In order to save manpower and time costs,and to achieve simultaneous detection of multiple animal-derived components in meat and meat products,this study used multiple nucleotide polymorphism(MNP)marker technology bas...In order to save manpower and time costs,and to achieve simultaneous detection of multiple animal-derived components in meat and meat products,this study used multiple nucleotide polymorphism(MNP)marker technology based on the principle of high-throughput sequencing,and established a multi-locus 10 animalderived components identification method of cattle,goat,sheep,donkey,horse,chicken,duck,goose,pigeon,quail in meat and meat products.The specific loci of each species could be detected and the species could be accurately identified,including 5 loci for cattle and duck,3 loci for sheep,9 loci for chicken and horse,10 loci for goose and pigeon,6 loci for quail and 1 locus for donkey and goat,and an adulteration model was established to simulate commercially available samples.The results showed that the method established in this study had high throughput,good repeatability and accuracy,and was able to identify 10 animalderived components simultaneously with 100%repeatability accuracy.The detection limit was 0.1%(m/m)in simulated samples of chicken,duck and horse.Using the method established in this study to test commercially available samples,4 samples from 14 commercially available samples were detected to be inconsistent with the labels,of which 2 did not contain the target ingredient and 2 were adulterated with small amounts of other ingredients.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
In recent years,intensive human activities have increased the intensity of desertification,driving continual desertification process of peripheral meadows.To investigate the effects of restoration on soil microbial co...In recent years,intensive human activities have increased the intensity of desertification,driving continual desertification process of peripheral meadows.To investigate the effects of restoration on soil microbial communities,we analyzed vegetation-soil relationships in the Hulun Buir Sandy Land,northern China.Through the use of high-throughput sequencing,we examined the structure and diversity in the bacterial and fungal communities within the 0-20 cm soil layer after 9-15 a of restoration.Different slope positions were analyzed and spatial heterogeneity was assessed.The results showed progressive improvements in soil properties and vegetation with the increase of restoration duration,and the following order was as follows:bottom slope>middle slope>crest slope.During the restoration in the Hulun Buir Sandy Land,the bacterial communities were dominated by Proteobacteria,Actinobacteria,and Acidobacteria,whereas the fungal communities were dominated by Ascomycota and Basidiomycota.Eutrophic bacterial abundance increased with the restoration duration,whereas oligotrophic bacterial and fungal abundance levels decreased.The soil bacterial abundance significantly increased with the increasing restoration duration,whereas the fungal diversity decreased after 11 a of restoration,except that at the crest slope.Redundancy analysis showed that pH,soil moisture content,total nitrogen,and vegetation-related factors affected the bacterial community structure(45.43%of the total variance explained).Canonical correspondence analysis indicated that pH,total phosphorus,and vegetation-related factors shaped the bacterial community structure(31.82%of the total variance explained).Structural equation modeling highlighted greater bacterial responses(R^(2)=0.49-0.79)to changes in environmental factors than those of fungi(R^(2)=0.20-0.48).The soil bacterial community was driven mainly by pH,soil moisture content,electrical conductivity,plant coverage,and litter dry weight.The abundance and diversity of the soil fungal community were mainly driven by plant coverage,litter dry weight,and herbaceous aboveground biomass,while there was no significant correlation between the soil fungal community structure and environmental factors.These findings highlighted divergent microbial succession patterns and environmental sensitivities during sandy grassland restoration.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
In this review,the advantages and advances in applying high-throughput sequencing(HTS)in the management of viral diseases in citrus,along with some challenges,are discussed to provide perspectives on future prospects....In this review,the advantages and advances in applying high-throughput sequencing(HTS)in the management of viral diseases in citrus,along with some challenges,are discussed to provide perspectives on future prospects.Since the initial implementation of HTS in citrus virology,a substantial number of citrus viruses have been identified,with a notable increase in the last 7 years.The acquisition of viral genomes and various HTS-based omics analyses serve as crucial pillars for advancing research in the etiology,epidemiology,pathology,evolution,ecology,and biotechnology of citrus viruses.HTS has notably contributed to disease diagnosis,such as the diagnoses of concave gum and impietratura,as well as to the surveillance of new virus risks and the preparation of virus-free materials.However,certain inherent defects in HTS and coupled bioinformatics analysis,such as challenges with sequence assembly and the detection of viral dark matter,require improvement to enhance practical efficiency.In addition,the utilization of HTS for the systematic management of citrus viral diseases remains limited,and drawing insights from other virus-plant pathosystems while integrating emerging compatible techniques and ideas may broaden its specific applications.展开更多
Chinese traditional fermented foods have a very long history dating back thousands of years and have become an indispensable part of Chinese dietary culture. A plethora of research has been conducted to unravel the co...Chinese traditional fermented foods have a very long history dating back thousands of years and have become an indispensable part of Chinese dietary culture. A plethora of research has been conducted to unravel the composition and dynamics of microbial consortia associated with Chinese traditional fermented foods using culture- dependent as well as culture-independent methods, like different high-throughput sequencing （HTS） techniques. These HTS techniques enable us to understand the relationship between a food product and its microbes to a greater extent than ever before. Considering the importance of Chinese traditional fermented products, the objective of this paper is to review the diversity and dynamics of microbiota in Chinese traditional fermented foods revealed by HTS approaches.展开更多
This study was conducted to investigate the phylogenetic diversity of archaea in the rumen of adult and elderly yaks. Six domesticated female yaks, 3 adult yaks （（5.3±0.6） years old）, and 3 elderly yaks （（1...This study was conducted to investigate the phylogenetic diversity of archaea in the rumen of adult and elderly yaks. Six domesticated female yaks, 3 adult yaks （（5.3±0.6） years old）, and 3 elderly yaks （（10.7±0.6） years old）, were used for the rumen contents collection. Illumina MiSeq high-throughput sequencing technology was applied to examine the archaeal composition of rumen contents. A total of 92 901 high-quality archaeal sequences were analyzed, and these were assigned to 2 033 operational taxonomic units （OTUs）. Among these, 974 OTUs were unique to adult yaks while 846 OTUs were unique to elderly yaks; 213 OTUs were shared by both groups. At the phylum level, more than 99% of the obtained OTUs belonged to the Euryarchaeota phylum. At the genus level, the archaea could be divided into 7 archaeal genera. The 7 genera （i.e., Methanobrevibacter, Methanobacterium, Methanosphaera, Thermogymnomonas, Methanomicrobiu, Meth- animicrococcus and the unclassified genus） were shared by all yaks, and their total abundance accounted for 99% of the rumen archaea. The most abundant archaea in elderly and adult yaks were Methanobrevibacterand Thermogymnomonas, respectively. The abundance of Methanobacteria （class）, Methanobacteriales （order）, Methanobacteriaceae （family）, and Methanobrevibacter （genus） in elderly yaks was significantly higher than in adult yaks. In contrast, the abundance of Ther-mogymnomonas in elderly yaks was 34% lower than in adult yaks, though the difference was not statistically significant. The difference in abundance of other archaea was not significant between the two groups. These results suggested that the structure of archaea in the rumen of yaks changed with age. This is the first study to compare the phytogenetic differences of rumen archaeal structure and composition using the yak model.展开更多
Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and h...Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and high-throughput data. Currently, high-throughput sequencing technology has been widely applied in multi-level researches on genomics, transcriptomics and epigenomics. And it has fundamentally changed the way we approach problems in basic and translational researches and created many new possibilities. This paper presented a general description of high-throughput sequencing technology and a comprehensive review of its application with plain, concisely and precisely. In order to help researchers finish their work faster and better, promote science amateurs and understand it easier and better.展开更多
This study aimed to investigate the eff ect of LyPB on the intestinal microfl ora of giant pandas with indigestion,using high-throughput sequencing(HTS)technology.The species distribution and microfl oral density and ...This study aimed to investigate the eff ect of LyPB on the intestinal microfl ora of giant pandas with indigestion,using high-throughput sequencing(HTS)technology.The species distribution and microfl oral density and diversity before and after administration of the LyPB probiotic agent were analyzed.LyPB evidently has the ability to adjust the fl oral imbalance in the panda’s intestine.To test the eff ects of LyPB on the microfl ora of the panda gut,fecal samples were taken from a healthy giant panda(Anan)without administration of LyPB and from a dyspeptic giant panda Yangyang before and after LyPB administration.Compared with the sample obtained from healthy Anan(anan-c)and that obtained from dyspeptic Yangyang before LyPB administration(yangyang1),the sample taken from Yangyang(yangyang2)after LyPB administration displayed a signifi cant increase in the operational taxonomic unit index.An increase in the Chao index indicated an increase in the microfl oral richness,while an increase in the Shannon index indicated an increase in microfl oral diversity.At phylum and genus levels,a signifi cant increase was observed in the density of probiotic bacteria of phylum fi rmicutes,genus Streptococcus,while a drastic reduction in the density of Escherichia coli/Escherichia coli Shigella/bacteria of genus Shigella was observed.Data obtained in this study shows that LyPB preparations successfully improve the microbial structure within the panda’s intestinal canal by signifi cantly increasing the eff ective microbial community and decreasing the number of pathogenic microbes.展开更多
Bacterial community presumably plays an essential role in inhibiting pathogen colonization and maintaining the health of scallop larvae, but limiting data are available for Yesso scallop （Patinopecten yessoensisis Ja...Bacterial community presumably plays an essential role in inhibiting pathogen colonization and maintaining the health of scallop larvae, but limiting data are available for Yesso scallop （Patinopecten yessoensisis Jay, 1857） larval development stages. The aim of this study was to characterize and compare the bacterial communities associating with Yesso scallop larval development at fertilized egg S l, trochophora S2, D-shaped larvae S3, umbo larvae S4, and juvenile scallop S5 stages by Illumina high-throughput sequencing. Genomic DNA was extracted from the larvae and their associating baetera, and a gene segment covering V3-V4 region of 16S rRNA gene was amplified and sequenced using an Illumina Miseq sequencer. Overall, 106760 qualified sequences with an average length of 449 bp were obtained. Sequences were compared with those retrieved from 16S rRNA gene databases, and 4 phyla, 7 classes, 15 orders, 21 families, 31 genera were identified. Proteobacteria was predominant phylum, accounting for more than 99%, at all 5 larval development stages. At genus level, Pseudomonas was dominant at stages S1 （80.60%）, S2 （87.77%） and S5 （68.71%）, followed by Photobacterium （17.06%） and Aeromonas （1.64%） at stage S1, Serratia （6.94%）, Stenotrophomonas （3.08%） and Acinetobacter （1.2%） at stage S2, Shewanella （25.95%） and Pseudoalteromonas （4.57%） at stage S5. Moreover, genus Pseudoal- teromonas became dominant at stages S3 （44.85%） and S4 （56.02%）, followed by Photobacterium （29.82%）, Pseudomonas （11.86%）, Aliivibrio （8.60%） and Shewanella （3.39%） at stage S3, Pseudomonas （18.16%）, Aliivibrio （14.29%）, Shewanella （4.11%）, Psychro- monas （4.04%） and Psychrobacter （1.81%） at stage S4. From the results, we concluded that the bacterial community changed sig- nificantly at different development stages of Yesso Scallop larvae.展开更多
Torque teno virus(TTV) has been found to be prevalent world-wide in healthy populations and in patients with various diseases, but its etiological role has not yet been determined. Using high-throughput unbiased seque...Torque teno virus(TTV) has been found to be prevalent world-wide in healthy populations and in patients with various diseases, but its etiological role has not yet been determined. Using high-throughput unbiased sequencing to screen for viruses in the serum of a patient with persistent high fever who died of suspected viral infection and prolonged weakness, we identified the complete genome sequence of a TTV(isolate Hebei-1). The genome of TTV-Hebei-1 is 3649 bp in length, encoding four putative open reading frames, and it has a G+C content of 49%. Genomic comparison and a BLASTN search revealed that the assembled genome of TTV-Hebei-1 represented a novel isolate, with a genome sequence that was highly heterologous to the sequences of other reported TTV strains. A phylogenetic tree constructed using the complete genome sequence showed that TTV-Hebei-1 and an uncharacterized Taiwan Residents strain, TW53A37, constitute a new TTV genotype. The patient was strongly suspected of carrying a viral infection and died eventually without any other possible causes being apparent. No virus other than the novel TTV was identified in his serum sample. Although a direct causal link between the novel TTV genotype infection and the patient's disease could not be confirmed, the findings suggest that surveillance of this novel TTV genotype is necessary and that its role in disease deserves to be explored.展开更多
Differentially expressed genes are thought to regulate the development and progression of oral squamous cell carcinomas （OSCC）. The purpose of this study was to screen differentially expressed mRNAs in OSCC and matc...Differentially expressed genes are thought to regulate the development and progression of oral squamous cell carcinomas （OSCC）. The purpose of this study was to screen differentially expressed mRNAs in OSCC and matched paraneoplastic normal tissues, and to explore the intrinsic mechanism of OSCC development and progres- sion. We obtained the differentially expressed mRNA expression profiles in 10 pairs of fresh-frozen OSCC tissue specimens and matched paraneoplastic normal tissue specimens by high-throughput RNA sequencing. By using Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment analyses, the functional significance of the differentially expressed genes were analyzed. We identified 1,120 sig- nificantly up-regulated mRNAs and 178 significantly down-regulated mRNAs in OSCC, compared to normal tissue. The differentially expressed mRNAs were involved in 20 biological processes and 68 signal pathways. Compared to adjacent normal tissue, the expression of MAGEAll was up-regulated; TCHH was down-regulated. These find- ings were verified by real-time PCR. These differentially expressed mRNAs may function as oncogenes or tumor suppressors in the development and progression of OSCC. This study provides novel insights into OSCC. However, further work is needed to determine if these differentially expressed mRNAs have potential roles as diagnostic bio- markers and candidate therapeutic targets for OSCC.展开更多
OBJECTIVE:To explore the mechanism of Xianglian Huazhuo formula(香连化浊方,XLHZ)blocking the development of chronic atrophic gastritis(CAG)to gastric cancer(GC)through bioinformatics analysis and in vitro.METHODS:Path...OBJECTIVE:To explore the mechanism of Xianglian Huazhuo formula(香连化浊方,XLHZ)blocking the development of chronic atrophic gastritis(CAG)to gastric cancer(GC)through bioinformatics analysis and in vitro.METHODS:Pathological morphology of gastric mucosa of rats were observed.High-throughput sequencing was used to analyze the miRNA expression profile of gastric mucosa.The miRanda,miRDB and miRWalk databases were used to predict the differential target genes.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis were performed for differential target genes.Real-time quantitative reverse transcription polymerase chain reaction(qRTPCR)was used to verify the differentially expressed miRNAs and target genes.Western blot,EdU,wound healing and flow cytometry were used to observe the effect of XLHZ on epithelial-mesenchymal transition(EMT)markers,proliferation,migration,apoptosis and cell cycle of CAG cells in vitro.RESULTS:A total of five differentially expressed miRNAs and four differential target genes were screened in this study.GO analysis showed that the target genes were enriched in regulation of neuron development,regulation of transcription factor activity and regulation of RNA polymerase.KEGG pathways database differences in gene enrichment of target genes in the Wnt signaling pathway,Phospholipase D signaling pathway and mitogen-activated protein kinase signaling pathway.qRTPCR confirmed that miRNAs and its target genes were consistent with the screening results.In vitro,our study revealed that XLHZ could increase the expression of Ecadherin,decrease the expression of transforming growth factorβ1,vimentin andβ-catenin,inhibite the proliferation and migration of CAG cells,cause cell cycle arrest at G0/G1 and G2/M phase,induce the apoptosis of CAG cells,and prevent the progression of CAG to GC.CONCLUSION:This study provided a new idea for the mechanism of blocking the progression of CAG to GC by XLHZ,which may be related to the expression of miR-20a-3p,miR-320-3p,miR-34b-5p,miR-483-3p and miR-883-3p and their target genes transferrin receptor,nuclear receptor subfamily 4 member 2,delta like canonical Notch ligand 1 and a kinase anchor protein 12 in CAG.In the future,we will continue to investigate the linkage between the active ingredients of XLHZ and the relevant miRNAs and their target genes,so as to provide more sufficient experimental basis for clinically effective prevention of CAG to GC.展开更多
Background: RNA editing is a co/posttranscriptional modification mechanism that increases the diversity of transcripts, with potential functional consequences. The advent of next-generation sequencing technologies has...Background: RNA editing is a co/posttranscriptional modification mechanism that increases the diversity of transcripts, with potential functional consequences. The advent of next-generation sequencing technologies has enabled the identification of RNA edits at unprecedented throughput and resolution. However, our knowledge of RNA editing in swine is still limited.Results: Here, we utilized RES-Scanner to identify RNA editing sites in the brain, subcutaneous fat, heart, liver,muscle, lung and ovary in three 180-day-old Large White gilts based on matched strand-specific RNA sequencing and whole-genome resequencing datasets. In total, we identified 74863 editing sites, and 92.1% of these sites caused adenosine-to-guanosine(A-to-G) conversion. Most A-to-G sites were located in noncoding regions and generally had low editing levels. In total, 151 A-to-G sites were detected in coding regions(CDS), including 94 sites that could lead to nonsynonymous amino acid changes. We provide further evidence supporting a previous observation that pig transcriptomes are highly editable at PRE-1 elements. The number of A-to-G editing sites ranged from 4155(muscle) to 25001(brain) across the seven tissues. The expression levels of the ADAR enzymes could explain some but not all of this variation across tissues. The functional analysis of the genes with tissuespecific editing sites in each tissue revealed that RNA editing might play important roles in tissue function.Specifically, more pathways showed significant enrichment in the fat and liver than in other tissues, while no pathway was enriched in the muscle.Conclusions: This study identified a total of 74863 nonredundant RNA editing sites in seven tissues and revealed the potential importance of RNA editing in tissue function. Our findings largely extend the porcine editome and enhance our understanding of RNA editing in swine.展开更多
Huguangyan Maar Lake is a typical maar lake in the southeast of China. It is well preserved and not disturbed by anthropogenic activities. In this study, microbial community structures in sediment and water samples fr...Huguangyan Maar Lake is a typical maar lake in the southeast of China. It is well preserved and not disturbed by anthropogenic activities. In this study, microbial community structures in sediment and water samples from Huguangyan Maar Lake were investigated using a high-throughput sequencing method. We found significant differences between the microbial community compositions of the water and the sediment. The sediment samples contained more diverse Bacteria and Archaea than did the water samples. Actinobacteria, Betaproteobacteria, Cyanobacteria, and Deltaproteobacteria predominated in the water samples while Deltaproteobacteria, Anaerolineae, Nitrospira, and Dehalococcoidia were the major bacterial groups in the sediment. As for Archaea, Woesearchaeota (DHVEG-6), unclassified Archaea, and Deep Sea Euryarchaeotic Group were detected at higher abundances in the water, whereas the Miscellaneous Crenarchaeotic Group, Thermoplasmata, and Methanomicrobia were significantly more abundant in the sediment. Interactions between Bacteria and Archaea were common in both the water column and the sediment. The concentrations of major nutrients (NO^3-, PO4^3-, SiO3^2- and NH4^+) shaped the microbial population structures in the water. At the higher phylogenetic levels including phylum and class, many of the dominant groups were those that were also abundant in other lakes;however, novel microbial populations (unclassified) were often seen at the lower phylogenetic levels. Our study lays a foundation for examining microbial biogeochemical cycling in sequestered lakes or reservoirs.展开更多
Delivery of safe and pathogen-free drinking water is crucial to public health.However,there exist challenges to the maintenance of the sterility of drinking water throughout the drinking water distribution systems（D...Delivery of safe and pathogen-free drinking water is crucial to public health.However,there exist challenges to the maintenance of the sterility of drinking water throughout the drinking water distribution systems（DWDS）.Microbial growth in DWDS,such as growth of opportunistic pathogenic microorganisms,can lead to severe health problems in consumers（Berry et al.,2006;Brettar and Hofle,2006;Lu et al.,2014;Zhang et al.,2015）.展开更多
Objective Viral encephalitis is an infectious disease severely affecting human health.It is caused by a wide variety of viral pathogens,including herpes viruses,flaviviruses,enteroviruses,and other viruses.The laborat...Objective Viral encephalitis is an infectious disease severely affecting human health.It is caused by a wide variety of viral pathogens,including herpes viruses,flaviviruses,enteroviruses,and other viruses.The laboratory diagnosis of viral encephalitis is a worldwide challenge.Recently,high-throughput sequencing technology has provided new tools for diagnosing central nervous system infections.Thus,In this study,we established a multipathogen detection platform for viral encephalitis based on amplicon sequencing.Methods We designed nine pairs of specific polymerase chain reaction(PCR)primers for the 12 viruses by reviewing the relevant literature.The detection ability of the primers was verified by software simulation and the detection of known positive samples.Amplicon sequencing was used to validate the samples,and consistency was compared with Sanger sequencing.Results The results showed that the target sequences of various pathogens were obtained at a coverage depth level greater than 20×,and the sequence lengths were consistent with the sizes of the predicted amplicons.The sequences were verified using the National Center for Biotechnology Information BLAST,and all results were consistent with the results of Sanger sequencing.Conclusion Amplicon-based high-throughput sequencing technology is feasible as a supplementary method for the pathogenic detection of viral encephalitis.It is also a useful tool for the high-volume screening of clinical samples.展开更多
Acanthogobius ommaturus,a fish species of the Family Gobiidae,is a marine commercial fish perched on the bottom of seawater.In this study,Illumina high-throughput sequencing technology was applied to obtain the candid...Acanthogobius ommaturus,a fish species of the Family Gobiidae,is a marine commercial fish perched on the bottom of seawater.In this study,Illumina high-throughput sequencing technology was applied to obtain the candidate microsatellite markers of A.ommaturus.A total of 4746 microsatellite-rich fragments were found,of which 4542 microsatellites are with primer fragments,containing 971 dinucleotide sequences,2643 trinucleotide sequences,569 tetranucleotide sequences,406 pentanucleotide sequences,and 212 hexanucleotide sequences.Based on the results of high-throughput sequencing,a total of 141 pairs of the microsatellite primers were designed and screened.And then 24 polymorphic primers were finally obtained by polyacrylamide gel electrophoresis.In total,271 alleles were detected in the 24 pairs of primers.The number of alleles for different primers ranged from 5 to 19.The average number of effective alleles(Na)was 11.292;the average observed heterozygosity(Ho)of the 24 pairs of primers was 0.665,the average expected heterozygosity(He)was 0.880,and the average polymorphic information content was 0.846.All sites were highly polymorphic(PIC>0.50).展开更多
Upland cotton （Gossypium hirsutum L.） is an allotetraploid species originated from interspecific hybridization between AA-genome diploid （G. arboretum） and DD-genome diploid （G. raimondii） （Wendel et al., 1992...Upland cotton （Gossypium hirsutum L.） is an allotetraploid species originated from interspecific hybridization between AA-genome diploid （G. arboretum） and DD-genome diploid （G. raimondii） （Wendel et al., 1992）. Cotton fibers are single-celled trichomes that emerge from the ovule epidermal cells. Indexed by the number of days post-anthesis （dpa）, fiber morphogenesis includes four distinct but overlapping steps： initiation （0-3 dpa）, elongation （3-20 dpa）, secondary cell wall thickening （15-45 dpa） and maturation （40-60 dpa） （Yang et al., 2008, Du et al., 2013）. The efficiency and duration of each morphogenesis stage is important to the quality attributes of the mature fiber. Cell elongation is critical for fiber length, whereas secondary cell wall thickening is important for fiber fineness and strength （Meinert and Delmer, 1977）.展开更多
基金financially supported by National Key R&D Program(2021YFF0701905)。
文摘In order to save manpower and time costs,and to achieve simultaneous detection of multiple animal-derived components in meat and meat products,this study used multiple nucleotide polymorphism(MNP)marker technology based on the principle of high-throughput sequencing,and established a multi-locus 10 animalderived components identification method of cattle,goat,sheep,donkey,horse,chicken,duck,goose,pigeon,quail in meat and meat products.The specific loci of each species could be detected and the species could be accurately identified,including 5 loci for cattle and duck,3 loci for sheep,9 loci for chicken and horse,10 loci for goose and pigeon,6 loci for quail and 1 locus for donkey and goat,and an adulteration model was established to simulate commercially available samples.The results showed that the method established in this study had high throughput,good repeatability and accuracy,and was able to identify 10 animalderived components simultaneously with 100%repeatability accuracy.The detection limit was 0.1%(m/m)in simulated samples of chicken,duck and horse.Using the method established in this study to test commercially available samples,4 samples from 14 commercially available samples were detected to be inconsistent with the labels,of which 2 did not contain the target ingredient and 2 were adulterated with small amounts of other ingredients.
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 Ecological Environment Survey and Assessment(2024-vertical-0107)the Fundamental Research Funds for the Central Public-interest Scientific Institution(2023YSKY-26)the Hulun Buir Grassland Ecological Restoration Comprehensive Survey Project(DD20230474).
文摘In recent years,intensive human activities have increased the intensity of desertification,driving continual desertification process of peripheral meadows.To investigate the effects of restoration on soil microbial communities,we analyzed vegetation-soil relationships in the Hulun Buir Sandy Land,northern China.Through the use of high-throughput sequencing,we examined the structure and diversity in the bacterial and fungal communities within the 0-20 cm soil layer after 9-15 a of restoration.Different slope positions were analyzed and spatial heterogeneity was assessed.The results showed progressive improvements in soil properties and vegetation with the increase of restoration duration,and the following order was as follows:bottom slope>middle slope>crest slope.During the restoration in the Hulun Buir Sandy Land,the bacterial communities were dominated by Proteobacteria,Actinobacteria,and Acidobacteria,whereas the fungal communities were dominated by Ascomycota and Basidiomycota.Eutrophic bacterial abundance increased with the restoration duration,whereas oligotrophic bacterial and fungal abundance levels decreased.The soil bacterial abundance significantly increased with the increasing restoration duration,whereas the fungal diversity decreased after 11 a of restoration,except that at the crest slope.Redundancy analysis showed that pH,soil moisture content,total nitrogen,and vegetation-related factors affected the bacterial community structure(45.43%of the total variance explained).Canonical correspondence analysis indicated that pH,total phosphorus,and vegetation-related factors shaped the bacterial community structure(31.82%of the total variance explained).Structural equation modeling highlighted greater bacterial responses(R^(2)=0.49-0.79)to changes in environmental factors than those of fungi(R^(2)=0.20-0.48).The soil bacterial community was driven mainly by pH,soil moisture content,electrical conductivity,plant coverage,and litter dry weight.The abundance and diversity of the soil fungal community were mainly driven by plant coverage,litter dry weight,and herbaceous aboveground biomass,while there was no significant correlation between the soil fungal community structure and environmental factors.These findings highlighted divergent microbial succession patterns and environmental sensitivities during sandy grassland restoration.
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 National Natural Science Foundation of China(Grant Nos.32370005,32072389)Chongqing Science Funds for Distinguished Young Scientists(Grant No.CSTB2022NSCQ-JQX0027)+3 种基金Innovation Research 2035 Pilot Plan of Southwest University(Grant Nos.SWU-XDPY22002,SWUXDZD22002)Special Fund for Youth Team of Southwest University(Grant No.SWU-XJLJ202310)Chongqing Talents of Exceptional Young Talents Project(Grant No.cstc2022ycjh-bgzxm0143)Chongqing Municipal Training Program of Innovation and Entrepreneurship for Undergraduates(Grant No.S202310635160)。
文摘In this review,the advantages and advances in applying high-throughput sequencing(HTS)in the management of viral diseases in citrus,along with some challenges,are discussed to provide perspectives on future prospects.Since the initial implementation of HTS in citrus virology,a substantial number of citrus viruses have been identified,with a notable increase in the last 7 years.The acquisition of viral genomes and various HTS-based omics analyses serve as crucial pillars for advancing research in the etiology,epidemiology,pathology,evolution,ecology,and biotechnology of citrus viruses.HTS has notably contributed to disease diagnosis,such as the diagnoses of concave gum and impietratura,as well as to the surveillance of new virus risks and the preparation of virus-free materials.However,certain inherent defects in HTS and coupled bioinformatics analysis,such as challenges with sequence assembly and the detection of viral dark matter,require improvement to enhance practical efficiency.In addition,the utilization of HTS for the systematic management of citrus viral diseases remains limited,and drawing insights from other virus-plant pathosystems while integrating emerging compatible techniques and ideas may broaden its specific applications.
基金supported by the National Natural Science Foundation of China(Nos.31371826 and 31571808)the China Postdoctoral Science Foundation Funded Project(No.2016M592002)
文摘Chinese traditional fermented foods have a very long history dating back thousands of years and have become an indispensable part of Chinese dietary culture. A plethora of research has been conducted to unravel the composition and dynamics of microbial consortia associated with Chinese traditional fermented foods using culture- dependent as well as culture-independent methods, like different high-throughput sequencing （HTS） techniques. These HTS techniques enable us to understand the relationship between a food product and its microbes to a greater extent than ever before. Considering the importance of Chinese traditional fermented products, the objective of this paper is to review the diversity and dynamics of microbiota in Chinese traditional fermented foods revealed by HTS approaches.
基金the International Cooperation Project of the Ministry of Sciences and Technology of China(2014DFA32860)the National Natural Science Foundation of China(31402104)for their financial support
文摘This study was conducted to investigate the phylogenetic diversity of archaea in the rumen of adult and elderly yaks. Six domesticated female yaks, 3 adult yaks （（5.3±0.6） years old）, and 3 elderly yaks （（10.7±0.6） years old）, were used for the rumen contents collection. Illumina MiSeq high-throughput sequencing technology was applied to examine the archaeal composition of rumen contents. A total of 92 901 high-quality archaeal sequences were analyzed, and these were assigned to 2 033 operational taxonomic units （OTUs）. Among these, 974 OTUs were unique to adult yaks while 846 OTUs were unique to elderly yaks; 213 OTUs were shared by both groups. At the phylum level, more than 99% of the obtained OTUs belonged to the Euryarchaeota phylum. At the genus level, the archaea could be divided into 7 archaeal genera. The 7 genera （i.e., Methanobrevibacter, Methanobacterium, Methanosphaera, Thermogymnomonas, Methanomicrobiu, Meth- animicrococcus and the unclassified genus） were shared by all yaks, and their total abundance accounted for 99% of the rumen archaea. The most abundant archaea in elderly and adult yaks were Methanobrevibacterand Thermogymnomonas, respectively. The abundance of Methanobacteria （class）, Methanobacteriales （order）, Methanobacteriaceae （family）, and Methanobrevibacter （genus） in elderly yaks was significantly higher than in adult yaks. In contrast, the abundance of Ther-mogymnomonas in elderly yaks was 34% lower than in adult yaks, though the difference was not statistically significant. The difference in abundance of other archaea was not significant between the two groups. These results suggested that the structure of archaea in the rumen of yaks changed with age. This is the first study to compare the phytogenetic differences of rumen archaeal structure and composition using the yak model.
基金Supported by the National Natural Science Foundations of China(3127218631301791)
文摘Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and high-throughput data. Currently, high-throughput sequencing technology has been widely applied in multi-level researches on genomics, transcriptomics and epigenomics. And it has fundamentally changed the way we approach problems in basic and translational researches and created many new possibilities. This paper presented a general description of high-throughput sequencing technology and a comprehensive review of its application with plain, concisely and precisely. In order to help researchers finish their work faster and better, promote science amateurs and understand it easier and better.
文摘This study aimed to investigate the eff ect of LyPB on the intestinal microfl ora of giant pandas with indigestion,using high-throughput sequencing(HTS)technology.The species distribution and microfl oral density and diversity before and after administration of the LyPB probiotic agent were analyzed.LyPB evidently has the ability to adjust the fl oral imbalance in the panda’s intestine.To test the eff ects of LyPB on the microfl ora of the panda gut,fecal samples were taken from a healthy giant panda(Anan)without administration of LyPB and from a dyspeptic giant panda Yangyang before and after LyPB administration.Compared with the sample obtained from healthy Anan(anan-c)and that obtained from dyspeptic Yangyang before LyPB administration(yangyang1),the sample taken from Yangyang(yangyang2)after LyPB administration displayed a signifi cant increase in the operational taxonomic unit index.An increase in the Chao index indicated an increase in the microfl oral richness,while an increase in the Shannon index indicated an increase in microfl oral diversity.At phylum and genus levels,a signifi cant increase was observed in the density of probiotic bacteria of phylum fi rmicutes,genus Streptococcus,while a drastic reduction in the density of Escherichia coli/Escherichia coli Shigella/bacteria of genus Shigella was observed.Data obtained in this study shows that LyPB preparations successfully improve the microbial structure within the panda’s intestinal canal by signifi cantly increasing the eff ective microbial community and decreasing the number of pathogenic microbes.
基金financial support from Zhang Zidao Sland Group Co.,Ltd. for the project (99801214)
文摘Bacterial community presumably plays an essential role in inhibiting pathogen colonization and maintaining the health of scallop larvae, but limiting data are available for Yesso scallop （Patinopecten yessoensisis Jay, 1857） larval development stages. The aim of this study was to characterize and compare the bacterial communities associating with Yesso scallop larval development at fertilized egg S l, trochophora S2, D-shaped larvae S3, umbo larvae S4, and juvenile scallop S5 stages by Illumina high-throughput sequencing. Genomic DNA was extracted from the larvae and their associating baetera, and a gene segment covering V3-V4 region of 16S rRNA gene was amplified and sequenced using an Illumina Miseq sequencer. Overall, 106760 qualified sequences with an average length of 449 bp were obtained. Sequences were compared with those retrieved from 16S rRNA gene databases, and 4 phyla, 7 classes, 15 orders, 21 families, 31 genera were identified. Proteobacteria was predominant phylum, accounting for more than 99%, at all 5 larval development stages. At genus level, Pseudomonas was dominant at stages S1 （80.60%）, S2 （87.77%） and S5 （68.71%）, followed by Photobacterium （17.06%） and Aeromonas （1.64%） at stage S1, Serratia （6.94%）, Stenotrophomonas （3.08%） and Acinetobacter （1.2%） at stage S2, Shewanella （25.95%） and Pseudoalteromonas （4.57%） at stage S5. Moreover, genus Pseudoal- teromonas became dominant at stages S3 （44.85%） and S4 （56.02%）, followed by Photobacterium （29.82%）, Pseudomonas （11.86%）, Aliivibrio （8.60%） and Shewanella （3.39%） at stage S3, Pseudomonas （18.16%）, Aliivibrio （14.29%）, Shewanella （4.11%）, Psychro- monas （4.04%） and Psychrobacter （1.81%） at stage S4. From the results, we concluded that the bacterial community changed sig- nificantly at different development stages of Yesso Scallop larvae.
基金supported by a grant from the National Natural Science Foundation of China (No. 81072350)the National Hi-Tech Research and Development (863) Program of China (No. 2012AA022-003)+2 种基金the China Mega-Project on Major Drug Development (No. 2011ZX09401-023)the China Mega-Project on Infectious Disease Prevention (No. 2013ZX10004-605, No. 2013ZX10004-607, No. 2013ZX10004-217, and No. 2011ZX10004-001) the State Key Laboratory of Pathogen and BioSecurity Program (No. SKLPBS1113)
文摘Torque teno virus(TTV) has been found to be prevalent world-wide in healthy populations and in patients with various diseases, but its etiological role has not yet been determined. Using high-throughput unbiased sequencing to screen for viruses in the serum of a patient with persistent high fever who died of suspected viral infection and prolonged weakness, we identified the complete genome sequence of a TTV(isolate Hebei-1). The genome of TTV-Hebei-1 is 3649 bp in length, encoding four putative open reading frames, and it has a G+C content of 49%. Genomic comparison and a BLASTN search revealed that the assembled genome of TTV-Hebei-1 represented a novel isolate, with a genome sequence that was highly heterologous to the sequences of other reported TTV strains. A phylogenetic tree constructed using the complete genome sequence showed that TTV-Hebei-1 and an uncharacterized Taiwan Residents strain, TW53A37, constitute a new TTV genotype. The patient was strongly suspected of carrying a viral infection and died eventually without any other possible causes being apparent. No virus other than the novel TTV was identified in his serum sample. Although a direct causal link between the novel TTV genotype infection and the patient's disease could not be confirmed, the findings suggest that surveillance of this novel TTV genotype is necessary and that its role in disease deserves to be explored.
基金supported by a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD,2014-37)
文摘Differentially expressed genes are thought to regulate the development and progression of oral squamous cell carcinomas （OSCC）. The purpose of this study was to screen differentially expressed mRNAs in OSCC and matched paraneoplastic normal tissues, and to explore the intrinsic mechanism of OSCC development and progres- sion. We obtained the differentially expressed mRNA expression profiles in 10 pairs of fresh-frozen OSCC tissue specimens and matched paraneoplastic normal tissue specimens by high-throughput RNA sequencing. By using Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment analyses, the functional significance of the differentially expressed genes were analyzed. We identified 1,120 sig- nificantly up-regulated mRNAs and 178 significantly down-regulated mRNAs in OSCC, compared to normal tissue. The differentially expressed mRNAs were involved in 20 biological processes and 68 signal pathways. Compared to adjacent normal tissue, the expression of MAGEAll was up-regulated; TCHH was down-regulated. These find- ings were verified by real-time PCR. These differentially expressed mRNAs may function as oncogenes or tumor suppressors in the development and progression of OSCC. This study provides novel insights into OSCC. However, further work is needed to determine if these differentially expressed mRNAs have potential roles as diagnostic bio- markers and candidate therapeutic targets for OSCC.
基金Construction Project of National Clinical Research Base of Traditional Chinese Medicine(Science Letter[2018]No.131,State Office of Traditional Chinese Medicine)Natural Science Foundation of Hebei Province:Study on the Mechanism of Action of Traditional Chinese Medicine on Disease and Syndrome(No.H2023423001)+6 种基金Key Research Project of the Ministry of Science and Technology(No.2018YFC1704100)Key Research Project of the Ministry of Science and Technology:Li Diangui Famous Old Chinese Medicine of Traditional Chinese Medicine Academic View Characteristic,Diagnosis and Treatment Methods and Experience of Prevention and Control of Major Diseases(No.2018YFC1704102)Provincial Science and Technology Program of Hebei Province:Prevention and Treatment of Gastric Cancer by Blocking the"Inflammation-Cancer Transformation"Based on the Theory of Turbidimetric Toxicity(No.21377724D)Provincial Science and Technology Program of Hebei Province:to Study the Clinical Efficacy and Mechanism of Huazhuo Jiedu Formula in the Treatment of Chronic Atrophic Gastritis based on Epidermal Growth Factor Receptor/Mitogen Activated Protein Kinase/Extracellular Signal-Regulated Kinase Signaling Pathway(No.21377740D)Scientific Research Project of Hebei Administration of Traditional Chinese Medicine:Clinical Study of Huazhuo Jiedu Formula Blocking the Pathological Evolution of Chronic Atrophic Gastritis(No.2022026)Scientific Research Project of Hebei Administration of Traditional Chinese Medicine:Study on the Medication Rules of Spleen and Stomach Diseases of Famous Yanzhao Medical Doctors Based on Data Mining(No.2022032)Scientific Research Project of Hebei Administration of Traditional Chinese Medicine:to Explore the Mechanism of Xianglian Huazhuo Formula in the Treatment of Chronic Atrophic Gastritis based on Transcriptomics(No.2023022)。
文摘OBJECTIVE:To explore the mechanism of Xianglian Huazhuo formula(香连化浊方,XLHZ)blocking the development of chronic atrophic gastritis(CAG)to gastric cancer(GC)through bioinformatics analysis and in vitro.METHODS:Pathological morphology of gastric mucosa of rats were observed.High-throughput sequencing was used to analyze the miRNA expression profile of gastric mucosa.The miRanda,miRDB and miRWalk databases were used to predict the differential target genes.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis were performed for differential target genes.Real-time quantitative reverse transcription polymerase chain reaction(qRTPCR)was used to verify the differentially expressed miRNAs and target genes.Western blot,EdU,wound healing and flow cytometry were used to observe the effect of XLHZ on epithelial-mesenchymal transition(EMT)markers,proliferation,migration,apoptosis and cell cycle of CAG cells in vitro.RESULTS:A total of five differentially expressed miRNAs and four differential target genes were screened in this study.GO analysis showed that the target genes were enriched in regulation of neuron development,regulation of transcription factor activity and regulation of RNA polymerase.KEGG pathways database differences in gene enrichment of target genes in the Wnt signaling pathway,Phospholipase D signaling pathway and mitogen-activated protein kinase signaling pathway.qRTPCR confirmed that miRNAs and its target genes were consistent with the screening results.In vitro,our study revealed that XLHZ could increase the expression of Ecadherin,decrease the expression of transforming growth factorβ1,vimentin andβ-catenin,inhibite the proliferation and migration of CAG cells,cause cell cycle arrest at G0/G1 and G2/M phase,induce the apoptosis of CAG cells,and prevent the progression of CAG to GC.CONCLUSION:This study provided a new idea for the mechanism of blocking the progression of CAG to GC by XLHZ,which may be related to the expression of miR-20a-3p,miR-320-3p,miR-34b-5p,miR-483-3p and miR-883-3p and their target genes transferrin receptor,nuclear receptor subfamily 4 member 2,delta like canonical Notch ligand 1 and a kinase anchor protein 12 in CAG.In the future,we will continue to investigate the linkage between the active ingredients of XLHZ and the relevant miRNAs and their target genes,so as to provide more sufficient experimental basis for clinically effective prevention of CAG to GC.
基金supported by the National Key Technology R&D Program of China(2015BAD03B02–2)Beijing Natural Science Foundation(6174047)+1 种基金earmarked fund for Modern Agro-industry Technology Research System(CARS-35)Agricultural Science and Technology Innovation Program(ASTIP-IAS02)
文摘Background: RNA editing is a co/posttranscriptional modification mechanism that increases the diversity of transcripts, with potential functional consequences. The advent of next-generation sequencing technologies has enabled the identification of RNA edits at unprecedented throughput and resolution. However, our knowledge of RNA editing in swine is still limited.Results: Here, we utilized RES-Scanner to identify RNA editing sites in the brain, subcutaneous fat, heart, liver,muscle, lung and ovary in three 180-day-old Large White gilts based on matched strand-specific RNA sequencing and whole-genome resequencing datasets. In total, we identified 74863 editing sites, and 92.1% of these sites caused adenosine-to-guanosine(A-to-G) conversion. Most A-to-G sites were located in noncoding regions and generally had low editing levels. In total, 151 A-to-G sites were detected in coding regions(CDS), including 94 sites that could lead to nonsynonymous amino acid changes. We provide further evidence supporting a previous observation that pig transcriptomes are highly editable at PRE-1 elements. The number of A-to-G editing sites ranged from 4155(muscle) to 25001(brain) across the seven tissues. The expression levels of the ADAR enzymes could explain some but not all of this variation across tissues. The functional analysis of the genes with tissuespecific editing sites in each tissue revealed that RNA editing might play important roles in tissue function.Specifically, more pathways showed significant enrichment in the fat and liver than in other tissues, while no pathway was enriched in the muscle.Conclusions: This study identified a total of 74863 nonredundant RNA editing sites in seven tissues and revealed the potential importance of RNA editing in tissue function. Our findings largely extend the porcine editome and enhance our understanding of RNA editing in swine.
基金Supported by the National Natural Science Foundation of China(Nos.41576123,41706129)the Guangdong Natural Science Foundation(Nos.2015A030313326,2016A030312004)+2 种基金the International Science and Technology Cooperation Project(No.GASI-IPOVI-04)the Project of Enhancing School with Innovation of Guangdong Ocean University(No.GDOU2016050243)the Program for Scientific Research Start-Up Funds of Guangdong Ocean University(No.E15030)
文摘Huguangyan Maar Lake is a typical maar lake in the southeast of China. It is well preserved and not disturbed by anthropogenic activities. In this study, microbial community structures in sediment and water samples from Huguangyan Maar Lake were investigated using a high-throughput sequencing method. We found significant differences between the microbial community compositions of the water and the sediment. The sediment samples contained more diverse Bacteria and Archaea than did the water samples. Actinobacteria, Betaproteobacteria, Cyanobacteria, and Deltaproteobacteria predominated in the water samples while Deltaproteobacteria, Anaerolineae, Nitrospira, and Dehalococcoidia were the major bacterial groups in the sediment. As for Archaea, Woesearchaeota (DHVEG-6), unclassified Archaea, and Deep Sea Euryarchaeotic Group were detected at higher abundances in the water, whereas the Miscellaneous Crenarchaeotic Group, Thermoplasmata, and Methanomicrobia were significantly more abundant in the sediment. Interactions between Bacteria and Archaea were common in both the water column and the sediment. The concentrations of major nutrients (NO^3-, PO4^3-, SiO3^2- and NH4^+) shaped the microbial population structures in the water. At the higher phylogenetic levels including phylum and class, many of the dominant groups were those that were also abundant in other lakes;however, novel microbial populations (unclassified) were often seen at the lower phylogenetic levels. Our study lays a foundation for examining microbial biogeochemical cycling in sequestered lakes or reservoirs.
文摘Delivery of safe and pathogen-free drinking water is crucial to public health.However,there exist challenges to the maintenance of the sterility of drinking water throughout the drinking water distribution systems（DWDS）.Microbial growth in DWDS,such as growth of opportunistic pathogenic microorganisms,can lead to severe health problems in consumers（Berry et al.,2006;Brettar and Hofle,2006;Lu et al.,2014;Zhang et al.,2015）.
基金supported by the National Key Research and Development Program(grant number:2022YFC2305304).
文摘Objective Viral encephalitis is an infectious disease severely affecting human health.It is caused by a wide variety of viral pathogens,including herpes viruses,flaviviruses,enteroviruses,and other viruses.The laboratory diagnosis of viral encephalitis is a worldwide challenge.Recently,high-throughput sequencing technology has provided new tools for diagnosing central nervous system infections.Thus,In this study,we established a multipathogen detection platform for viral encephalitis based on amplicon sequencing.Methods We designed nine pairs of specific polymerase chain reaction(PCR)primers for the 12 viruses by reviewing the relevant literature.The detection ability of the primers was verified by software simulation and the detection of known positive samples.Amplicon sequencing was used to validate the samples,and consistency was compared with Sanger sequencing.Results The results showed that the target sequences of various pathogens were obtained at a coverage depth level greater than 20×,and the sequence lengths were consistent with the sizes of the predicted amplicons.The sequences were verified using the National Center for Biotechnology Information BLAST,and all results were consistent with the results of Sanger sequencing.Conclusion Amplicon-based high-throughput sequencing technology is feasible as a supplementary method for the pathogenic detection of viral encephalitis.It is also a useful tool for the high-volume screening of clinical samples.
基金Supported by the National Natural Science Foundation of China(Nos.41776171,41506158)the Fund of Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization,Ministry of Agriculture and Rural Affairs,China(No.FREU2018-04)。
文摘Acanthogobius ommaturus,a fish species of the Family Gobiidae,is a marine commercial fish perched on the bottom of seawater.In this study,Illumina high-throughput sequencing technology was applied to obtain the candidate microsatellite markers of A.ommaturus.A total of 4746 microsatellite-rich fragments were found,of which 4542 microsatellites are with primer fragments,containing 971 dinucleotide sequences,2643 trinucleotide sequences,569 tetranucleotide sequences,406 pentanucleotide sequences,and 212 hexanucleotide sequences.Based on the results of high-throughput sequencing,a total of 141 pairs of the microsatellite primers were designed and screened.And then 24 polymorphic primers were finally obtained by polyacrylamide gel electrophoresis.In total,271 alleles were detected in the 24 pairs of primers.The number of alleles for different primers ranged from 5 to 19.The average number of effective alleles(Na)was 11.292;the average observed heterozygosity(Ho)of the 24 pairs of primers was 0.665,the average expected heterozygosity(He)was 0.880,and the average polymorphic information content was 0.846.All sites were highly polymorphic(PIC>0.50).
基金supported by the grants from the State Key Basic Research and Development Plan (No. 2010CB126003)the National Transgenic Animals and Plants Research Project (Nos. 2011ZX08005-003 and 2011ZX08009-003)
文摘Upland cotton （Gossypium hirsutum L.） is an allotetraploid species originated from interspecific hybridization between AA-genome diploid （G. arboretum） and DD-genome diploid （G. raimondii） （Wendel et al., 1992）. Cotton fibers are single-celled trichomes that emerge from the ovule epidermal cells. Indexed by the number of days post-anthesis （dpa）, fiber morphogenesis includes four distinct but overlapping steps： initiation （0-3 dpa）, elongation （3-20 dpa）, secondary cell wall thickening （15-45 dpa） and maturation （40-60 dpa） （Yang et al., 2008, Du et al., 2013）. The efficiency and duration of each morphogenesis stage is important to the quality attributes of the mature fiber. Cell elongation is critical for fiber length, whereas secondary cell wall thickening is important for fiber fineness and strength （Meinert and Delmer, 1977）.
