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
High-temperature Daqu(HTD),a microbial starter crucial for saccharification,fermentation,and aroma development in Maotai-flavor Baijiu production,is still produced through labor-intensive manual processes.Mechanizatio...High-temperature Daqu(HTD),a microbial starter crucial for saccharification,fermentation,and aroma development in Maotai-flavor Baijiu production,is still produced through labor-intensive manual processes.Mechanization of HTD production,essential for scalability and consistency,requires the identification,pure cultivation and utilization of key microorganisms from its traditional complex microbiome.To establish a bacterial collection of HTD systematically,this study designed and screened 51 culture conditions targeting samples from 4 critical fermentation stages across 3 distinct geographical production regions.Through iterative optimization of these conditions,we isolated and identified 852 pure colonies,representing 60 genera and 122 species,achieving cultivation efficiency reaches from 21.43%to 42.86%.More importantly,45 microbial genera(113 microbial species)were cultured but not sequenced(CBNS),including 11 actinobacterial genera.Solid-state simulated fermentation experiments showed the ecological importance of these CBNS Actinobacteria,revealing their capacity to suppress off-odor-producing molds.This study represents the first systematic cultivation of HTD microorganisms,achieving a two-fold increase in culturable diversity.Our findings underscore the critical role of culture-dependent methods in assessing microbial diversity and elucidating ecological functions within HTD fermentation,providing a framework for enhancing bacterial cultivation from complex consortia.展开更多
Next-generation sequencing technologies have significantly advanced our comprehension of microbial diversity and ecological roles within fermented foods.However,culture-based approaches remain essential for a comprehe...Next-generation sequencing technologies have significantly advanced our comprehension of microbial diversity and ecological roles within fermented foods.However,culture-based approaches remain essential for a comprehensive understanding of these complex ecosystems.This study integrated culture-dependent and culture-independent techniques to elucidate the microbial diversity and flavor-forming potential of fungi in high-temperature Daqu,a critical solid-state fermentation process in Maotai-flavor Baijiu production.Through iterative cultivation strategies,we successfully isolated and identified 660 pure eukaryotic colonies,representing 33 genera and 58 species,from Daqu samples.This approach significantly improved cultivation efficiency from 20.7 to 63.2%.In addition,despite the optimization of ITS rRNA primer sets to enhance the detection of eukaryotic microorganisms,we still identified 21 genera(comprising 27 species)that were culturable but not detected by high-throughput sequencing analysis.Fermentation experiments demonstrated the robust growth and substantial ethyl acetate production potential of these fungal species,particularly Kluyveromyces marxianus,which exhibited exceptional performance at elevated temperatures(45℃).This study advanced culture-dependent techniques to improve the isolation of eukaryotic microorganisms from Daqu.These findings highlight the importance of culture-based approaches in characterizing microbial diversity and function.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
Severe fever with thrombocytopenia syndrome(SFTS),caused by Dabie bandavirus(DBV),triggers aberrant immune activation and cytokine storms,contributing to poor prognosis;however,its immune dysfunction mechanism remains...Severe fever with thrombocytopenia syndrome(SFTS),caused by Dabie bandavirus(DBV),triggers aberrant immune activation and cytokine storms,contributing to poor prognosis;however,its immune dysfunction mechanism remains unclear.Current management relies on symptomatic treatment and glucocorticoids,but no standardized treatment guidelines exist.This study investigated the mechanisms of abnormal lymphocyte function in acute-phase SFTS and the effects of glucocorticoid treatment on lymphoid cells using single-cell RNA sequencing(scRNA-seq)and bioinformatics analysis.We enrolled three healthy volunteers and 13 patients with acute SFTS and divided them into four groups.ScRNA-seq was performed on peripheral blood mononuclear cells from all 16 participants,capturing transcripts from the 3′ends of mRNA.Bioinformatics analyses were used to profile patient immunological signatures,characterize subpopulation compositions,infer developmental trajectories,and assess lymphoid cell interactions.We obtained 120886 lymphoid cells,which were clustered into 23 functionally heterogeneous subsets.Results showed that patients with severe SFTS exhibited stronger inflammatory and adaptive immune responses.Glucocorticoid treatment suppressed inflammation and the interferon response but also inhibited the production of virus-specific antibodies.These findings suggest that appropriate glucocorticoid administration may alleviate the hyperinflammatory state in severe SFTS during the acute phase,although it is not recommended as a conventional treatment because of its potential to suppress antiviral immunity.This study provides insights into SFTS immunopathology and informs the optimized clinical use of glucocorticoids.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
In this study,we introduce the sequence space l^(μ)(p,Δ^(m)) with a fractional order μ.Furthermore,we give some topological properties of this space.Also we introduce α-,β-,andγ-duals of l^(μ)(p,Δ^(m)) and its...In this study,we introduce the sequence space l^(μ)(p,Δ^(m)) with a fractional order μ.Furthermore,we give some topological properties of this space.Also we introduce α-,β-,andγ-duals of l^(μ)(p,Δ^(m)) and its some matrix mappings.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
Aberrant RNA modification has been linked to the pathogenesis of various diseases;however,its specific molecular mechanisms in spinal cord injury remain poorly understood.The objective of this study was to explore RNA...Aberrant RNA modification has been linked to the pathogenesis of various diseases;however,its specific molecular mechanisms in spinal cord injury remain poorly understood.The objective of this study was to explore RNA modification-related biomarkers of spinal cord injury.The mRNA expression profiles of mice with spinal cord injury were retrieved from the Gene Expression Omnibus(GEO)database(GSE18179).We identified 185 differentially expressed genes using bioinformatics approaches.Functional enrichment analysis demonstrated aberrant activation or inhibition of common metabolism-related pathways,including sulfur metabolism and steroid biosynthesis,in mice with spinal cord injury.An integrated strategy comprising weighted gene co-expression network analysis,a random forest model,a support vector machine model,and a generalized linear model was employed to identify four genes whose aberrant RNA modification was linked to spinal cord injury:Elovl6,Idi1,Sqle,and Stbd1.We verified the expression levels and diagnostic performance of these four genes in the original training dataset and mouse samples via receiver operating characteristic curve analysis.Quantitative reverse transcription-polymerase chain reaction demonstrated variations in the mRNA levels of the four genes between the Sham and spinal cord injury groups at different time points following injury.We also constructed microRNA-mRNA and transcription factor-mRNA interaction networks using Cytoscape.Additionally,we evaluated the proportions of 22 types of immune cells in the spinal cords of mice using the CIBERSORT tool,revealing significant alterations in the numbers of memory B cells,resting dendritic cells,M0 macrophages,activated mast cells,resting mast cells,and CD8+T cells in spinal cord injury mice compared with Sham controls.Microglia and T cells were identified as key cell types by single-cell sequencing analysis.These findings provide new directions for the development of RNA modification-related therapeutic strategies for spinal cord injury and suggest that Elovl6,Idi1,Sqle,and Stbd1 are potential biomarkers 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
Background:This study aims to analyze the genotypes and antibiotic resistance characteristics of Clostridioides difficile(C.difficile)isolated from children under 5 years old with diarrhea in Yunnan Province.Methods:F...Background:This study aims to analyze the genotypes and antibiotic resistance characteristics of Clostridioides difficile(C.difficile)isolated from children under 5 years old with diarrhea in Yunnan Province.Methods:Fecal samples from children under 5 years of age with diarrhea in Kunming city from 2013-2019 were collected for anaerobic culture,isolation,and identification of C.difficile.The antibiotic susceptibility tests and molecular typing of isolated strains were also performed.Results:44 strains of C.difficile were isolated from 896 fecal samples.Of these,40 strains(90.9%)were positive for both tcdA and tcdB,while 4 strains(9.1%)were negative for both.All isolates were negative for cdtA and cdtB.The isolates were classified into 13 STs,the predominant types were ST3(13 strains,29.5%),ST35(8 strains,18.2%),and ST54(5 strains,11.4%).All the strains were susceptible to metronidazole,amoxicillin/clavulanic acid,vancomycin,and amoxicillin.The highest resistance rate was observed against gentamicin(86.36%),followed by polymyxin E(84.09%),quinupristin-dalfopristin(61.36%),and ceftazidime(36.36%).Some patients with diarrhea had C.difficile co-infections with other pathogens,including norovirus,adenovirus,rotavirus or Salmonella or Escherichia coli.Conclusion:C.difficile strains isolated from children under 5 years of age are mostly toxigenic,and the MLST results are highly diverse.Monitoring and prevention of C.difficile should be strengthened.展开更多
Penduline tits(genus Remiz)are small passerines distributed across Europe,Central and East Asia,and North Africa,renowned for their elaborate nests and unusually diverse mating systems.However,the taxonomy and evoluti...Penduline tits(genus Remiz)are small passerines distributed across Europe,Central and East Asia,and North Africa,renowned for their elaborate nests and unusually diverse mating systems.However,the taxonomy and evolutionary relationships within this genus have remained contentious due to overlapping breeding distributions and extensive hybridization.Using broad-range geographic sampling and whole-genome sequencing,here we report the phylogenetic relationships within this genus.Our results from maximum likelihood trees,species trees,population structure,and PCA analyses consistently identify four distinct,well-supported monophyletic clades.Based on these robust results,we support dividing Remiz into four species:the Eurasian Penduline Tit(R.pendulinus),Black-headed Penduline Tit(R.macronyx),White-crowned Penduline Tit(R.coronatus),and Chinese Penduline Tit(R.consobrinus).Among these species,R.consobrinus diverged earlier from other species,followed by R.coronatus,and then,R.pendulinus and R.macronyx.R.pendulinus and R.macronyx showed shallow genetic differentiation with recent divergence(~87,000 years ago)and ongoing gene flow.Our findings demonstrate the effectiveness of phylogenomic approaches in resolving taxonomic ambiguities and provide a robust evolutionary framework for tracing the diversification of life history traits,particularly nest structures and mating systems,across the genus.展开更多
The occurrence of severe thalassemia,an inherited blood disorder that is either blood-transfusiondependent or fatal,can be mitigated through carrier screening.Here,we aim to evaluate the effectiveness and outcomes of ...The occurrence of severe thalassemia,an inherited blood disorder that is either blood-transfusiondependent or fatal,can be mitigated through carrier screening.Here,we aim to evaluate the effectiveness and outcomes of pre-conceptional and early pregnancy screening initiatives for severe thalassemia prevention in a diverse population of 28,043 women.Using next-generation sequencing(NGS),we identify 4,226(15.07%)thalassemia carriers across 29 ethnic groups and categorize them into high-(0.75%),low-(25.86%),and unknown-risk(69.19%)groups based on their spouses'screening results.Post-screening follow-up reveals 59 fetuses with severe thalassemia exclusively in high-risk couples,underscoring the efficacy of risk classification.Among 25,053 live births over 6 months of age,two severe thalassemia infants were born to unknown-risk couples,which was attributed to incomplete screening and late NGS-based testing for a rare variant.Notably,64 rare variants are identified in 287 individuals,highlighting the genetic heterogeneity of thalassemia.We also observe that migrant flow significantly impacts carrier rates,with 93.90%of migrants to Chenzhou originating from high-prevalence regions in southern China.Our study demonstrates that NGS-based screening during pre-conception and early pregnancy is effective for severe thalassemia prevention,emphasizing the need for continuous screening efforts in areas with high and underestimated prevalence.展开更多
Anther is a key male reproductive organ that is essential for the plant life cycle,from the sporophyte to the gametophyte generation.To explore the isoform-level transcriptional landscape of developing anthers in maiz...Anther is a key male reproductive organ that is essential for the plant life cycle,from the sporophyte to the gametophyte generation.To explore the isoform-level transcriptional landscape of developing anthers in maize(Zea mays L.),we analyzed Iso-Seq data from anthers collected at 10 developmental stages,together with strand-specific RNA-seq,CAGE-seq,and PAS-seq data.Of the 152,026 high-confidence full-length isoforms identified,68.8%have not been described;these include 22,365 isoforms that originate from previously unannotated loci and 82,167 novel isoforms that originate from annotated protein-coding genes.Using our newly developed strategy to detect dynamic expression patterns of isoforms,we identify 13,899 differentially variable regions(DVRs);surprisingly,1275 genes contain more than two DVRs,revealing highly efficient utilization of limited genic regions.We identify 7876 long non-coding RNAs(lncRNAs)from 4098 loci,most of which were preferentially expressed during cell differentiation and meiosis.We also detected 371 long-range interactions involving intergenic lncRNAs(lincRNAs);interestingly,243 were lincRNA-gene ones,and the interacting genes were highly expressed in anthers,suggesting that many potential lncRNA regulators of key genes are required for anther development.This study provides valuable resources and fundamental information for studying the essential transcripts of key genes during anther development.展开更多
Recent advancements in genome sequencing have enabled the estimation of genetic load through deleterious mutation profiling.However,Chinese populations remain underexplored in this context.We analyze whole-exome seque...Recent advancements in genome sequencing have enabled the estimation of genetic load through deleterious mutation profiling.However,Chinese populations remain underexplored in this context.We analyze whole-exome sequencing data from 5002 individuals,encompassing major Han subgroups―North Han(NHan),South Han(S-Han),and Guangxi Han(G-Han)―as well as 13 ethnic minorities.Notably,G-Han exhibits significant genetic affinity with the Zhuang population.Systematic curation of 2110 ClinVar pathogenic or likely pathogenic variants reveals 93.4%are ultra-rare.Exceptions include GJB2 rs72474224-A(hearing loss),which shows higher frequencies in Zhuang and G-Han,and β-thalassemia-associated HBB variants(rs33986703-A and rs33950507-T),which are elevated in G-Han compared to other Han subgroups.Among 96 autosomal dominant mutation carriers,LDLR variants are predominant(~25%),with comparable frequencies across Han subgroups.Adaptive signatures highlight gene-environment interactions:MTHFR rs1801133-A(UV adaptation)declines southward,while ALDH2 rs671-A(alcohol metabolism)displays the opposite trend.ABCC11 rs17822931-A,associated with cold adaptation,is particularly low frequency in G-Han.Gene-based rare-variant collapsing analyses identify an elevated risk of retinitis pigmentosa in S-Han(PRPF4,TUB).Our findings demonstrate that genetic load in Chinese populations is influenced by demographic history,population structure,and regional adaptation,emphasizing the importance of population-specific frameworks in precision medicine.展开更多
Objectives:Tumor recurrence is a major determinant of poor prognosis in hepatocellular carcinoma(HCC),yet its cellular and molecular basis remains incompletely understood.This study aimed to identify recurrenceassocia...Objectives:Tumor recurrence is a major determinant of poor prognosis in hepatocellular carcinoma(HCC),yet its cellular and molecular basis remains incompletely understood.This study aimed to identify recurrenceassociated genes at single-cell resolution and to develop a prognostic model for predicting survival outcomes and immunotherapy responsiveness in HCC.Methods:Single-cell RNA sequencing data from 12 primary and 6 recurrent HCC samples were integrated and analyzed to identify genes characteristic of recurrence.After quality control,principal component analysis,and t-SNE-based clustering were used to identify highly variable genes for cell clustering and annotation.Based on macrophage characteristic genes,a recurrence-related risk score was constructed using a LASSOCox regression model,and a nomogram integrating clinical variables was developed.Prognostic performance was assessed using Kaplan-Meier analysis and time-dependent ROC curves.Immune infiltration profiling was performed to compare immune characteristics between risk groups defined by the prognostic model.Multivariate Cox regression was applied to identify independent prognostic biomarkers,which were subsequently validated by cell function experiments.Results:The risk model effectively stratified patients into high-and low-risk groups with distinct survival outcomes,demonstrating high predictive accuracy for 1-,3-,and 5-year survival.High-risk patients showed altered immune profiles and a reduced predicted response to immunotherapy.GRID2,RNF186,and SLC4A10 were identified as independent prognostic genes,with RNF186 promoting HCC cell proliferation in a SESN2-dependent manner.Conclusion:This prognostic model provides new insights into precision medicine and immunotherapy for HCC,highlighting the potential clinical significance of RNF186 as a therapeutic target.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:Bloodstream infections(BSIs) caused by gram-positive cocci(GPC) and gramnegative bacilli(GNB) are major causes of sepsis.However,their distinct effects on host responses remain poorly characterized at the s...BACKGROUND:Bloodstream infections(BSIs) caused by gram-positive cocci(GPC) and gramnegative bacilli(GNB) are major causes of sepsis.However,their distinct effects on host responses remain poorly characterized at the single-cell level.This study used single-cell transcriptomics to define pathogenspecific monocyte heterogeneity in BSIs to identify the mechanisms underlying clinical differences.METHODS:Single-cell RNA sequencing(sc RNA-seq) was performed on peripheral blood mononuclear cells obtained from healthy volunteers,two patients with GNB-BSI sepsis,and two patients with GPC-BSI sepsis.Differential gene expression,particularly in monocytes,was analyzed.The key findings were validated with clinical characteristics and outcomes of 45 patients with GNBBSI sepsis and 40 patients with GPC-BSI sepsis.The distinguishing performances of identified biomarkers were evaluated via receiver operating characteristic(ROC) curve.RESULTS:In pathogen-specific transcriptomes,54 identified genes were significantly associated with GNB-BSI(upregulated genes enriched in inflammatory pathways and downregulated genes enriched in oxidative phosphorylation).Twenty-one identified genes were associated with GPC-BSI(downregulated genes associated with cell adhesion molecules and upregulated genes involved in PI3K-Akt signaling).Nineteen genes were common to both groups,with distinct pathogen sensitivities.Patients with GNB-BSI presented with significantly greater disease severity,systemic inflammation and lymphopenia than patients with GPC-BSI.Conversely,patients with GPC-BSI had higher S100A12 and globulin levels and platelet counts.The combination of S100A12^(high) and procalcitonin(PCT)^(low) discriminated GPC-BSI from GNB-BSI(area under the curve=0.882,sensitivity 75%,specificity 91%;cutoff value 0.56).CONCLUSION:Sc RNA-seq reveals the heterogeneity of GPC-BSI and GNB-BSI.Compared with GPC-BSI,GNB-BSI causes severe inflammation and metabolic suppression,which are associated with poor outcomes.The S100A12^(high)+PCT^(low) combination may have potential to discriminate among the major causes of BSI.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 the Natural Science Foundation of Jiangsu Province(BK20242077).
文摘High-temperature Daqu(HTD),a microbial starter crucial for saccharification,fermentation,and aroma development in Maotai-flavor Baijiu production,is still produced through labor-intensive manual processes.Mechanization of HTD production,essential for scalability and consistency,requires the identification,pure cultivation and utilization of key microorganisms from its traditional complex microbiome.To establish a bacterial collection of HTD systematically,this study designed and screened 51 culture conditions targeting samples from 4 critical fermentation stages across 3 distinct geographical production regions.Through iterative optimization of these conditions,we isolated and identified 852 pure colonies,representing 60 genera and 122 species,achieving cultivation efficiency reaches from 21.43%to 42.86%.More importantly,45 microbial genera(113 microbial species)were cultured but not sequenced(CBNS),including 11 actinobacterial genera.Solid-state simulated fermentation experiments showed the ecological importance of these CBNS Actinobacteria,revealing their capacity to suppress off-odor-producing molds.This study represents the first systematic cultivation of HTD microorganisms,achieving a two-fold increase in culturable diversity.Our findings underscore the critical role of culture-dependent methods in assessing microbial diversity and elucidating ecological functions within HTD fermentation,providing a framework for enhancing bacterial cultivation from complex consortia.
基金supported by the Natural Science Foundation of Jiangsu Province.(BK20242077)。
文摘Next-generation sequencing technologies have significantly advanced our comprehension of microbial diversity and ecological roles within fermented foods.However,culture-based approaches remain essential for a comprehensive understanding of these complex ecosystems.This study integrated culture-dependent and culture-independent techniques to elucidate the microbial diversity and flavor-forming potential of fungi in high-temperature Daqu,a critical solid-state fermentation process in Maotai-flavor Baijiu production.Through iterative cultivation strategies,we successfully isolated and identified 660 pure eukaryotic colonies,representing 33 genera and 58 species,from Daqu samples.This approach significantly improved cultivation efficiency from 20.7 to 63.2%.In addition,despite the optimization of ITS rRNA primer sets to enhance the detection of eukaryotic microorganisms,we still identified 21 genera(comprising 27 species)that were culturable but not detected by high-throughput sequencing analysis.Fermentation experiments demonstrated the robust growth and substantial ethyl acetate production potential of these fungal species,particularly Kluyveromyces marxianus,which exhibited exceptional performance at elevated temperatures(45℃).This study advanced culture-dependent techniques to improve the isolation of eukaryotic microorganisms from Daqu.These findings highlight the importance of culture-based approaches in characterizing microbial diversity and function.
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 Natural Science Foundation of China(Grant No.81871242)the"YiQi"Fund Project(Grant Nos.2024YQZL01 and 2023YQFH05)the National Key Research and Development Program of China(Grant No.2022YFF0710100).
文摘Severe fever with thrombocytopenia syndrome(SFTS),caused by Dabie bandavirus(DBV),triggers aberrant immune activation and cytokine storms,contributing to poor prognosis;however,its immune dysfunction mechanism remains unclear.Current management relies on symptomatic treatment and glucocorticoids,but no standardized treatment guidelines exist.This study investigated the mechanisms of abnormal lymphocyte function in acute-phase SFTS and the effects of glucocorticoid treatment on lymphoid cells using single-cell RNA sequencing(scRNA-seq)and bioinformatics analysis.We enrolled three healthy volunteers and 13 patients with acute SFTS and divided them into four groups.ScRNA-seq was performed on peripheral blood mononuclear cells from all 16 participants,capturing transcripts from the 3′ends of mRNA.Bioinformatics analyses were used to profile patient immunological signatures,characterize subpopulation compositions,infer developmental trajectories,and assess lymphoid cell interactions.We obtained 120886 lymphoid cells,which were clustered into 23 functionally heterogeneous subsets.Results showed that patients with severe SFTS exhibited stronger inflammatory and adaptive immune responses.Glucocorticoid treatment suppressed inflammation and the interferon response but also inhibited the production of virus-specific antibodies.These findings suggest that appropriate glucocorticoid administration may alleviate the hyperinflammatory state in severe SFTS during the acute phase,although it is not recommended as a conventional treatment because of its potential to suppress antiviral immunity.This study provides insights into SFTS immunopathology and informs the optimized clinical use of glucocorticoids.
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.
文摘In this study,we introduce the sequence space l^(μ)(p,Δ^(m)) with a fractional order μ.Furthermore,we give some topological properties of this space.Also we introduce α-,β-,andγ-duals of l^(μ)(p,Δ^(m)) and its some matrix mappings.
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.
文摘Aberrant RNA modification has been linked to the pathogenesis of various diseases;however,its specific molecular mechanisms in spinal cord injury remain poorly understood.The objective of this study was to explore RNA modification-related biomarkers of spinal cord injury.The mRNA expression profiles of mice with spinal cord injury were retrieved from the Gene Expression Omnibus(GEO)database(GSE18179).We identified 185 differentially expressed genes using bioinformatics approaches.Functional enrichment analysis demonstrated aberrant activation or inhibition of common metabolism-related pathways,including sulfur metabolism and steroid biosynthesis,in mice with spinal cord injury.An integrated strategy comprising weighted gene co-expression network analysis,a random forest model,a support vector machine model,and a generalized linear model was employed to identify four genes whose aberrant RNA modification was linked to spinal cord injury:Elovl6,Idi1,Sqle,and Stbd1.We verified the expression levels and diagnostic performance of these four genes in the original training dataset and mouse samples via receiver operating characteristic curve analysis.Quantitative reverse transcription-polymerase chain reaction demonstrated variations in the mRNA levels of the four genes between the Sham and spinal cord injury groups at different time points following injury.We also constructed microRNA-mRNA and transcription factor-mRNA interaction networks using Cytoscape.Additionally,we evaluated the proportions of 22 types of immune cells in the spinal cords of mice using the CIBERSORT tool,revealing significant alterations in the numbers of memory B cells,resting dendritic cells,M0 macrophages,activated mast cells,resting mast cells,and CD8+T cells in spinal cord injury mice compared with Sham controls.Microglia and T cells were identified as key cell types by single-cell sequencing analysis.These findings provide new directions for the development of RNA modification-related therapeutic strategies for spinal cord injury and suggest that Elovl6,Idi1,Sqle,and Stbd1 are potential biomarkers 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 Yunnan Provincial Key Research and Development Program(grant No.202503AP140034)Infectious Disease Spectrum and Epidemiology Project of YNCDC(grant No.YNAPM2025-003).
文摘Background:This study aims to analyze the genotypes and antibiotic resistance characteristics of Clostridioides difficile(C.difficile)isolated from children under 5 years old with diarrhea in Yunnan Province.Methods:Fecal samples from children under 5 years of age with diarrhea in Kunming city from 2013-2019 were collected for anaerobic culture,isolation,and identification of C.difficile.The antibiotic susceptibility tests and molecular typing of isolated strains were also performed.Results:44 strains of C.difficile were isolated from 896 fecal samples.Of these,40 strains(90.9%)were positive for both tcdA and tcdB,while 4 strains(9.1%)were negative for both.All isolates were negative for cdtA and cdtB.The isolates were classified into 13 STs,the predominant types were ST3(13 strains,29.5%),ST35(8 strains,18.2%),and ST54(5 strains,11.4%).All the strains were susceptible to metronidazole,amoxicillin/clavulanic acid,vancomycin,and amoxicillin.The highest resistance rate was observed against gentamicin(86.36%),followed by polymyxin E(84.09%),quinupristin-dalfopristin(61.36%),and ceftazidime(36.36%).Some patients with diarrhea had C.difficile co-infections with other pathogens,including norovirus,adenovirus,rotavirus or Salmonella or Escherichia coli.Conclusion:C.difficile strains isolated from children under 5 years of age are mostly toxigenic,and the MLST results are highly diverse.Monitoring and prevention of C.difficile should be strengthened.
基金supported by the National Natural Science Foundation of China(32161143024,32500368,31970405)the Third Xinjiang Scientific Expedition Program(2022xjkk0200)+2 种基金INSF-NSFC Joint Research Project(No.4002006)HUN-REN-Debrecen University Reproductive Strategies Research Group grant(Ref 1102207)supported by the Postdoctoral Fellowship Program of CPSF under Grant Number GZC20240121。
文摘Penduline tits(genus Remiz)are small passerines distributed across Europe,Central and East Asia,and North Africa,renowned for their elaborate nests and unusually diverse mating systems.However,the taxonomy and evolutionary relationships within this genus have remained contentious due to overlapping breeding distributions and extensive hybridization.Using broad-range geographic sampling and whole-genome sequencing,here we report the phylogenetic relationships within this genus.Our results from maximum likelihood trees,species trees,population structure,and PCA analyses consistently identify four distinct,well-supported monophyletic clades.Based on these robust results,we support dividing Remiz into four species:the Eurasian Penduline Tit(R.pendulinus),Black-headed Penduline Tit(R.macronyx),White-crowned Penduline Tit(R.coronatus),and Chinese Penduline Tit(R.consobrinus).Among these species,R.consobrinus diverged earlier from other species,followed by R.coronatus,and then,R.pendulinus and R.macronyx.R.pendulinus and R.macronyx showed shallow genetic differentiation with recent divergence(~87,000 years ago)and ongoing gene flow.Our findings demonstrate the effectiveness of phylogenomic approaches in resolving taxonomic ambiguities and provide a robust evolutionary framework for tracing the diversification of life history traits,particularly nest structures and mating systems,across the genus.
基金supported by the National Natural Science Foundation of China(81760037)Yunling Scholar Project of Yunnan Province(YNWR-YLXZ-2019-0005)+1 种基金Hunan Provincial Innovation Platform and Talent Program(2018SK4004)Hunan Provincial Natural Science Foundation(2019JJ80048).
文摘The occurrence of severe thalassemia,an inherited blood disorder that is either blood-transfusiondependent or fatal,can be mitigated through carrier screening.Here,we aim to evaluate the effectiveness and outcomes of pre-conceptional and early pregnancy screening initiatives for severe thalassemia prevention in a diverse population of 28,043 women.Using next-generation sequencing(NGS),we identify 4,226(15.07%)thalassemia carriers across 29 ethnic groups and categorize them into high-(0.75%),low-(25.86%),and unknown-risk(69.19%)groups based on their spouses'screening results.Post-screening follow-up reveals 59 fetuses with severe thalassemia exclusively in high-risk couples,underscoring the efficacy of risk classification.Among 25,053 live births over 6 months of age,two severe thalassemia infants were born to unknown-risk couples,which was attributed to incomplete screening and late NGS-based testing for a rare variant.Notably,64 rare variants are identified in 287 individuals,highlighting the genetic heterogeneity of thalassemia.We also observe that migrant flow significantly impacts carrier rates,with 93.90%of migrants to Chenzhou originating from high-prevalence regions in southern China.Our study demonstrates that NGS-based screening during pre-conception and early pregnancy is effective for severe thalassemia prevention,emphasizing the need for continuous screening efforts in areas with high and underestimated prevalence.
基金supported by the Excellent Young Scientists Fund(Category B)(32422063)the National Key Research and Development Program of China(2022YFF1003500)the Zhengzhou University Qiushi Postdoctoral Research Funding Program.For open access,the authors have applied for a Creative Commons Attribution(CC BY)license for any Author Accepted Manuscript version arising from this submission.
文摘Anther is a key male reproductive organ that is essential for the plant life cycle,from the sporophyte to the gametophyte generation.To explore the isoform-level transcriptional landscape of developing anthers in maize(Zea mays L.),we analyzed Iso-Seq data from anthers collected at 10 developmental stages,together with strand-specific RNA-seq,CAGE-seq,and PAS-seq data.Of the 152,026 high-confidence full-length isoforms identified,68.8%have not been described;these include 22,365 isoforms that originate from previously unannotated loci and 82,167 novel isoforms that originate from annotated protein-coding genes.Using our newly developed strategy to detect dynamic expression patterns of isoforms,we identify 13,899 differentially variable regions(DVRs);surprisingly,1275 genes contain more than two DVRs,revealing highly efficient utilization of limited genic regions.We identify 7876 long non-coding RNAs(lncRNAs)from 4098 loci,most of which were preferentially expressed during cell differentiation and meiosis.We also detected 371 long-range interactions involving intergenic lncRNAs(lincRNAs);interestingly,243 were lincRNA-gene ones,and the interacting genes were highly expressed in anthers,suggesting that many potential lncRNA regulators of key genes are required for anther development.This study provides valuable resources and fundamental information for studying the essential transcripts of key genes during anther development.
基金supported by the National Natural Science Foundation of China(NSFC)grants(32030020,32288101,32470649,323B2013,32300499,32270665)the National Key Research and Development Program of China(2023YFC2605400)+1 种基金the Shanghai Science and Technology Commission Program(25JS2810100,23JS1410100,QNKJ2024023)the Office of Global Partnerships(Key Projects Development Fund).
文摘Recent advancements in genome sequencing have enabled the estimation of genetic load through deleterious mutation profiling.However,Chinese populations remain underexplored in this context.We analyze whole-exome sequencing data from 5002 individuals,encompassing major Han subgroups―North Han(NHan),South Han(S-Han),and Guangxi Han(G-Han)―as well as 13 ethnic minorities.Notably,G-Han exhibits significant genetic affinity with the Zhuang population.Systematic curation of 2110 ClinVar pathogenic or likely pathogenic variants reveals 93.4%are ultra-rare.Exceptions include GJB2 rs72474224-A(hearing loss),which shows higher frequencies in Zhuang and G-Han,and β-thalassemia-associated HBB variants(rs33986703-A and rs33950507-T),which are elevated in G-Han compared to other Han subgroups.Among 96 autosomal dominant mutation carriers,LDLR variants are predominant(~25%),with comparable frequencies across Han subgroups.Adaptive signatures highlight gene-environment interactions:MTHFR rs1801133-A(UV adaptation)declines southward,while ALDH2 rs671-A(alcohol metabolism)displays the opposite trend.ABCC11 rs17822931-A,associated with cold adaptation,is particularly low frequency in G-Han.Gene-based rare-variant collapsing analyses identify an elevated risk of retinitis pigmentosa in S-Han(PRPF4,TUB).Our findings demonstrate that genetic load in Chinese populations is influenced by demographic history,population structure,and regional adaptation,emphasizing the importance of population-specific frameworks in precision medicine.
文摘Objectives:Tumor recurrence is a major determinant of poor prognosis in hepatocellular carcinoma(HCC),yet its cellular and molecular basis remains incompletely understood.This study aimed to identify recurrenceassociated genes at single-cell resolution and to develop a prognostic model for predicting survival outcomes and immunotherapy responsiveness in HCC.Methods:Single-cell RNA sequencing data from 12 primary and 6 recurrent HCC samples were integrated and analyzed to identify genes characteristic of recurrence.After quality control,principal component analysis,and t-SNE-based clustering were used to identify highly variable genes for cell clustering and annotation.Based on macrophage characteristic genes,a recurrence-related risk score was constructed using a LASSOCox regression model,and a nomogram integrating clinical variables was developed.Prognostic performance was assessed using Kaplan-Meier analysis and time-dependent ROC curves.Immune infiltration profiling was performed to compare immune characteristics between risk groups defined by the prognostic model.Multivariate Cox regression was applied to identify independent prognostic biomarkers,which were subsequently validated by cell function experiments.Results:The risk model effectively stratified patients into high-and low-risk groups with distinct survival outcomes,demonstrating high predictive accuracy for 1-,3-,and 5-year survival.High-risk patients showed altered immune profiles and a reduced predicted response to immunotherapy.GRID2,RNF186,and SLC4A10 were identified as independent prognostic genes,with RNF186 promoting HCC cell proliferation in a SESN2-dependent manner.Conclusion:This prognostic model provides new insights into precision medicine and immunotherapy for HCC,highlighting the potential clinical significance of RNF186 as a therapeutic target.
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 the Key R&D Program of Ningxia Hui Autonomous Region (2023BEG02024)Natural Science Foundation of Ningxia (2025AAC030942)the University-level Research Project of Ningxia Medical University (XM2023019)。
文摘BACKGROUND:Bloodstream infections(BSIs) caused by gram-positive cocci(GPC) and gramnegative bacilli(GNB) are major causes of sepsis.However,their distinct effects on host responses remain poorly characterized at the single-cell level.This study used single-cell transcriptomics to define pathogenspecific monocyte heterogeneity in BSIs to identify the mechanisms underlying clinical differences.METHODS:Single-cell RNA sequencing(sc RNA-seq) was performed on peripheral blood mononuclear cells obtained from healthy volunteers,two patients with GNB-BSI sepsis,and two patients with GPC-BSI sepsis.Differential gene expression,particularly in monocytes,was analyzed.The key findings were validated with clinical characteristics and outcomes of 45 patients with GNBBSI sepsis and 40 patients with GPC-BSI sepsis.The distinguishing performances of identified biomarkers were evaluated via receiver operating characteristic(ROC) curve.RESULTS:In pathogen-specific transcriptomes,54 identified genes were significantly associated with GNB-BSI(upregulated genes enriched in inflammatory pathways and downregulated genes enriched in oxidative phosphorylation).Twenty-one identified genes were associated with GPC-BSI(downregulated genes associated with cell adhesion molecules and upregulated genes involved in PI3K-Akt signaling).Nineteen genes were common to both groups,with distinct pathogen sensitivities.Patients with GNB-BSI presented with significantly greater disease severity,systemic inflammation and lymphopenia than patients with GPC-BSI.Conversely,patients with GPC-BSI had higher S100A12 and globulin levels and platelet counts.The combination of S100A12^(high) and procalcitonin(PCT)^(low) discriminated GPC-BSI from GNB-BSI(area under the curve=0.882,sensitivity 75%,specificity 91%;cutoff value 0.56).CONCLUSION:Sc RNA-seq reveals the heterogeneity of GPC-BSI and GNB-BSI.Compared with GPC-BSI,GNB-BSI causes severe inflammation and metabolic suppression,which are associated with poor outcomes.The S100A12^(high)+PCT^(low) combination may have potential to discriminate among the major causes of BSI.
