GSE5296)and single-cell RNA sequencing data(GSE162610)were acquired from gene expression databases.We then conducted differential analysis and immune infiltration analysis.Atf3 and Piezo1 were identified as key ferroptosis genes through random forest and least absolute shrinkage and selection operator algorithms.Further analysis of single-cell RNA sequencing data revealed a close relationship between ferroptosis and cell types such as macrophages/microglia and their intrinsic state transition processes.Differences in transcription factor regulation and intercellular communication networks were found in ferroptosis-related cells,confirming the high expression of Atf3 and Piezo1 in these cells.Molecular docking analysis confirmed that the proteins encoded by these genes can bind cycloheximide.In a mouse model of T8 spinal cord injury,low-dose cycloheximide treatment was found to improve neurological function,decrease levels of the pro-inflammatory cytokine inducible nitric oxide synthase,and increase levels of the anti-inflammatory cytokine arginase 1.Correspondingly,the expression of the ferroptosis-related gene Gpx4 increased in macrophages/microglia,while the expression of Acsl4 decreased.Our findings reveal the important role of ferroptosis in the treatment of spinal cord injury,identify the key cell types and genes involved in ferroptosis after spinal cord injury,and validate the efficacy of potential drug therapies,pointing to new directions in the treatment of spinal cord injury.展开更多
Acrylamide(AA)is a common carcinogen that affects the development and function of the central nervous system(CNS).At present,the toxic injuries of common AA are mainly divided into acute and chronic attacks,and the da...Acrylamide(AA)is a common carcinogen that affects the development and function of the central nervous system(CNS).At present,the toxic injuries of common AA are mainly divided into acute and chronic attacks,and the damage caused to the CNS is different.To investigate whether different doses of AA have different effects on brain cells,we performed single-nucleus RNA sequencing of the brain.The findings indicated that short-term high-dose(acute)AA directly disrupted protein synthesis and protein structure stability on the endoplasmic reticulum.Additionally,acute AA was observed to downregulate genes that inhibit apoptosis and autophagy,promote apoptosis,accelerate cell aging,and affect cell function in glial cells(Glia).Longterm low-dose(chronic)AA exposure elevated Ca^(2+)concentration,increased protein autophosphorylation,and induced mitochondrial dysfunction,resulting in impaired axonal transport and disrupted metabolism of Kenyon cells(KCs).These findings highlight the cell type-specific effects of AA,where acute exposure disrupts Glia protein homeostasis,and chronic exposure impairs calcium signaling and axonal transport in KCs.Such results deepen our understanding of AA-induced neurotoxicity and lay the groundwork for developing targeted therapeutic strategies to mitigate its effects on the CNS.展开更多
Natural hybridization is known to play a vital role in speciation;however,the mechanisms underlying the early stages of natural hybridization remain unclear.Where two plant species come into contact,two driving forces...Natural hybridization is known to play a vital role in speciation;however,the mechanisms underlying the early stages of natural hybridization remain unclear.Where two plant species come into contact,two driving forces may balance the dynamic consequences of hybridization:fusion by hybridization-mediated gene flow,and separation by reproductive isolation(RI)(Ma et al.,2010a,b;Chang et al.,2022).展开更多
Background The cellular basis of testicular development and spermatogenesis for the extreme sperm density in chickens(100-fold higher than mammals)remains poorly defined.A comprehensive understanding of the molecular ...Background The cellular basis of testicular development and spermatogenesis for the extreme sperm density in chickens(100-fold higher than mammals)remains poorly defined.A comprehensive understanding of the molecular characteristics driving poultry testicular development is crucial for explaining this enhanced spermatogenic capacity.Results Here,we first established a single-cell transcriptome profile of chicken testes from hatching to maturity,identifying the dynamic transcriptional characteristics of germ cell fate transition and exploring the developmental characteristics of Sertoli cells and Leydig cells.Multi-species comparisons revealed a higher proportion of germ cells and the unique adaptations of Sertoli cells in chicken testes.Most importantly,our results demonstrated that Sertoli cells dominated in somatic composition of mature chicken testes,and proliferating Sertoli cells persisted in chicken testes even after sexual maturity,while no proliferating Sertoli cells in mammals.We also found a richer interaction network between chicken testicular cells,especially the specific activation of Sertoli cell interaction signals,such as TGF-β,BMP,EGF,and activin.These adaptations of Sertoli cells may support the spermatogenic superiority in chickens.Additionally,our results indicated that cAMP responsive element binding protein 5(CREB5)played a crucial role in maintaining the maturation and function of chicken Sertoli cells,and circadian rhythm promoted testosterone secretion and the development of Leydig cells.Conclusion Our study revealed that the sustained proliferative capacity of Sertoli cells,their enriched signaling network,and the regulatory roles of CREB5 and circadian rhythms collectively represented unique testicular adaptations in chickens.These findings may hold extraordinary significance in understanding the molecular characteristics of poultry testicular development,and provide a plausible framework for explaining enhanced spermatogenesis in poultry.展开更多
Soil cadmium(Cd)contamination poses significant risks to human health and environmental sustainability.Despite advances in bioremediation,effective bioagents with clear mechanistic insights for Cd detoxification are l...Soil cadmium(Cd)contamination poses significant risks to human health and environmental sustainability.Despite advances in bioremediation,effective bioagents with clear mechanistic insights for Cd detoxification are lacking.We first deciphered the whole-genome sequence of a novel Cd-tolerant Trichoderma nigricans T32781 and its in vivo heavy metal tolerance.In five independent pot and field trials,we revealed the T32781-induced alleviation mechanisms of plant-microbe-soil interactions in wheat and barley in response to Cd toxicity using a combination of agronomic,physiological,microbiome and metabolome approaches.We discovered that T32781 inoculation in soil significantly increased grain yield and decreased grain Cd concentration in barley and wheat exposed to different soil Cd levels.T32781 predominantly colonized soils,mitigating Cd toxicity by reducing soil Cd availability and promoting beneficial soil microbial communities and metabolites.These beneficial effects were further validated in the field,where the exogenous application of key metabolites induced by T32781 inoculation in soils and plants significantly increased grain yield and reduced grain Cd concentration in barley.This work highlights the potential of T32781 to enhance plantmicrobe-soil interactions and support sustainable and safe crop production in Cd-contaminated soils,addressing the increasing global demand for cereal production for food and feed.展开更多
Down syndrome(DS)is caused by an extra copy of chromosome 21(Hsa21).Children with DS have an increased frequency of respiratory tract infections,impaired alveolar and vascular development,and pulmonary hypertension.Ho...Down syndrome(DS)is caused by an extra copy of chromosome 21(Hsa21).Children with DS have an increased frequency of respiratory tract infections,impaired alveolar and vascular development,and pulmonary hypertension.How trisomy 21 causes lung diseases remains poorly understood.In this study,we use the Dp16 mouse model,which contains a segmental chromosomal duplication of the entire Hsa21 syntenic region on mouse chromosome 16,to explore the gene dosage effects on DS-related lung diseases.The Dp16 mice present impaired alveolar development and inflammatory-like pathological changes.Single-cell RNA sequencing(scRNA-seq)analysis highlights increased APP-related interactions among male Dp16 lung cells.Specifically,altered antigen processing and presentation with increased MHC-II signaling are found in Dp16 immune cells.Reduced angiogenesis and altered inflammatory responses of Dp16 endothelial cells are also suggested.Moreover,scRNA-seq indicates hyperplasia of Dp16 vascular smooth muscle cells,which is validated by tissue immunofluorescence assessment.Transthoracic echocardiography further shows the existence of pulmonary hypertension in young Dp16 mice.Independent scRNA-seq analysis of the female lung cells recapitulates the majority of key findings identified in male mice,confirming the reproducibility of the results.Collectively,our results provide important clues for the further development of therapeutic approaches for DS-related lung diseases.展开更多
Tuberculosis(TB)continues to pose a significant threat to global public health,necessitating rapid and precise diagnostic methods and comprehensive detection of antimicrobial resistance(AMR)to facilitate timely clinic...Tuberculosis(TB)continues to pose a significant threat to global public health,necessitating rapid and precise diagnostic methods and comprehensive detection of antimicrobial resistance(AMR)to facilitate timely clinical management.Traditional diagnostic techniques suffer from extended turnaround times and limited ability to comprehensively profile AMR,often resulting in delayed therapeutic interventions.Highthroughput sequencing(HTS)technologies have revolutionized pathogen research by significantly improving diagnostic speed and accuracy.In the context of TB,diverse sequencing strategies and platforms are being employed to fulfill specific research goals,ranging from elucidating the molecular mechanisms underlying AMR to characterizing the genomic diversity among clinical isolates.This review systematically examines current progress in the application of HTS for rapid pathogen identification,comprehensive AMR profiling,epidemiological studies,advances in novel drugs,and vaccine development.Furthermore,we address existing technological limitations and bioinformatics challenges and explore the future directions necessary for effectively integrating HTS-based methodologies into global TB control efforts.展开更多
Macrophages in the brain barrier system include microglia in the brain parenchyma,border-associated macrophages at the brain’s borders,and recruited macrophages.They are responsible for neural development,maintenance...Macrophages in the brain barrier system include microglia in the brain parenchyma,border-associated macrophages at the brain’s borders,and recruited macrophages.They are responsible for neural development,maintenance of homeostasis,and orchestrating immune responses.With the rapid exploitation and development of new technologies,there is a deeper understanding of macrophages in the brain barrier system.Here we review the origin,development,important molecules,and functions of macrophages,mainly focusing on microglia and border-associated macrophages.We also highlight some advances in single-cell sequencing and significant cell markers.We anticipate that more advanced methods will emerge to study resident and recruited macrophages in the future,opening new horizons for neuroimmunology and related peripheral immune fields.展开更多
This study establishes and validates a method for the precise quantification of aquatic microbial loads using microbial diversity absolute quantitative sequencing.By adding synthetic spike-in DNA to water samples from...This study establishes and validates a method for the precise quantification of aquatic microbial loads using microbial diversity absolute quantitative sequencing.By adding synthetic spike-in DNA to water samples from the Dahei River prior to DNA extraction and 16S rRNA gene sequencing,it generates standard curves to convert sequencing data into absolute microbial copy numbers.The method,which is proved highly accurate(R^(2)>0.99),reveals a clear contrast between the river sites:the upstream community has not only a significantly higher total microbial load but also a completely different makeup of species compared to the downstream site.This approach effectively overcomes the limitations of relative abundance analysis,providing a powerful tool for environmental monitoring,and proposes key steps for future standardization to ensure data comparability and integration.展开更多
Breast cancer is a malignant tumor originating from breast epithelial tissue.In essence,breast epithelial cells undergo gene mutation under the influence of carcinogenic factors,leading to abnormal cell proliferation ...Breast cancer is a malignant tumor originating from breast epithelial tissue.In essence,breast epithelial cells undergo gene mutation under the influence of carcinogenic factors,leading to abnormal cell proliferation and loss of organism regulation,ultimately leading to the formation of tumors with invasive and metastatic capabilities.Carcinogenic factors of breast cancer involve multiple cellular and molecular mechanisms.Among them,disseminated tumor cells(DTCs)are considered important for treating breast cancer.However,traditional bulk sequencing techniques have limitations,such as the inability to distinguish individual cell differences and dilution of information from key cell subpopulations(such as cancer stem cells and rare immune cells).Single-cell sequencing(scRNA-seq)overcomes the heterogeneity of tumors that traditional sequencing cannot capture by analysing the molecular characteristics of single cells,providing a highresolution perspective for precise typing of breast cancer,exploration of the mechanism of the microenvironment,and personalized treatment.Through this technology,researchers can identify specific gene expression profiles of different cell subpopulations,thus providing a new basis for the molecular typing and personalized treatment of breast cancer.This article explains how single-cell sequencing is used to describe the origin of disseminated tumor cells(DTCs),analyse tumor heterogeneity,metastasis,etc.,and review the current literature on the use of scRNA-seq in breast cancer treatment.In the future,cell separation and processing steps in single-cell sequencing will be further improved to ensure the accuracy of the results and broader application in clinical diagnosis and treatment.展开更多
As an important resource in data link,time slots should be strategically allocated to enhance transmission efficiency and resist eavesdropping,especially considering the tremendous increase in the number of nodes and ...As an important resource in data link,time slots should be strategically allocated to enhance transmission efficiency and resist eavesdropping,especially considering the tremendous increase in the number of nodes and diverse communication needs.It is crucial to design control sequences with robust randomness and conflict-freeness to properly address differentiated access control in data link.In this paper,we propose a hierarchical access control scheme based on control sequences to achieve high utilization of time slots and differentiated access control.A theoretical bound of the hierarchical control sequence set is derived to characterize the constraints on the parameters of the sequence set.Moreover,two classes of optimal hierarchical control sequence sets satisfying the theoretical bound are constructed,both of which enable the scheme to achieve maximum utilization of time slots.Compared with the fixed time slot allocation scheme,our scheme reduces the symbol error rate by up to 9%,which indicates a significant improvement in anti-interference and eavesdropping capabilities.展开更多
Open earthen pond-based larviculture is the main method for rearing Chinese mitten crab(Eriocheir sinensis)larvae in China.Bacterioplankton play a vital role in aquaculture ecosystems,but their community succession th...Open earthen pond-based larviculture is the main method for rearing Chinese mitten crab(Eriocheir sinensis)larvae in China.Bacterioplankton play a vital role in aquaculture ecosystems,but their community succession throughout the larval nursery stages of E.sinensis in such systems is still poorly understood.Using 16S rRNA gene amplicon sequencing,this study characterized the dynamics of bacterioplankton communities during a complete E.sinensis larval rearing cycle in open earthen ponds.Results presented a distinct,unidirectional succession in bacterioplankton composition,characterized by a decrease in Alphaproteobacteria and an increase in Actinobacteria.Live feeds(Brachionus plicatilis and Artemia salina)significantly affected bacterioplankton communities directly through their biological activities and indirectly by modifying the structure of phytoplankton composition.In addition to live feeds,water temperature and dissolved oxygen were key environmental factors affecting the structure of bacterioplankton communities.Biotic interactions,specifically with phytoplankton and copepods,were key drivers of bacterioplankton succession.Routine feeding practices during larval cultivation decreased bacterioplankton network complexity and strengthened community stability.Keystone taxa,specifically OTU783(Rhodobacteraceae)and OTU1235(Microbacteriaceae),played an essential role in maintaining the community stability through recruiting more rare species during the later stages despite their low abundances.These outcomes advance our understanding of the mechanisms central to bacterioplankton community succession and stability in E.sinensis larviculture systems,offering critical insights for developing sustainable aquaculture management strategies.展开更多
Hodgkin lymphoma(HL)is a heterogenous lymphoproliferative disorder of B-cell origin and represents one of the most common malignancies in children and young adults.In addition to well-known underlying factors-such as ...Hodgkin lymphoma(HL)is a heterogenous lymphoproliferative disorder of B-cell origin and represents one of the most common malignancies in children and young adults.In addition to well-known underlying factors-such as Epstein-Barr virus infection-the familial aggregation demonstrated in large population studies suggested a genetic predisposition.First-degree relatives of patients with HL have an approximately threefold increased risk of developing the disease compared to the general population.These observations have recently prompted several whole-genome studies in affected families,identifying variants possibly implicated in lymphomagenesis,including alterations in DICER1(a member of the ribonuclease III family),POT1(protection of telomeres 1),KDR(kinase insert domain receptor),KLHDC8B(kelch domain-containing protein 8B),PAX5(paired box protein 5),GATA3(GATA binding protein 3),IRF7(interferon regulatory factor 7),EEF2KMT(eukaryotic elongation factor 2 lysine methyltransferase),and POLR1E(RNA polymerase I subunit E).In this article,we review current insights into the etiopathogenesis and risks of familial HL,and present case reports involving two sisters diagnosed with HL nearly 17 years apart.Recognizing the risk for first-degree relatives may potentially increase awareness of early symptoms among family members of HL patients,leading to earlier diagnosis and better outcomes.Conversely,understanding that the hereditary risk,though higher than in the general population,remains relatively low may provide reassurance for affected families.展开更多
Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome,demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches...Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome,demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches.While the study represents a valuable methodological step forward,it remains limited by singlecenter design,lack of quantitative calibration,and insufficient control for contamination and inter-laboratory variability.This editorial critically appraises these methodological gaps and emphasizes that future efforts must focus on harmonized,consensus-driven workflows to ensure reproducibility and clinical reliability.The translational potential of multi-region 16S lies in moving from descriptive microbial profiling to actionable clinical integration,particularly for recurrence prediction,treatment-response monitoring,and perioperative complication risk assessment.By addressing these methodological,economic,and ethical challenges,the field can advance toward evidence-based and clinically deployable microbiome-guided precision oncology.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
文摘The plant genome possesses a large number of microRNAs （miRNAs） mainly 21-24 nucleotides in length. They play a vital role in regulation of target gene expression at various stages throughout the whole plant life cycle. Here we sequenced and analyzed ~ 10 million non-coding RNAs （ncRNAs） derived from fiber tissue of the allotetraploid cotton （Gossypium hirsutum） 7 days post-anthesis using ncRNA-seq technology. In terms of distinct reads, 24 nt ncRNA is by far the dominant species, followed by 21 nt and 23 nt ncRNAs. Using ab initio prediction, we identified and characterized a total of 562 candidate miRNA gene loci on the recently assembled D5 genome of the diploid cotton G. raimondii. Of all the 562 predicted miRNAs, 22 were previously discovered in cotton species and 187 had sequence conservation and homology to homologous miRNAs of other plant species. Nucleotide bias analysis showed that the 9th and 1st positions were significantly conserved among different types of miRNA genes. Among the 463 putative miRNA target genes, most significant up/down-regulation occurred in 10-20 days post-anthesis, indicating that miRNAs played an important role during the elongation and secondary cell wall synthesis stages of cotton fiber development. The discovery of new miRNA genes will help understand the mechanisms of miRNA generation and regulation in cotton.
基金Supported by Coordenao de Aperfeioamento de Pessoal de Nível Superior(CAPES)in Brazil,processes BEX 12954-12-8 and 11517-12-3,to Barbosa EGV and Aburjaile FF
文摘Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft(partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.
基金supported by Qingdao Key Medical and Health Discipline ProjectThe Intramural Research Program of the Affiliated Hospital of Qingdao University,No. 4910Qingdao West Coast New Area Science and Technology Project,No. 2020-55 (all to SW)。
文摘Border-associated macrophages are located at the interface between the brain and the periphery, including the perivascular spaces, choroid plexus, and meninges. Until recently, the functions of border-associated macrophages have been poorly understood and largely overlooked. However, a recent study reported that border-associated macrophages participate in stroke-induced inflammation, although many details and the underlying mechanisms remain unclear. In this study, we performed a comprehensive single-cell analysis of mouse border-associated macrophages using sequencing data obtained from the Gene Expression Omnibus(GEO) database(GSE174574 and GSE225948). Differentially expressed genes were identified, and enrichment analysis was performed to identify the transcription profile of border-associated macrophages. CellChat analysis was conducted to determine the cell communication network of border-associated macrophages. Transcription factors were predicted using the ‘pySCENIC' tool. We found that, in response to hypoxia, borderassociated macrophages underwent dynamic transcriptional changes and participated in the regulation of inflammatory-related pathways. Notably, the tumor necrosis factor pathway was activated by border-associated macrophages following ischemic stroke. The pySCENIC analysis indicated that the activity of signal transducer and activator of transcription 3(Stat3) was obviously upregulated in stroke, suggesting that Stat3 inhibition may be a promising strategy for treating border-associated macrophages-induced neuroinflammation. Finally, we constructed an animal model to investigate the effects of border-associated macrophages depletion following a stroke. Treatment with liposomes containing clodronate significantly reduced infarct volume in the animals and improved neurological scores compared with untreated animals. Taken together, our results demonstrate comprehensive changes in border-associated macrophages following a stroke, providing a theoretical basis for targeting border-associated macrophages-induced neuroinflammation in stroke treatment.
基金supported by the National Science Foundation of China,Nos.82325031(to FX),82030059(to YC),82102290(to YG),U23A20485(to YC)Noncommunicable Chronic Diseases-National Science and Technology Major Project,No.2023ZD0505504(to FX),2023ZD0505500(to YC)the Key R&D Program of Shandong Province,No.2022ZLGX03(to YC).
文摘Global brain ischemia and neurological deficit are consequences of cardiac arrest that lead to high mortality.Despite advancements in resuscitation science,our limited understanding of the cellular and molecular mechanisms underlying post-cardiac arrest brain injury have hindered the development of effective neuroprotective strategies.Previous studies primarily focused on neuronal death,potentially overlooking the contributions of non-neuronal cells and intercellular communication to the pathophysiology of cardiac arrest-induced brain injury.To address these gaps,we hypothesized that single-cell transcriptomic analysis could uncover previously unidentified cellular subpopulations,altered cell communication networks,and novel molecular mechanisms involved in post-cardiac arrest brain injury.In this study,we performed a single-cell transcriptomic analysis of the hippocampus from pigs with ventricular fibrillation-induced cardiac arrest at 6 and 24 hours following the return of spontaneous circulation,and from sham control pigs.Sequencing results revealed changes in the proportions of different cell types,suggesting post-arrest disruption in the blood-brain barrier and infiltration of neutrophils.These results were validated through western blotting,quantitative reverse transcription-polymerase chain reaction,and immunofluorescence staining.We also identified and validated a unique subcluster of activated microglia with high expression of S100A8,which increased over time following cardiac arrest.This subcluster simultaneously exhibited significant M1/M2 polarization and expressed key functional genes related to chemokines and interleukins.Additionally,we revealed the post-cardiac arrest dysfunction of oligodendrocytes and the differentiation of oligodendrocyte precursor cells into oligodendrocytes.Cell communication analysis identified enhanced post-cardiac arrest communication between neutrophils and microglia that was mediated by neutrophil-derived resistin,driving pro-inflammatory microglial polarization.Our findings provide a comprehensive single-cell map of the post-cardiac arrest hippocampus,offering potential novel targets for neuroprotection and repair following cardiac arrest.
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,No.81972073(to HZ)a grant from the Taishan Scholars Program ofShandong Province-Young Taishan Scholars,No.tsqn201909197(to HZ)+1 种基金a grant from Tianjin Key Medical Discipline(Specialty)Construct Project,No.TJYXZDXK-027A(to SF)a grant from Academic Expert International Innovation Summit,No.22JRRCRC00010(to SF).
文摘Ferroptosis,a type of cell death that mainly involves iron metabolism imbalance and lipid peroxidation,is strongly correlated with the phagocytic response caused by bleeding after spinal cord injury.Thus,in this study,bulk RNA sequencing data(GSE47681 and GSE5296)and single-cell RNA sequencing data(GSE162610)were acquired from gene expression databases.We then conducted differential analysis and immune infiltration analysis.Atf3 and Piezo1 were identified as key ferroptosis genes through random forest and least absolute shrinkage and selection operator algorithms.Further analysis of single-cell RNA sequencing data revealed a close relationship between ferroptosis and cell types such as macrophages/microglia and their intrinsic state transition processes.Differences in transcription factor regulation and intercellular communication networks were found in ferroptosis-related cells,confirming the high expression of Atf3 and Piezo1 in these cells.Molecular docking analysis confirmed that the proteins encoded by these genes can bind cycloheximide.In a mouse model of T8 spinal cord injury,low-dose cycloheximide treatment was found to improve neurological function,decrease levels of the pro-inflammatory cytokine inducible nitric oxide synthase,and increase levels of the anti-inflammatory cytokine arginase 1.Correspondingly,the expression of the ferroptosis-related gene Gpx4 increased in macrophages/microglia,while the expression of Acsl4 decreased.Our findings reveal the important role of ferroptosis in the treatment of spinal cord injury,identify the key cell types and genes involved in ferroptosis after spinal cord injury,and validate the efficacy of potential drug therapies,pointing to new directions in the treatment of spinal cord injury.
基金supported by the National Natural Science Foundation of China Project(32230081).
文摘Acrylamide(AA)is a common carcinogen that affects the development and function of the central nervous system(CNS).At present,the toxic injuries of common AA are mainly divided into acute and chronic attacks,and the damage caused to the CNS is different.To investigate whether different doses of AA have different effects on brain cells,we performed single-nucleus RNA sequencing of the brain.The findings indicated that short-term high-dose(acute)AA directly disrupted protein synthesis and protein structure stability on the endoplasmic reticulum.Additionally,acute AA was observed to downregulate genes that inhibit apoptosis and autophagy,promote apoptosis,accelerate cell aging,and affect cell function in glial cells(Glia).Longterm low-dose(chronic)AA exposure elevated Ca^(2+)concentration,increased protein autophosphorylation,and induced mitochondrial dysfunction,resulting in impaired axonal transport and disrupted metabolism of Kenyon cells(KCs).These findings highlight the cell type-specific effects of AA,where acute exposure disrupts Glia protein homeostasis,and chronic exposure impairs calcium signaling and axonal transport in KCs.Such results deepen our understanding of AA-induced neurotoxicity and lay the groundwork for developing targeted therapeutic strategies to mitigate its effects on the CNS.
基金supported by the National Natural Science Foundation of China(U23A20160,32360336)Guizhou Provincial Key Technology R&D Program(Qian KeHe ZhiCheng[2023]YiBan035).
文摘Natural hybridization is known to play a vital role in speciation;however,the mechanisms underlying the early stages of natural hybridization remain unclear.Where two plant species come into contact,two driving forces may balance the dynamic consequences of hybridization:fusion by hybridization-mediated gene flow,and separation by reproductive isolation(RI)(Ma et al.,2010a,b;Chang et al.,2022).
基金supported by“National Key Research and Development Program of China”(Grant No.2021YFF1000701)“National Natural Science Foundation of China”(Grant No.U22A20509)。
文摘Background The cellular basis of testicular development and spermatogenesis for the extreme sperm density in chickens(100-fold higher than mammals)remains poorly defined.A comprehensive understanding of the molecular characteristics driving poultry testicular development is crucial for explaining this enhanced spermatogenic capacity.Results Here,we first established a single-cell transcriptome profile of chicken testes from hatching to maturity,identifying the dynamic transcriptional characteristics of germ cell fate transition and exploring the developmental characteristics of Sertoli cells and Leydig cells.Multi-species comparisons revealed a higher proportion of germ cells and the unique adaptations of Sertoli cells in chicken testes.Most importantly,our results demonstrated that Sertoli cells dominated in somatic composition of mature chicken testes,and proliferating Sertoli cells persisted in chicken testes even after sexual maturity,while no proliferating Sertoli cells in mammals.We also found a richer interaction network between chicken testicular cells,especially the specific activation of Sertoli cell interaction signals,such as TGF-β,BMP,EGF,and activin.These adaptations of Sertoli cells may support the spermatogenic superiority in chickens.Additionally,our results indicated that cAMP responsive element binding protein 5(CREB5)played a crucial role in maintaining the maturation and function of chicken Sertoli cells,and circadian rhythm promoted testosterone secretion and the development of Leydig cells.Conclusion Our study revealed that the sustained proliferative capacity of Sertoli cells,their enriched signaling network,and the regulatory roles of CREB5 and circadian rhythms collectively represented unique testicular adaptations in chickens.These findings may hold extraordinary significance in understanding the molecular characteristics of poultry testicular development,and provide a plausible framework for explaining enhanced spermatogenesis in poultry.
基金supported by the National Natural Science Foundation of China(NSFC-ASRT International Joint Research Project 3211101286)Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding,China(2021C02064-3)。
文摘Soil cadmium(Cd)contamination poses significant risks to human health and environmental sustainability.Despite advances in bioremediation,effective bioagents with clear mechanistic insights for Cd detoxification are lacking.We first deciphered the whole-genome sequence of a novel Cd-tolerant Trichoderma nigricans T32781 and its in vivo heavy metal tolerance.In five independent pot and field trials,we revealed the T32781-induced alleviation mechanisms of plant-microbe-soil interactions in wheat and barley in response to Cd toxicity using a combination of agronomic,physiological,microbiome and metabolome approaches.We discovered that T32781 inoculation in soil significantly increased grain yield and decreased grain Cd concentration in barley and wheat exposed to different soil Cd levels.T32781 predominantly colonized soils,mitigating Cd toxicity by reducing soil Cd availability and promoting beneficial soil microbial communities and metabolites.These beneficial effects were further validated in the field,where the exogenous application of key metabolites induced by T32781 inoculation in soils and plants significantly increased grain yield and reduced grain Cd concentration in barley.This work highlights the potential of T32781 to enhance plantmicrobe-soil interactions and support sustainable and safe crop production in Cd-contaminated soils,addressing the increasing global demand for cereal production for food and feed.
基金supported by the Fundamental Research Funds for the Central Universities(226-2022-00035)the National Natural Science Foundation of China(81600986).
文摘Down syndrome(DS)is caused by an extra copy of chromosome 21(Hsa21).Children with DS have an increased frequency of respiratory tract infections,impaired alveolar and vascular development,and pulmonary hypertension.How trisomy 21 causes lung diseases remains poorly understood.In this study,we use the Dp16 mouse model,which contains a segmental chromosomal duplication of the entire Hsa21 syntenic region on mouse chromosome 16,to explore the gene dosage effects on DS-related lung diseases.The Dp16 mice present impaired alveolar development and inflammatory-like pathological changes.Single-cell RNA sequencing(scRNA-seq)analysis highlights increased APP-related interactions among male Dp16 lung cells.Specifically,altered antigen processing and presentation with increased MHC-II signaling are found in Dp16 immune cells.Reduced angiogenesis and altered inflammatory responses of Dp16 endothelial cells are also suggested.Moreover,scRNA-seq indicates hyperplasia of Dp16 vascular smooth muscle cells,which is validated by tissue immunofluorescence assessment.Transthoracic echocardiography further shows the existence of pulmonary hypertension in young Dp16 mice.Independent scRNA-seq analysis of the female lung cells recapitulates the majority of key findings identified in male mice,confirming the reproducibility of the results.Collectively,our results provide important clues for the further development of therapeutic approaches for DS-related lung diseases.
基金supported by the CAMS Innovation Fund for Medical Sciences(CIFMS)(2021-I2M-1-038 and 2023-I2M-2-001)the Non-profit Central Research Institute Fund of the Chinese Academy of Medical Sciences(2019PT310029 and 2023-PT310-04).
文摘Tuberculosis(TB)continues to pose a significant threat to global public health,necessitating rapid and precise diagnostic methods and comprehensive detection of antimicrobial resistance(AMR)to facilitate timely clinical management.Traditional diagnostic techniques suffer from extended turnaround times and limited ability to comprehensively profile AMR,often resulting in delayed therapeutic interventions.Highthroughput sequencing(HTS)technologies have revolutionized pathogen research by significantly improving diagnostic speed and accuracy.In the context of TB,diverse sequencing strategies and platforms are being employed to fulfill specific research goals,ranging from elucidating the molecular mechanisms underlying AMR to characterizing the genomic diversity among clinical isolates.This review systematically examines current progress in the application of HTS for rapid pathogen identification,comprehensive AMR profiling,epidemiological studies,advances in novel drugs,and vaccine development.Furthermore,we address existing technological limitations and bioinformatics challenges and explore the future directions necessary for effectively integrating HTS-based methodologies into global TB control efforts.
基金supported by Ministry of Science and Technology China Brain Initiative Grant,No.2022ZD0204702(to ZY)the National Natural Science Foundation of China,No.82371357(to LC)+2 种基金Foundation for Military Medicine,No.16QNP085(to ZY)Navy Medical University Basic Medical College“Yi Zhang”Basic Medical Talent Development and Support Program,Nos.JCYZRC-D-022(to TC)and JCYZRC-D-024(to HD)Science and Technology Innovation Special Fund of Shanghai Baoshan District,No.2023-E-05(to YW).
文摘Macrophages in the brain barrier system include microglia in the brain parenchyma,border-associated macrophages at the brain’s borders,and recruited macrophages.They are responsible for neural development,maintenance of homeostasis,and orchestrating immune responses.With the rapid exploitation and development of new technologies,there is a deeper understanding of macrophages in the brain barrier system.Here we review the origin,development,important molecules,and functions of macrophages,mainly focusing on microglia and border-associated macrophages.We also highlight some advances in single-cell sequencing and significant cell markers.We anticipate that more advanced methods will emerge to study resident and recruited macrophages in the future,opening new horizons for neuroimmunology and related peripheral immune fields.
基金supported by the National Natural Science Foundation of China(Grant No.32160172)the Key Science-Technology Project of Inner Mongolia(2023KYPT0010)+1 种基金the Natural Science Foundation of Inner Mongolia Autonomous Region of China(Grant No.2025QN03006)the 2023 Inner Mongolia Public Institution High-level Talent Introduction Scientific Research Support Project.
文摘This study establishes and validates a method for the precise quantification of aquatic microbial loads using microbial diversity absolute quantitative sequencing.By adding synthetic spike-in DNA to water samples from the Dahei River prior to DNA extraction and 16S rRNA gene sequencing,it generates standard curves to convert sequencing data into absolute microbial copy numbers.The method,which is proved highly accurate(R^(2)>0.99),reveals a clear contrast between the river sites:the upstream community has not only a significantly higher total microbial load but also a completely different makeup of species compared to the downstream site.This approach effectively overcomes the limitations of relative abundance analysis,providing a powerful tool for environmental monitoring,and proposes key steps for future standardization to ensure data comparability and integration.
文摘Breast cancer is a malignant tumor originating from breast epithelial tissue.In essence,breast epithelial cells undergo gene mutation under the influence of carcinogenic factors,leading to abnormal cell proliferation and loss of organism regulation,ultimately leading to the formation of tumors with invasive and metastatic capabilities.Carcinogenic factors of breast cancer involve multiple cellular and molecular mechanisms.Among them,disseminated tumor cells(DTCs)are considered important for treating breast cancer.However,traditional bulk sequencing techniques have limitations,such as the inability to distinguish individual cell differences and dilution of information from key cell subpopulations(such as cancer stem cells and rare immune cells).Single-cell sequencing(scRNA-seq)overcomes the heterogeneity of tumors that traditional sequencing cannot capture by analysing the molecular characteristics of single cells,providing a highresolution perspective for precise typing of breast cancer,exploration of the mechanism of the microenvironment,and personalized treatment.Through this technology,researchers can identify specific gene expression profiles of different cell subpopulations,thus providing a new basis for the molecular typing and personalized treatment of breast cancer.This article explains how single-cell sequencing is used to describe the origin of disseminated tumor cells(DTCs),analyse tumor heterogeneity,metastasis,etc.,and review the current literature on the use of scRNA-seq in breast cancer treatment.In the future,cell separation and processing steps in single-cell sequencing will be further improved to ensure the accuracy of the results and broader application in clinical diagnosis and treatment.
基金supported by the National Science Foundation of China(No.62171387)the Science and Technology Program of Sichuan Province(No.2024NSFSC0468)the China Postdoctoral Science Foundation(No.2019M663475).
文摘As an important resource in data link,time slots should be strategically allocated to enhance transmission efficiency and resist eavesdropping,especially considering the tremendous increase in the number of nodes and diverse communication needs.It is crucial to design control sequences with robust randomness and conflict-freeness to properly address differentiated access control in data link.In this paper,we propose a hierarchical access control scheme based on control sequences to achieve high utilization of time slots and differentiated access control.A theoretical bound of the hierarchical control sequence set is derived to characterize the constraints on the parameters of the sequence set.Moreover,two classes of optimal hierarchical control sequence sets satisfying the theoretical bound are constructed,both of which enable the scheme to achieve maximum utilization of time slots.Compared with the fixed time slot allocation scheme,our scheme reduces the symbol error rate by up to 9%,which indicates a significant improvement in anti-interference and eavesdropping capabilities.
基金supported by the National Key R&D Program(No.2022YFD2400700)from the Ministry of Science and Technology of Chinathe Open Competition Project(No.JBGS[2021]127)from the Department of Agriculture and Rural Affairs of Jiangsu Provincepartially supported by the platform project of Shanghai Collaborative Innovation Center for Cultivating Elite Breeds and Green-culture of Aquaculture Animals(No.2021-KJ-02-12)。
文摘Open earthen pond-based larviculture is the main method for rearing Chinese mitten crab(Eriocheir sinensis)larvae in China.Bacterioplankton play a vital role in aquaculture ecosystems,but their community succession throughout the larval nursery stages of E.sinensis in such systems is still poorly understood.Using 16S rRNA gene amplicon sequencing,this study characterized the dynamics of bacterioplankton communities during a complete E.sinensis larval rearing cycle in open earthen ponds.Results presented a distinct,unidirectional succession in bacterioplankton composition,characterized by a decrease in Alphaproteobacteria and an increase in Actinobacteria.Live feeds(Brachionus plicatilis and Artemia salina)significantly affected bacterioplankton communities directly through their biological activities and indirectly by modifying the structure of phytoplankton composition.In addition to live feeds,water temperature and dissolved oxygen were key environmental factors affecting the structure of bacterioplankton communities.Biotic interactions,specifically with phytoplankton and copepods,were key drivers of bacterioplankton succession.Routine feeding practices during larval cultivation decreased bacterioplankton network complexity and strengthened community stability.Keystone taxa,specifically OTU783(Rhodobacteraceae)and OTU1235(Microbacteriaceae),played an essential role in maintaining the community stability through recruiting more rare species during the later stages despite their low abundances.These outcomes advance our understanding of the mechanisms central to bacterioplankton community succession and stability in E.sinensis larviculture systems,offering critical insights for developing sustainable aquaculture management strategies.
文摘Hodgkin lymphoma(HL)is a heterogenous lymphoproliferative disorder of B-cell origin and represents one of the most common malignancies in children and young adults.In addition to well-known underlying factors-such as Epstein-Barr virus infection-the familial aggregation demonstrated in large population studies suggested a genetic predisposition.First-degree relatives of patients with HL have an approximately threefold increased risk of developing the disease compared to the general population.These observations have recently prompted several whole-genome studies in affected families,identifying variants possibly implicated in lymphomagenesis,including alterations in DICER1(a member of the ribonuclease III family),POT1(protection of telomeres 1),KDR(kinase insert domain receptor),KLHDC8B(kelch domain-containing protein 8B),PAX5(paired box protein 5),GATA3(GATA binding protein 3),IRF7(interferon regulatory factor 7),EEF2KMT(eukaryotic elongation factor 2 lysine methyltransferase),and POLR1E(RNA polymerase I subunit E).In this article,we review current insights into the etiopathogenesis and risks of familial HL,and present case reports involving two sisters diagnosed with HL nearly 17 years apart.Recognizing the risk for first-degree relatives may potentially increase awareness of early symptoms among family members of HL patients,leading to earlier diagnosis and better outcomes.Conversely,understanding that the hereditary risk,though higher than in the general population,remains relatively low may provide reassurance for affected families.
文摘Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome,demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches.While the study represents a valuable methodological step forward,it remains limited by singlecenter design,lack of quantitative calibration,and insufficient control for contamination and inter-laboratory variability.This editorial critically appraises these methodological gaps and emphasizes that future efforts must focus on harmonized,consensus-driven workflows to ensure reproducibility and clinical reliability.The translational potential of multi-region 16S lies in moving from descriptive microbial profiling to actionable clinical integration,particularly for recurrence prediction,treatment-response monitoring,and perioperative complication risk assessment.By addressing these methodological,economic,and ethical challenges,the field can advance toward evidence-based and clinically deployable microbiome-guided precision oncology.
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.
