Genomic data have demonstrated considerable traction in accelerating contemporary studies in traditional medicine. However,the lack of a uniform format and dispersed storage limits the full potential of herb genomic d...Genomic data have demonstrated considerable traction in accelerating contemporary studies in traditional medicine. However,the lack of a uniform format and dispersed storage limits the full potential of herb genomic data. In this study, we developed a Global Pharmacopoeia Genome Database(GPGD). The database contains 34,346 records for 903 herb species from eight global pharmacopoeias(Brazilian, Egyptian, European, Indian, Japanese, Korean, the Pharmacopoeia of the People’s Republic of China, and U.S. Pharmacopoeia’s Herbal Medicines Compendium). In particular, the GPGD contains 21,872 DNA barcodes from 867 species, 2,203 organelle genomes from 674 species, 55 whole genomes from 49 species, 534 genomic sequencing datasets from 366 species, and 9,682 transcriptome datasets from 350 species. Among the organelle genomes, 534 genomes from 366 species were newly generated in this study. Whole genomes, organelle genomes, genomic fragments, transcriptomes, and DNA barcodes were uniformly formatted and arranged by species. The GPGD is publicly accessible at http://www.gpgenome.com and serves as an essential resource for species identification, decomposition of biosynthetic pathways, and molecular-assisted breeding analysis. Thus, the database is an invaluable resource for future studies on herbal medicine safety, drug discovery, and the protection and rational use of herbal resources.展开更多
Secretion systems, macromolecules to pass which can mediate the across cellular membranes, are essential for virulent and genetic material exchange among bacterial species[1]. Type IV secretion system （T4SS） is one ...Secretion systems, macromolecules to pass which can mediate the across cellular membranes, are essential for virulent and genetic material exchange among bacterial species[1]. Type IV secretion system （T4SS） is one of the secretion systems and it usually consists of 12 genes： VirB1, VirB2 ...VirB11, and VirD4[2]. The structure and molecular mechanisms of these genes have been well analyzed in Gram-negative strains[3] and Gram-positive strains were once believed to be lack of T4SS. However, some recent studies revealed that one or more virB/D genes also exist in some kinds of Gram-positive bacteria and play similar role, and form a T4SS-like system[3]. The VirBl-like, VirB4, VirB6, and VirD4 genes were identified in the chromosome of Gram-positive bacterium Streptococcus suis in our previous studies and their role as important mobile elements for horizontal transfer to recipients in an 89 K pathogenicity island （PAl） was demonstrated[45]. However, their structure and molecular mechanisms in other strains, especially in Gram-positive strains, are remained unclear.展开更多
Genetic genealogy provides crucial insights into the complex biological relationships within contemporary and ancient human populations by analyzing shared alleles and chromosomal segments that are identical by descen...Genetic genealogy provides crucial insights into the complex biological relationships within contemporary and ancient human populations by analyzing shared alleles and chromosomal segments that are identical by descent to understand kinship,migration patterns,and population dynamics.Within forensic science,forensic investigative genetic genealogy(FIGG)has gained prominence by leveraging next-generation sequencing technologies and population-specific genomic resources,opening useful investigative avenues.In this review,we synthesize current knowledge,underscore recent advancements,and discuss the growing role of FIGG in forensic genomics.FIGG has been pivotal in revitalizing dormant inquiries and offering genetic leads in numerous cold cases.Its effectiveness relies on the extensive single-nucleotide polymorphism profiles contributed by individuals from diverse populations to specialized genomic databases.Advances in computational genomics and the growth of human genomic databases have spurred a profound shift in the application of genetic genealogy across forensics,anthropology,and ancient DNA studies.As the field progresses,FIGG is evolving from a nascent practice into a more sophisticated and specialized discipline,shaping the future of forensic investigations.展开更多
BACKGROUNDGastric cancer(GC)has a high prevalence and mortality overall.GEN1 is associatedwith abnormal centrosome amplification,DNA damage and increasedapoptosis.To date,little is known about the function and mechani...BACKGROUNDGastric cancer(GC)has a high prevalence and mortality overall.GEN1 is associatedwith abnormal centrosome amplification,DNA damage and increasedapoptosis.To date,little is known about the function and mechanism of GEN1 inGC.AIMTo explore the cellular processes associated with GC will help to elucidate themechanism of the occurrence and development of GC and discover potentialtherapeutic targets.METHODSThe detection of GEN1 expression at mRNA and protein levels was done by realtimequantitative polymerase chain reaction and western blotting.The function ofGEN1 was verified by loss-of-function experiments in AGS cells.The genes coexpressedwith GEN1 were searched from the stomach adenocarcinomas(STAD)data in The Cancer Genome Atlas database.Kyoto Encyclopedia of Genes andGenomes(KEGG)enrichment analysis of the genes co-expressed with GEN1 tofurther identify the pathways involved in GEN1.Rescue experiments usingferroptosis inhibitor ferrostatin-1 and chemotherapeutic sensitivity assays withcisplatin were also performed.RESULTSSignificant up-regulation of GEN1 was observed in GC cell lines AGS and MGC-803.Inhibition of GEN1 induced cell apoptosis and decreased cell proliferation,cycle progression,migration in AGS cells.There were 264 genes co-expressedwith GEN1 in STAD cohort(r>0.4,P<0.001).KEGG enrichment analysis showed that GEN1 might be associated with the cell cycle,Fanconi anemia pathway,homologous recombination,oocytemeiosis and cellular senescence in GC.Furthermore,CCNA2,CCNB1,CCNB2,cyclin-dependent kinase(CDK)1,CDK2 and polo-like kinase 1 protein levels were lower in GEN1-knockdown AGS cells,manifesting that GEN1 wasassociated with the cell cycle pathway in AGS cells.Downregulation of GEN1 decreased adenosine triphosphatecontent and elevated reactive oxygen species in AGS cells,suggesting that GEN1 silencing led to mitochondrialdysfunction in AGS cells.In addition,GEN1 silencing caused an overt decrease in FTH1 and GPX4 protein levelsand a significant elevation in ACSL4 protein levels,implying that GEN1 silencing promoted AGS cell ferroptosis.Treatment with ferrostatin-1 rescued cell viability loss induced by GEN1 knockdown,confirming ferroptosis as akey death mechanism.Additionally,GEN1-deficient AGS cells showed enhanced sensitivity to cisplatin,with asignificantly reduced half-maximal inhibitory concentration compared to control cells.CONCLUSIONGEN1 promotes GC cell proliferation and migration while suppressing apoptosis and ferroptosis.Targeting GEN1not only disrupts mitochondrial function and cell cycle progression but also sensitizes GC cells to ferroptosis andchemotherapy.These findings highlight GEN1 as a potential therapeutic target for enhancing treatment efficacy ingastric cancer.展开更多
The Genome Warehouse(GWH),accessible at https://ngdc.cncb.ac.cn/gwh,is an extensively-utilized public repository dedicated to the deposition,management,and sharing of genome assembly sequences,annotations,and metadata...The Genome Warehouse(GWH),accessible at https://ngdc.cncb.ac.cn/gwh,is an extensively-utilized public repository dedicated to the deposition,management,and sharing of genome assembly sequences,annotations,and metadata.This paper highlights noteworthy enhancements to the GWH since the 2021 version,emphasizing substantial advancements in web interfaces for data submission,database functionality updates,and re-source integration.Key updates include the reannotation of released prokaryotic genomes,mirroring of genome resources from National Center for Biotechnology Information(NCBl)GenBank and Reference Sequence Database(RefSeq),integration of Poxviridae sequences,implementation of an online batch submission system,enhancements to the quality control system,advanced search capabilities,and the introduction of a controlled-access mechanism for human genome data.These improvements collectively enhance the ease and security of data submission and access as well as genome data value,thereby improving convenience and utility for researchers in the genomics field.展开更多
Human mitochondrial DNA(mt DNA)harbors essential mutations linked to aging,neurodegenerative diseases,and complex muscle disorders.Due to its uniparental and haploid inheritance,mt DNA captures matrilineal evolutionar...Human mitochondrial DNA(mt DNA)harbors essential mutations linked to aging,neurodegenerative diseases,and complex muscle disorders.Due to its uniparental and haploid inheritance,mt DNA captures matrilineal evolutionary trajectories,playing a crucial role in population and medical genetics.However,critical questions about the genomic diversity patterns,inheritance models,and evolutionary and medical functions of mt DNA remain unresolved or underexplored,particularly in the transition from traditional genotyping to largescale genomic analyses.This review summarizes recent advancements in data-driven genomic research and technological innovations that address these questions and clarify the biological impact of nuclear-mitochondrial segments(NUMTs)and mt DNA variants on human health,disease,and evolution.We propose a streamlined pipeline to comprehensively identify mt DNA and NUMT genomic diversity using advanced sequencing and computational technologies.Haplotype-resolved mt DNA sequencing and assembly can distinguish authentic mt DNA variants from NUMTs,reduce diagnostic inaccuracies,and provide clearer insights into heteroplasmy patterns and the authenticity of paternal inheritance.This review emphasizes the need for integrative multi-omics approaches and emerging long-read sequencing technologies to gain new insights into mutation mechanisms,the influence of heteroplasmy and paternal inheritance on mt DNA diversity and disease susceptibility,and the detailed functions of NUMTs.展开更多
Objective To experimentally validate clinical samples,analyze the mRNA expression of the FYVE domain containing phosphatidylinositol 3-phosphate 5 kinase(PIKFYVE)gene,and its clinical significance based on the Cancer ...Objective To experimentally validate clinical samples,analyze the mRNA expression of the FYVE domain containing phosphatidylinositol 3-phosphate 5 kinase(PIKFYVE)gene,and its clinical significance based on the Cancer Genome Atlas(TCGA)database in hepatocellular carcinoma(HCC).MethodssData information on 424 clinical samples(including 374 cases of HCC tissues and 50 cases of non-tumorous liver tissues)were collected based on the TCGA database.Cox regression analysis and the Kaplan-Meier method were used to analyze the relationship between mRNA expression of the PIKFYVE gene and the clinical characteristics as well as survival prognosis in patients with HCC.The relationship betwen the PIKFYVE gene and immune cell infiltration was examined by correlation analysis with 24 kinds of immune cells.In addition,the mRNA expression level of the PIKFYVE gene and RACalpha serine/threonine-protein kinase(AKT1),phosphatase and tensin homolog(PTEN),protein kinase C alpha(PRKCA),inositol polyphosphate-5-phosphatase(INPP5D),phosphoinositide-3-kinase regulatory subunit 1(PIK3R1),inositol polyphosphate 4-phosphatase type II(INPP4B)and phospholipase C beta 4(PLCB4)gene correlations were analyzed in HCC tissues.At the same time,paraffin sections of highly differentiated,moderately differentiated,poorly differentiated,and non-tumor liver tissues from patients with HCC were collected from the Department of Pathology of the First Affiliated Hospital of Xinjiang Medical University.The histopathological observation was performed by HE staining.Immunohistochemistry was used to verify the expression levels of the PIKFYVE and Ki67 proteins in each clinical sample.The t-test was used for intergroup comparison of continuous data.The X test and Wilcoxon rank sum test were used for intergroup comparison of enumeration data.The Kaplan-Meier method was used for survival analysis.Results The expression level of the PIKFYVE gene was higher in the HCC tumor than that in normal liver tissue(P<0.01).The overall survival time of patients was significantly longer in the low expression group than that in the high expression group(HR=1.57,95%CI:1.10-2.25,P=0.014).The results of univariate Cox regression analysis showed that tumor stage,pathological grade,tumor status,residual tumor,and PIKFYVE expression level all had an effect on OS(P<0.05).The PIKFYVE prognostic risk model had a proportionate score of HR=1.533(95%CI:1.077-2.181,P=0.018).Multivariate Cox risk regression analysis showed that the PIKFYVE prognostic risk model had a proportionate score of HR=1.481(95%CI:0.886-2.476,P=0.134)and an area under the receiver operating characteristic curve of 0.559,indicating that it had predictive value for survival prediction.The results of the correlation analysis showed that the expression level of PIKFYVE was strongly correlated with immune cell infiltration and TP53(P<0.01).The results of immunohistochemical staining showed that the expression level of PIKFYVECwas significantly higher in HCC tissue samples than that in non-tumor liver tissues(P<0.01),and was negatively correlated with the degree of differentiation.Conclusion PIKFYVE,as an independent risk factor,is expected to be developed into a biomarker for clinical diagnosis,offering a reference for novel therapeutic agents in HCC.展开更多
Pineapple is the third most crucial tropical fruit worldwide and available in five varieties.Genomes of different pineapple varieties have been released to date;however,none of them are complete,with all exhibiting su...Pineapple is the third most crucial tropical fruit worldwide and available in five varieties.Genomes of different pineapple varieties have been released to date;however,none of them are complete,with all exhibiting substantial gaps and representing only two of the five pineapple varieties.This significantly hinders the advancement of pineapple breeding efforts.In this study,we sequenced the genomes of three varieties:a wild pineapple variety,a fiber pineapple variety,and a globally cultivated edible pineapple variety.We constructed the first gap-free reference genome(Ref)for pineapple.By consolidating multiple sources of evidence and manually revising each gene structure annotation,we identified 26,656 proteincoding genes.The BUSCO evaluation indicated a completeness of 99.2%,demonstrating the high quality of the gene structure annotations in this genome.Utilizing these resources,we identified 7,209 structural variations across the three varieties.Approximately 30.8%of pineapple genes were located within±5 kb of structural variations,including 30 genes associated with anthocyanin synthesis.Further analysis and functional experiments demonstrated that the high expression of AcMYB528 aligns with the accumulation of anthocyanins in the leaves,both of which may be affected by a 1.9-kb insertion fragment.In addition,we developed the Ananas Genome Database,which offers data browsing,retrieval,analysis,and download functions.The construction of this database addresses the lack of pineapple genome resource databases.In summary,we acquired a seamless pineapple reference genome with highquality gene structure annotations,providing a solid foundation for pineapple genomics and a valuable reference for pineapple breeding.展开更多
Pyridoxal kinase （PLK） （EC 2.7.1.35） catalyzes the ATP-dependent phosphorylation of pyridoxal, generating pyridoxal-5＇-phosphate （PLP）, an important cofactor for many enzymatic reactions. Bombyx mori, similar t...Pyridoxal kinase （PLK） （EC 2.7.1.35） catalyzes the ATP-dependent phosphorylation of pyridoxal, generating pyridoxal-5＇-phosphate （PLP）, an important cofactor for many enzymatic reactions. Bombyx mori, similar to mammals, relies on a nutritional source of vitamin B6 to synthesize PLP. This article describes how a cDNA encoding PLK was cloned from Bombyx mori using the PCR method （GenBank accession number： DQ452397）. The cDNA has an 894 bp open reading frame and encodes a protein of 298 amino acid residues with a molecular mass of 33.1 k.Da. The amino acid sequence shares 48.6% identity with that of human PLK, and it also contains signature conserved motifs of the PLK family. However, the protein is 10 or more amino acids shorter than the PLK from mammals and plants, and several amino acid residues conserved in the PLK from mammals and plants are changed in the protein. The cDNA cloned was expressed successfully in Escherichia coli using the T7 promoter/T7 RNA polymerase expression system, and the crude extracts containing the expressed product were found to have strong PLK enzymatic activity with a value of 30 nmol/min/mg, confirming that the cDNA encodes the functional PLK of Bombyx mori. This is the first identification of a gene encoding PLK in insects.展开更多
BACKGROUND Self-renewal of gastric cancer stem cells(GCSCs)is considered to be the underlying cause of the metastasis,drug resistance,and recurrence of gastric cancer(GC).AIM To characterize the expression of stem cel...BACKGROUND Self-renewal of gastric cancer stem cells(GCSCs)is considered to be the underlying cause of the metastasis,drug resistance,and recurrence of gastric cancer(GC).AIM To characterize the expression of stem cell-related genes in GC.METHODS RNA sequencing results and clinical data for gastric adenoma and adenocarcinoma samples were obtained from The Cancer Genome Atlas database,and the results of the GC mRNA expression-based stemness index(mRNAsi)were analyzed.Weighted gene coexpression network analysis was then used to find modules of interest and their key genes.Survival analysis of key genes was performed using the online tool Kaplan-Meier Plotter,and the online database Oncomine was used to assess the expression of key genes in GC.RESULTS mRNAsi was significantly upregulated in GC tissues compared to normal gastric tissues(P<0.0001).A total of 16 modules were obtained from the gene coexpression network;the brown module was most positively correlated with mRNAsi.Sixteen key genes(BUB1,BUB1 B,NCAPH,KIF14,RACGAP1,RAD54 L,TPX2,KIF15,KIF18 B,CENPF,TTK,KIF4 A,SGOL2,PLK4,XRCC2,a n d C1 orf112)were identified in the brown module.The functional and pathway enrichment analyses showed that the key genes were significantly enriched in the spindle cellular component,the sister chromatid segregation biological process,the motor activity molecular function,and the cell cycle and homologous recombination pathways.Survival analysis and Oncomine analysis revealed that the prognosis of patients with GC and the expression of three genes(RAD54 L,TPX2,and XRCC2)were consistently related.CONCLUSION Sixteen key genes are primarily associated with stem cell self-renewal and cell proliferation characteristics.RAD54 L,TPX2,and XRCC2 are the most likely therapeutic targets for inhibiting the stemness characteristics of GC cells.展开更多
Copy number variations have been found in patients with neural tube abnormalities.In this study,we performed genome-wide screening using high-resolution array-based comparative genomic hybridization in three children ...Copy number variations have been found in patients with neural tube abnormalities.In this study,we performed genome-wide screening using high-resolution array-based comparative genomic hybridization in three children with tethered spinal cord syndrome and two healthy parents.Of eight copy number variations,four were non-polymorphic.These non-polymorphic copy number variations were associated with Angelman and Prader-Willi syndromes,and microcephaly.Gene function enrichment analysis revealed that COX8 C,a gene associated with metabolic disorders of the nervous system,was located in the copy number variation region of Patient 1.Our results indicate that array-based comparative genomic hybridization can be used to diagnose tethered spinal cord syndrome.Our results may help determine the pathogenesis of tethered spinal cord syndrome and prevent occurrence of this disease.展开更多
Objective This study aimed to construct a prognostic model for rectal adenocarcinomas based on immune-related long noncoding RNAs(lncRNAs)and verify its prediction efficiency.Methods Transcript data and clinical data ...Objective This study aimed to construct a prognostic model for rectal adenocarcinomas based on immune-related long noncoding RNAs(lncRNAs)and verify its prediction efficiency.Methods Transcript data and clinical data of rectal adenocarcinomas were downloaded from The Cancer Genome Atlas(TCGA)database.Perl software(strawberry version)and R language(version 3.6.1)were used to analyze the immune-related genes and immune-related lncRNAs of rectal adenocarcinomas,and the differentially expressed immune-related lncRNAs were screened according to the criteria|log2FC|>1 and P<0.05.The key immune-related lncRNAs were screened using single-factor Cox regression analysis and lasso regression analysis.Multivariate Cox regression analysis was performed to construct an immune-related lncRNA prognostic model using the risk scores.Next,we evaluated the effectiveness of the model through Kaplan-Meier(K-M)survival analysis,ROC curve analysis,and independent prognostic analysis of clinical features.In addition,prognostic biomarkers of immune-related lncRNAs in the model were analyzed by K-M survival analysis.Results In this study,we obtained gene expression profile matrices of 89 rectal adenocarcinomas and 2 paracancerous specimens from TCGA database and applied immunologic signatures to these transcripts.Through R and Perl software analysis,we obtained 847 immune-related lncRNAs and 331 protein-encoded immune-related genes in rectal adenocarcinomas.Eight important immune-related lncRNAs related to the prognosis of rectal adenocarcinomas were identified using univariate Cox regression and lasso regression analysis.Furthermore,four immune-related lncRNAs were identified as prognostic markers of rectal adenocarcinomas via multivariate Cox regression analysis.The prognostic risk model was as follows:risk score=(-4.084)*expression LINC01871+(3.112)*expression AL158152.2+(7.616)*expression PXN-AS1+(-0.867)*expression HCP5.The independent prognostic effect of the rectal adenocarcinoma risk score model was revealed through K-M analysis,ROC curve analysis,and univariate,and multivariate Cox regression analysis(P=0.035).LINC01871(P=0.006),PXN-AS1(P=0.008),and AL158152.2(P=0.0386)were closely correlated with the prognosis of rectal adenocarcinomas through the K-M survival analysis.Conclusion We constructed a prognostic model of rectal adenocarcinomas based on four immune-related lncRNAs by analyzing the data based on TCGA database,with high prediction accuracy.We also identified two biomarkers with poor prognosis(PXN-AS1 and AL158152.2)and one biomarker with good prognosis(LINC01871).展开更多
Objective The aim of this study was to construct a prognostic model of esophageal adenocarcinoma(EAC)based on immune-related long noncoding RNAs(immune-related lncRNAs)and identify prognostic biomarkers using the Canc...Objective The aim of this study was to construct a prognostic model of esophageal adenocarcinoma(EAC)based on immune-related long noncoding RNAs(immune-related lncRNAs)and identify prognostic biomarkers using the Cancer Genome Atlas(TCGA)database.Methods Whole genomic mRNA expression and clinical data of esophageal adenocarcinoma were obtained from the TCGA database.The software Strawberry Perl,R and R packets were used to identify the immune-related genes and lncRNAs of esophageal adenocarcinoma,and for data processing and analysis.The differentially expressed lncRNAs were detected while comparing esophageal adenocarcinoma and normal tissue samples.The key immune-related lncRNAs were screened using lasso regression analysis and univariate cox regression analysis,and used to construct the prognostic model using multivariate cox regression analysis.To evaluate the accuracy of the risk prognostic model,all esophageal adenocarcinomas were divided into high-risk and low-risk groups according to the median risk score,after which Kaplan-Meier(K-M)survival curves,operating characteristic(ROC)curve and independent prognostic analysis of clinical traits were created.In addition,statistically significant immune-related lncRNAs and potential prognostic biomarkers were identified using the prognostic model and multifactor cox regression analysis for k-m survival analysis.Results A total of 1322 differentially expressed immune-related lncRNAs were identified,28 of which were associated with prognosis via univariate cox regression analysis.In addition,K-M survival analysis showed that the total survival time of the higher risk group was significantly shorter than that of the lower risk group(P=1.063e-10).The area under the ROC curve of 5-year total survival rate was 0.90.The risk score showed independent prognostic risk for esophageal adenocarcinoma via single factor and multifactorial independent prognostic analyses.In addition,the HR and 95%CI of each key immune-related lncRNA were calculated using multivariate Cox regression.Using k-m survival analysis,we found that 5 out of 12 key significant immune-related lncRNAs had independent prognostic value[AL136115.1(P=0.006),AC079684.1(P=0.008),AC07916394.1(P=0.0386),AC087620.1(P=0.041)and MIRLET7BHG(P=0.044)].Conclusion The present study successfully constructed a prognostic model of esophageal adenocarcinoma based on the TCGA database,with moderate predictive accuracy.The model consisted of the expression level of 12 immune-related lncRNAs.Furthermore,the study identified one favorable prognostic biomarker,MIRLET7BHG,and four poor prognostic biomarkers(AL136115.1,AC079684.1,AC016394.1,and AC087620.1).展开更多
Background:Snail intermediate hosts play active roles in the transmission of snail-borne trematode infections in Africa.A good knowledge of snail-borne diseases epidemiology particularly snail intermediate host popula...Background:Snail intermediate hosts play active roles in the transmission of snail-borne trematode infections in Africa.A good knowledge of snail-borne diseases epidemiology particularly snail intermediate host populations would provide the necessary impetus to complementing existing control strategy.Main body:This review highlights the importance of molecular approaches in differentiating snail hosts population structure and the need to provide adequate information on snail host populations by updating snail hosts genome database for Africa,in order to equip different stakeholders with adequate information on the ecology of snail intermediate hosts and their roles in the transmission of different diseases.Also,we identify the gaps and areas where there is need for urgent intervention to facilitate effective integrated control of schistosomiasis and other snail-borne trematode infections.Conclusions:Prioritizing snail studies,especially snail differentiation using molecular tools will boost disease surveillance and also enhance efficient schistosomaisis control programme in Africa.展开更多
Commercial and customized microarrays are valuable tools for the analysis of holistic expression patterns,but require the integration of the latest genomic information.This study provides a comprehensive workflow impl...Commercial and customized microarrays are valuable tools for the analysis of holistic expression patterns,but require the integration of the latest genomic information.This study provides a comprehensive workflow implemented in an R package(rePROBE)to assign the entire probes and to annotate the probe sets based on up-to-date genomic and transcriptomic information.The rePROBE package can be applied to available gene expression microarray platforms and addresses both public and custom databases.The revised probe assignment and updated probe-set annotation are applied to commercial microarrays available for different livestock species,i.e.,chicken(Gallus gallus;ChiGene-1_0-st:443,579 probes and 18,530 probe sets),pig(Sus scrofa;PorGene-1_1-st:592,005 probes and 25,779 probe sets),and cattle(Bos Taurus;BovGene-1_0-st:530,717 probes and 24,759 probe sets),as well as available for human(Homo sapiens;HuGene-1_0-st)and mouse(Mus musculus HT_MG-430_PM).Using current species-specific transcriptomic information(RefSeq,Ensembl,and partially non-redundant nucleotide sequences)and genomic information,the applied workflow reveals 297,574 probes(15,689 probe sets)for chicken,384,715 probes(21,673 probe sets)for pig,363,077 probes(21,238 probe sets)for cattle,481,168 probes(23,495 probe sets)for human,and 324,942 probes(32,494 probe sets)for mouse.These are representative of 12,641,15,758,18,046,20,167,and 16,335 unique genes that are both annotated and positioned for chicken,pig,cattle,human,and mouse,respectively.Additionally,the workflow collects information on the number of single nucleotide polymorphisms(SNPs)within respective targeted genomic regions and thus provides a detailed basis for comprehensive analyses such as expression quantitative trait locus(eQTL)studies to identify quantitative and functional traits.The rePROBE R package is freely available at https://github.com/friederhadlich/rePROBE.展开更多
An ever-growing number of resources on model organisms have emerged with the continued development of sequencing technologies. In this paper, we review 13 databases of model organisms, most of which are reported by th...An ever-growing number of resources on model organisms have emerged with the continued development of sequencing technologies. In this paper, we review 13 databases of model organisms, most of which are reported by the National Institutes of Health of the United States（NIH; http：//www.nih.gov/science/models/）. We provide a brief description for each database, as well as detail its data source and types, functions, tools, and availability of access. In addition,we also provide a quality assessment about these databases. Significantly, the organism databases instituted in the early 1990s––such as the Mouse Genome Database（MGD）, Saccharomyces Genome Database（SGD）, and Fly Base––have developed into what are now comprehensive, core authority resources. Furthermore, all of the databases mentioned here update continually according to user feedback and with advancing technologies.展开更多
基金supported by the National Key Research and Development Program of China (2019YFC1711100)the National Natural Science Foundation of China and Karst Science Research Center of Guizhou Province (U1812403-1)+4 种基金the Special Foundation for National Science and Technology Basic Research Program of China (2018FY100701)the Fundamental Research Funds for the Central Public Welfare Research Institutes (ZXKT17027, ZXKT18014)the Open Research Fund of Chengdu University of Traditional Chinese Medicine Key Laboratory of Systematic Research of Distinctive Chinese Medicine Resources in Southwest China (2020GZ2011016)the Funds for Fostering Outstanding Scholars in Science and Technology (Innovation) (ZZ13-YQ-047)Innovation Fund of China Academy of Chinese Medical Sciences
文摘Genomic data have demonstrated considerable traction in accelerating contemporary studies in traditional medicine. However,the lack of a uniform format and dispersed storage limits the full potential of herb genomic data. In this study, we developed a Global Pharmacopoeia Genome Database(GPGD). The database contains 34,346 records for 903 herb species from eight global pharmacopoeias(Brazilian, Egyptian, European, Indian, Japanese, Korean, the Pharmacopoeia of the People’s Republic of China, and U.S. Pharmacopoeia’s Herbal Medicines Compendium). In particular, the GPGD contains 21,872 DNA barcodes from 867 species, 2,203 organelle genomes from 674 species, 55 whole genomes from 49 species, 534 genomic sequencing datasets from 366 species, and 9,682 transcriptome datasets from 350 species. Among the organelle genomes, 534 genomes from 366 species were newly generated in this study. Whole genomes, organelle genomes, genomic fragments, transcriptomes, and DNA barcodes were uniformly formatted and arranged by species. The GPGD is publicly accessible at http://www.gpgenome.com and serves as an essential resource for species identification, decomposition of biosynthetic pathways, and molecular-assisted breeding analysis. Thus, the database is an invaluable resource for future studies on herbal medicine safety, drug discovery, and the protection and rational use of herbal resources.
基金supported by the National Natural Science Foundation of China (No. 81201322)the Priority Project on Infectious Disease Control and Prevention 2011ZX10004-001 and 2013ZX10003006-002 by the Chinese Ministry of Science and Technology and the Chinese Ministry of Healththe Foundation of State Key Laboratory for Infectious Disease Prevention and Control (Grand No. 2011SKLID303)
文摘Secretion systems, macromolecules to pass which can mediate the across cellular membranes, are essential for virulent and genetic material exchange among bacterial species[1]. Type IV secretion system （T4SS） is one of the secretion systems and it usually consists of 12 genes： VirB1, VirB2 ...VirB11, and VirD4[2]. The structure and molecular mechanisms of these genes have been well analyzed in Gram-negative strains[3] and Gram-positive strains were once believed to be lack of T4SS. However, some recent studies revealed that one or more virB/D genes also exist in some kinds of Gram-positive bacteria and play similar role, and form a T4SS-like system[3]. The VirBl-like, VirB4, VirB6, and VirD4 genes were identified in the chromosome of Gram-positive bacterium Streptococcus suis in our previous studies and their role as important mobile elements for horizontal transfer to recipients in an 89 K pathogenicity island （PAl） was demonstrated[45]. However, their structure and molecular mechanisms in other strains, especially in Gram-positive strains, are remained unclear.
基金supported by the National Natural Science Foundation of China(82202078)the Major Project of the National Social Science Foundation of China(23&ZD203)+3 种基金the Open Project of the Key Laboratory of Forensic Genetics of the Ministry of Public Security(2022FGKFKT05)the Center for Archaeological Science of Sichuan University(23SASA01)the 1‧3‧5 Project for Disciplines of Excellence,West China Hospital,Sichuan University(ZYJC20002)the Sichuan Science and Technology Program(2024NSFSC1518).
文摘Genetic genealogy provides crucial insights into the complex biological relationships within contemporary and ancient human populations by analyzing shared alleles and chromosomal segments that are identical by descent to understand kinship,migration patterns,and population dynamics.Within forensic science,forensic investigative genetic genealogy(FIGG)has gained prominence by leveraging next-generation sequencing technologies and population-specific genomic resources,opening useful investigative avenues.In this review,we synthesize current knowledge,underscore recent advancements,and discuss the growing role of FIGG in forensic genomics.FIGG has been pivotal in revitalizing dormant inquiries and offering genetic leads in numerous cold cases.Its effectiveness relies on the extensive single-nucleotide polymorphism profiles contributed by individuals from diverse populations to specialized genomic databases.Advances in computational genomics and the growth of human genomic databases have spurred a profound shift in the application of genetic genealogy across forensics,anthropology,and ancient DNA studies.As the field progresses,FIGG is evolving from a nascent practice into a more sophisticated and specialized discipline,shaping the future of forensic investigations.
文摘BACKGROUNDGastric cancer(GC)has a high prevalence and mortality overall.GEN1 is associatedwith abnormal centrosome amplification,DNA damage and increasedapoptosis.To date,little is known about the function and mechanism of GEN1 inGC.AIMTo explore the cellular processes associated with GC will help to elucidate themechanism of the occurrence and development of GC and discover potentialtherapeutic targets.METHODSThe detection of GEN1 expression at mRNA and protein levels was done by realtimequantitative polymerase chain reaction and western blotting.The function ofGEN1 was verified by loss-of-function experiments in AGS cells.The genes coexpressedwith GEN1 were searched from the stomach adenocarcinomas(STAD)data in The Cancer Genome Atlas database.Kyoto Encyclopedia of Genes andGenomes(KEGG)enrichment analysis of the genes co-expressed with GEN1 tofurther identify the pathways involved in GEN1.Rescue experiments usingferroptosis inhibitor ferrostatin-1 and chemotherapeutic sensitivity assays withcisplatin were also performed.RESULTSSignificant up-regulation of GEN1 was observed in GC cell lines AGS and MGC-803.Inhibition of GEN1 induced cell apoptosis and decreased cell proliferation,cycle progression,migration in AGS cells.There were 264 genes co-expressedwith GEN1 in STAD cohort(r>0.4,P<0.001).KEGG enrichment analysis showed that GEN1 might be associated with the cell cycle,Fanconi anemia pathway,homologous recombination,oocytemeiosis and cellular senescence in GC.Furthermore,CCNA2,CCNB1,CCNB2,cyclin-dependent kinase(CDK)1,CDK2 and polo-like kinase 1 protein levels were lower in GEN1-knockdown AGS cells,manifesting that GEN1 wasassociated with the cell cycle pathway in AGS cells.Downregulation of GEN1 decreased adenosine triphosphatecontent and elevated reactive oxygen species in AGS cells,suggesting that GEN1 silencing led to mitochondrialdysfunction in AGS cells.In addition,GEN1 silencing caused an overt decrease in FTH1 and GPX4 protein levelsand a significant elevation in ACSL4 protein levels,implying that GEN1 silencing promoted AGS cell ferroptosis.Treatment with ferrostatin-1 rescued cell viability loss induced by GEN1 knockdown,confirming ferroptosis as akey death mechanism.Additionally,GEN1-deficient AGS cells showed enhanced sensitivity to cisplatin,with asignificantly reduced half-maximal inhibitory concentration compared to control cells.CONCLUSIONGEN1 promotes GC cell proliferation and migration while suppressing apoptosis and ferroptosis.Targeting GEN1not only disrupts mitochondrial function and cell cycle progression but also sensitizes GC cells to ferroptosis andchemotherapy.These findings highlight GEN1 as a potential therapeutic target for enhancing treatment efficacy ingastric cancer.
基金supported by the Science&Technology Fundamental Resources Investigation Program(Grant No.2022FY101203 to Xuetong Zhao)the International Partnership Program of the Chinese Academy of Sciences(Grant No.161GJHZ2022002MI to Yiming Bao)+2 种基金the Professional Association of the Alliance of International Science Organizations(Grant No.ANSO-PA-2023-07 to Yiming Bao)the CAS Key Technology Talent Program to Meili Chen,the Open Biodiversity and Health Big Data Programme of IUBS to Yiming Bao,the National Key R&D Program of China(Grant No.2023YFC2605700 to Wenming Zhao)the National Natural Science Foundation of China(Grant Nos.32170678 to Wenming Zhao,32170669 to Jingfa Xiao,and 32030021 to Zhang Zhang).
文摘The Genome Warehouse(GWH),accessible at https://ngdc.cncb.ac.cn/gwh,is an extensively-utilized public repository dedicated to the deposition,management,and sharing of genome assembly sequences,annotations,and metadata.This paper highlights noteworthy enhancements to the GWH since the 2021 version,emphasizing substantial advancements in web interfaces for data submission,database functionality updates,and re-source integration.Key updates include the reannotation of released prokaryotic genomes,mirroring of genome resources from National Center for Biotechnology Information(NCBl)GenBank and Reference Sequence Database(RefSeq),integration of Poxviridae sequences,implementation of an online batch submission system,enhancements to the quality control system,advanced search capabilities,and the introduction of a controlled-access mechanism for human genome data.These improvements collectively enhance the ease and security of data submission and access as well as genome data value,thereby improving convenience and utility for researchers in the genomics field.
基金supported by the National Natural Science Foundation of China(82202078 and 82402203)the National Natural Science Foundation of Chongqing(CSTB2024NSCQLZX0005)+4 种基金the Major Project of the National Social Science Foundation of China(23&ZD203)the Open Project of the Key Laboratory of Forensic Genetics of the Ministry of Public Security(2022FGKFKT05)the Center for Archaeological Science of Sichuan University(23SASA01)the 1.3.5 Project for Disciplines of Excellence,West China Hospital,Sichuan University(ZYJC20002)the Sichuan Science and Technology Program(2024NSFSC1518)。
文摘Human mitochondrial DNA(mt DNA)harbors essential mutations linked to aging,neurodegenerative diseases,and complex muscle disorders.Due to its uniparental and haploid inheritance,mt DNA captures matrilineal evolutionary trajectories,playing a crucial role in population and medical genetics.However,critical questions about the genomic diversity patterns,inheritance models,and evolutionary and medical functions of mt DNA remain unresolved or underexplored,particularly in the transition from traditional genotyping to largescale genomic analyses.This review summarizes recent advancements in data-driven genomic research and technological innovations that address these questions and clarify the biological impact of nuclear-mitochondrial segments(NUMTs)and mt DNA variants on human health,disease,and evolution.We propose a streamlined pipeline to comprehensively identify mt DNA and NUMT genomic diversity using advanced sequencing and computational technologies.Haplotype-resolved mt DNA sequencing and assembly can distinguish authentic mt DNA variants from NUMTs,reduce diagnostic inaccuracies,and provide clearer insights into heteroplasmy patterns and the authenticity of paternal inheritance.This review emphasizes the need for integrative multi-omics approaches and emerging long-read sequencing technologies to gain new insights into mutation mechanisms,the influence of heteroplasmy and paternal inheritance on mt DNA diversity and disease susceptibility,and the detailed functions of NUMTs.
文摘Objective To experimentally validate clinical samples,analyze the mRNA expression of the FYVE domain containing phosphatidylinositol 3-phosphate 5 kinase(PIKFYVE)gene,and its clinical significance based on the Cancer Genome Atlas(TCGA)database in hepatocellular carcinoma(HCC).MethodssData information on 424 clinical samples(including 374 cases of HCC tissues and 50 cases of non-tumorous liver tissues)were collected based on the TCGA database.Cox regression analysis and the Kaplan-Meier method were used to analyze the relationship between mRNA expression of the PIKFYVE gene and the clinical characteristics as well as survival prognosis in patients with HCC.The relationship betwen the PIKFYVE gene and immune cell infiltration was examined by correlation analysis with 24 kinds of immune cells.In addition,the mRNA expression level of the PIKFYVE gene and RACalpha serine/threonine-protein kinase(AKT1),phosphatase and tensin homolog(PTEN),protein kinase C alpha(PRKCA),inositol polyphosphate-5-phosphatase(INPP5D),phosphoinositide-3-kinase regulatory subunit 1(PIK3R1),inositol polyphosphate 4-phosphatase type II(INPP4B)and phospholipase C beta 4(PLCB4)gene correlations were analyzed in HCC tissues.At the same time,paraffin sections of highly differentiated,moderately differentiated,poorly differentiated,and non-tumor liver tissues from patients with HCC were collected from the Department of Pathology of the First Affiliated Hospital of Xinjiang Medical University.The histopathological observation was performed by HE staining.Immunohistochemistry was used to verify the expression levels of the PIKFYVE and Ki67 proteins in each clinical sample.The t-test was used for intergroup comparison of continuous data.The X test and Wilcoxon rank sum test were used for intergroup comparison of enumeration data.The Kaplan-Meier method was used for survival analysis.Results The expression level of the PIKFYVE gene was higher in the HCC tumor than that in normal liver tissue(P<0.01).The overall survival time of patients was significantly longer in the low expression group than that in the high expression group(HR=1.57,95%CI:1.10-2.25,P=0.014).The results of univariate Cox regression analysis showed that tumor stage,pathological grade,tumor status,residual tumor,and PIKFYVE expression level all had an effect on OS(P<0.05).The PIKFYVE prognostic risk model had a proportionate score of HR=1.533(95%CI:1.077-2.181,P=0.018).Multivariate Cox risk regression analysis showed that the PIKFYVE prognostic risk model had a proportionate score of HR=1.481(95%CI:0.886-2.476,P=0.134)and an area under the receiver operating characteristic curve of 0.559,indicating that it had predictive value for survival prediction.The results of the correlation analysis showed that the expression level of PIKFYVE was strongly correlated with immune cell infiltration and TP53(P<0.01).The results of immunohistochemical staining showed that the expression level of PIKFYVECwas significantly higher in HCC tissue samples than that in non-tumor liver tissues(P<0.01),and was negatively correlated with the degree of differentiation.Conclusion PIKFYVE,as an independent risk factor,is expected to be developed into a biomarker for clinical diagnosis,offering a reference for novel therapeutic agents in HCC.
基金supported by National Natural Science Foundation of China(32272677)National Key R&D Program of China(2019YFD1001104)+1 种基金Central Publicinterest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences(1630032024026,1630032024001,1630052023011)Hainan Provincial Natural Science Foundation of China(323QN279)。
文摘Pineapple is the third most crucial tropical fruit worldwide and available in five varieties.Genomes of different pineapple varieties have been released to date;however,none of them are complete,with all exhibiting substantial gaps and representing only two of the five pineapple varieties.This significantly hinders the advancement of pineapple breeding efforts.In this study,we sequenced the genomes of three varieties:a wild pineapple variety,a fiber pineapple variety,and a globally cultivated edible pineapple variety.We constructed the first gap-free reference genome(Ref)for pineapple.By consolidating multiple sources of evidence and manually revising each gene structure annotation,we identified 26,656 proteincoding genes.The BUSCO evaluation indicated a completeness of 99.2%,demonstrating the high quality of the gene structure annotations in this genome.Utilizing these resources,we identified 7,209 structural variations across the three varieties.Approximately 30.8%of pineapple genes were located within±5 kb of structural variations,including 30 genes associated with anthocyanin synthesis.Further analysis and functional experiments demonstrated that the high expression of AcMYB528 aligns with the accumulation of anthocyanins in the leaves,both of which may be affected by a 1.9-kb insertion fragment.In addition,we developed the Ananas Genome Database,which offers data browsing,retrieval,analysis,and download functions.The construction of this database addresses the lack of pineapple genome resource databases.In summary,we acquired a seamless pineapple reference genome with highquality gene structure annotations,providing a solid foundation for pineapple genomics and a valuable reference for pineapple breeding.
基金This work was supported by the Foundation of Talented Person Development of Anhui Province in 2004.
文摘Pyridoxal kinase （PLK） （EC 2.7.1.35） catalyzes the ATP-dependent phosphorylation of pyridoxal, generating pyridoxal-5＇-phosphate （PLP）, an important cofactor for many enzymatic reactions. Bombyx mori, similar to mammals, relies on a nutritional source of vitamin B6 to synthesize PLP. This article describes how a cDNA encoding PLK was cloned from Bombyx mori using the PCR method （GenBank accession number： DQ452397）. The cDNA has an 894 bp open reading frame and encodes a protein of 298 amino acid residues with a molecular mass of 33.1 k.Da. The amino acid sequence shares 48.6% identity with that of human PLK, and it also contains signature conserved motifs of the PLK family. However, the protein is 10 or more amino acids shorter than the PLK from mammals and plants, and several amino acid residues conserved in the PLK from mammals and plants are changed in the protein. The cDNA cloned was expressed successfully in Escherichia coli using the T7 promoter/T7 RNA polymerase expression system, and the crude extracts containing the expressed product were found to have strong PLK enzymatic activity with a value of 30 nmol/min/mg, confirming that the cDNA encodes the functional PLK of Bombyx mori. This is the first identification of a gene encoding PLK in insects.
基金the National Natural Science Foundation of China,No.81560389Key Research and Development Program of Jiangxi Province,No.20181BBG70015。
文摘BACKGROUND Self-renewal of gastric cancer stem cells(GCSCs)is considered to be the underlying cause of the metastasis,drug resistance,and recurrence of gastric cancer(GC).AIM To characterize the expression of stem cell-related genes in GC.METHODS RNA sequencing results and clinical data for gastric adenoma and adenocarcinoma samples were obtained from The Cancer Genome Atlas database,and the results of the GC mRNA expression-based stemness index(mRNAsi)were analyzed.Weighted gene coexpression network analysis was then used to find modules of interest and their key genes.Survival analysis of key genes was performed using the online tool Kaplan-Meier Plotter,and the online database Oncomine was used to assess the expression of key genes in GC.RESULTS mRNAsi was significantly upregulated in GC tissues compared to normal gastric tissues(P<0.0001).A total of 16 modules were obtained from the gene coexpression network;the brown module was most positively correlated with mRNAsi.Sixteen key genes(BUB1,BUB1 B,NCAPH,KIF14,RACGAP1,RAD54 L,TPX2,KIF15,KIF18 B,CENPF,TTK,KIF4 A,SGOL2,PLK4,XRCC2,a n d C1 orf112)were identified in the brown module.The functional and pathway enrichment analyses showed that the key genes were significantly enriched in the spindle cellular component,the sister chromatid segregation biological process,the motor activity molecular function,and the cell cycle and homologous recombination pathways.Survival analysis and Oncomine analysis revealed that the prognosis of patients with GC and the expression of three genes(RAD54 L,TPX2,and XRCC2)were consistently related.CONCLUSION Sixteen key genes are primarily associated with stem cell self-renewal and cell proliferation characteristics.RAD54 L,TPX2,and XRCC2 are the most likely therapeutic targets for inhibiting the stemness characteristics of GC cells.
文摘Copy number variations have been found in patients with neural tube abnormalities.In this study,we performed genome-wide screening using high-resolution array-based comparative genomic hybridization in three children with tethered spinal cord syndrome and two healthy parents.Of eight copy number variations,four were non-polymorphic.These non-polymorphic copy number variations were associated with Angelman and Prader-Willi syndromes,and microcephaly.Gene function enrichment analysis revealed that COX8 C,a gene associated with metabolic disorders of the nervous system,was located in the copy number variation region of Patient 1.Our results indicate that array-based comparative genomic hybridization can be used to diagnose tethered spinal cord syndrome.Our results may help determine the pathogenesis of tethered spinal cord syndrome and prevent occurrence of this disease.
基金Supported by a grant from the Health Commission of Hubei Province Scientific Research Project(No.WJ2019M118)。
文摘Objective This study aimed to construct a prognostic model for rectal adenocarcinomas based on immune-related long noncoding RNAs(lncRNAs)and verify its prediction efficiency.Methods Transcript data and clinical data of rectal adenocarcinomas were downloaded from The Cancer Genome Atlas(TCGA)database.Perl software(strawberry version)and R language(version 3.6.1)were used to analyze the immune-related genes and immune-related lncRNAs of rectal adenocarcinomas,and the differentially expressed immune-related lncRNAs were screened according to the criteria|log2FC|>1 and P<0.05.The key immune-related lncRNAs were screened using single-factor Cox regression analysis and lasso regression analysis.Multivariate Cox regression analysis was performed to construct an immune-related lncRNA prognostic model using the risk scores.Next,we evaluated the effectiveness of the model through Kaplan-Meier(K-M)survival analysis,ROC curve analysis,and independent prognostic analysis of clinical features.In addition,prognostic biomarkers of immune-related lncRNAs in the model were analyzed by K-M survival analysis.Results In this study,we obtained gene expression profile matrices of 89 rectal adenocarcinomas and 2 paracancerous specimens from TCGA database and applied immunologic signatures to these transcripts.Through R and Perl software analysis,we obtained 847 immune-related lncRNAs and 331 protein-encoded immune-related genes in rectal adenocarcinomas.Eight important immune-related lncRNAs related to the prognosis of rectal adenocarcinomas were identified using univariate Cox regression and lasso regression analysis.Furthermore,four immune-related lncRNAs were identified as prognostic markers of rectal adenocarcinomas via multivariate Cox regression analysis.The prognostic risk model was as follows:risk score=(-4.084)*expression LINC01871+(3.112)*expression AL158152.2+(7.616)*expression PXN-AS1+(-0.867)*expression HCP5.The independent prognostic effect of the rectal adenocarcinoma risk score model was revealed through K-M analysis,ROC curve analysis,and univariate,and multivariate Cox regression analysis(P=0.035).LINC01871(P=0.006),PXN-AS1(P=0.008),and AL158152.2(P=0.0386)were closely correlated with the prognosis of rectal adenocarcinomas through the K-M survival analysis.Conclusion We constructed a prognostic model of rectal adenocarcinomas based on four immune-related lncRNAs by analyzing the data based on TCGA database,with high prediction accuracy.We also identified two biomarkers with poor prognosis(PXN-AS1 and AL158152.2)and one biomarker with good prognosis(LINC01871).
基金a grant from the Health Commission of Hubei Province Scientific Research Project(No.WJ2019M118).
文摘Objective The aim of this study was to construct a prognostic model of esophageal adenocarcinoma(EAC)based on immune-related long noncoding RNAs(immune-related lncRNAs)and identify prognostic biomarkers using the Cancer Genome Atlas(TCGA)database.Methods Whole genomic mRNA expression and clinical data of esophageal adenocarcinoma were obtained from the TCGA database.The software Strawberry Perl,R and R packets were used to identify the immune-related genes and lncRNAs of esophageal adenocarcinoma,and for data processing and analysis.The differentially expressed lncRNAs were detected while comparing esophageal adenocarcinoma and normal tissue samples.The key immune-related lncRNAs were screened using lasso regression analysis and univariate cox regression analysis,and used to construct the prognostic model using multivariate cox regression analysis.To evaluate the accuracy of the risk prognostic model,all esophageal adenocarcinomas were divided into high-risk and low-risk groups according to the median risk score,after which Kaplan-Meier(K-M)survival curves,operating characteristic(ROC)curve and independent prognostic analysis of clinical traits were created.In addition,statistically significant immune-related lncRNAs and potential prognostic biomarkers were identified using the prognostic model and multifactor cox regression analysis for k-m survival analysis.Results A total of 1322 differentially expressed immune-related lncRNAs were identified,28 of which were associated with prognosis via univariate cox regression analysis.In addition,K-M survival analysis showed that the total survival time of the higher risk group was significantly shorter than that of the lower risk group(P=1.063e-10).The area under the ROC curve of 5-year total survival rate was 0.90.The risk score showed independent prognostic risk for esophageal adenocarcinoma via single factor and multifactorial independent prognostic analyses.In addition,the HR and 95%CI of each key immune-related lncRNA were calculated using multivariate Cox regression.Using k-m survival analysis,we found that 5 out of 12 key significant immune-related lncRNAs had independent prognostic value[AL136115.1(P=0.006),AC079684.1(P=0.008),AC07916394.1(P=0.0386),AC087620.1(P=0.041)and MIRLET7BHG(P=0.044)].Conclusion The present study successfully constructed a prognostic model of esophageal adenocarcinoma based on the TCGA database,with moderate predictive accuracy.The model consisted of the expression level of 12 immune-related lncRNAs.Furthermore,the study identified one favorable prognostic biomarker,MIRLET7BHG,and four poor prognostic biomarkers(AL136115.1,AC079684.1,AC016394.1,and AC087620.1).
基金The study is supported by Chinese National Science and Technology Major Program(grant no.2016ZX10004222-004)The funders played no role in the study design,data collection,and data analysis or interpretation。
文摘Background:Snail intermediate hosts play active roles in the transmission of snail-borne trematode infections in Africa.A good knowledge of snail-borne diseases epidemiology particularly snail intermediate host populations would provide the necessary impetus to complementing existing control strategy.Main body:This review highlights the importance of molecular approaches in differentiating snail hosts population structure and the need to provide adequate information on snail host populations by updating snail hosts genome database for Africa,in order to equip different stakeholders with adequate information on the ecology of snail intermediate hosts and their roles in the transmission of different diseases.Also,we identify the gaps and areas where there is need for urgent intervention to facilitate effective integrated control of schistosomiasis and other snail-borne trematode infections.Conclusions:Prioritizing snail studies,especially snail differentiation using molecular tools will boost disease surveillance and also enhance efficient schistosomaisis control programme in Africa.
基金partly funded by the Leibniz Science Campus Phosphorus Research Rostockfunding from the European Research Area Network on Sustainable Animal Production (ERA-NET Sus An) as part of the PEGa Sus project (Grant No. 2817ERA02D)The Research Institute for Farm Animal Biology (FBN) provided own matched funding
文摘Commercial and customized microarrays are valuable tools for the analysis of holistic expression patterns,but require the integration of the latest genomic information.This study provides a comprehensive workflow implemented in an R package(rePROBE)to assign the entire probes and to annotate the probe sets based on up-to-date genomic and transcriptomic information.The rePROBE package can be applied to available gene expression microarray platforms and addresses both public and custom databases.The revised probe assignment and updated probe-set annotation are applied to commercial microarrays available for different livestock species,i.e.,chicken(Gallus gallus;ChiGene-1_0-st:443,579 probes and 18,530 probe sets),pig(Sus scrofa;PorGene-1_1-st:592,005 probes and 25,779 probe sets),and cattle(Bos Taurus;BovGene-1_0-st:530,717 probes and 24,759 probe sets),as well as available for human(Homo sapiens;HuGene-1_0-st)and mouse(Mus musculus HT_MG-430_PM).Using current species-specific transcriptomic information(RefSeq,Ensembl,and partially non-redundant nucleotide sequences)and genomic information,the applied workflow reveals 297,574 probes(15,689 probe sets)for chicken,384,715 probes(21,673 probe sets)for pig,363,077 probes(21,238 probe sets)for cattle,481,168 probes(23,495 probe sets)for human,and 324,942 probes(32,494 probe sets)for mouse.These are representative of 12,641,15,758,18,046,20,167,and 16,335 unique genes that are both annotated and positioned for chicken,pig,cattle,human,and mouse,respectively.Additionally,the workflow collects information on the number of single nucleotide polymorphisms(SNPs)within respective targeted genomic regions and thus provides a detailed basis for comprehensive analyses such as expression quantitative trait locus(eQTL)studies to identify quantitative and functional traits.The rePROBE R package is freely available at https://github.com/friederhadlich/rePROBE.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences of China(Grant No.XDB13040500)
文摘An ever-growing number of resources on model organisms have emerged with the continued development of sequencing technologies. In this paper, we review 13 databases of model organisms, most of which are reported by the National Institutes of Health of the United States（NIH; http：//www.nih.gov/science/models/）. We provide a brief description for each database, as well as detail its data source and types, functions, tools, and availability of access. In addition,we also provide a quality assessment about these databases. Significantly, the organism databases instituted in the early 1990s––such as the Mouse Genome Database（MGD）, Saccharomyces Genome Database（SGD）, and Fly Base––have developed into what are now comprehensive, core authority resources. Furthermore, all of the databases mentioned here update continually according to user feedback and with advancing technologies.
