BACKGROUND Pancreatic cancer is a highly invasive malignant tumor. Expression levels of the autophagy-related protein microtubule-associated protein 1 A/1 B-light chain 3(LC3) and perineural invasion(PNI) are closely ...BACKGROUND Pancreatic cancer is a highly invasive malignant tumor. Expression levels of the autophagy-related protein microtubule-associated protein 1 A/1 B-light chain 3(LC3) and perineural invasion(PNI) are closely related to its occurrence and development. Our previous results showed that the high expression of LC3 was positively correlated with PNI in the patients with pancreatic cancer. In this study, we further searched for differential genes involved in autophagy of pancreatic cancer by gene expression profiling and analyzed their biological functions in pancreatic cancer, which provides a theoretical basis for elucidating the pathophysiological mechanism of autophagy in pancreatic cancer and PNI.AIM To identify differentially expressed genes involved in pancreatic cancer autophagy and explore the pathogenesis at the molecular level.METHODS Two sets of gene expression profiles of pancreatic cancer/normal tissue(GSE16515 and GSE15471) were collected from the Gene Expression Omnibus.Significance analysis of microarrays algorithm was used to screen differentially expressed genes related to pancreatic cancer. Gene Ontology(GO) analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis were used to analyze the functional enrichment of the differentially expressed genes. Protein interaction data containing only differentially expressed genes was downloaded from String database and screened. Module mining was carried out by Cytoscape software and ClusterOne plug-in. The interaction relationship between the modules was analyzed and the pivot nodes between the functional modules were determined according to the information of the functional modules and the data of reliable protein interaction network.RESULTS Based on the above two data sets of pancreatic tissue total gene expression, 6098 and 12928 differentially expressed genes were obtained by analysis of genes with higher phenotypic correlation. After extracting the intersection of the two differential gene sets, 4870 genes were determined. GO a展开更多
Ferroptosis plays a key role in aggravating the progression of spinal cord injury(SCI),but the specific mechanism remains unknown.In this study,we constructed a rat model of T10 SCI using a modified Allen method.We id...Ferroptosis plays a key role in aggravating the progression of spinal cord injury(SCI),but the specific mechanism remains unknown.In this study,we constructed a rat model of T10 SCI using a modified Allen method.We identified 48,44,and 27 ferroptosis genes that were differentially expressed at 1,3,and 7 days after SCI induction.Compared with the sham group and other SCI subgroups,the subgroup at 1 day after SCI showed increased expression of the ferroptosis marker acyl-CoA synthetase long-chain family member 4 and the oxidative stress marker malondialdehyde in the injured spinal cord while glutathione in the injured spinal cord was lower.These findings with our bioinformatics results suggested that 1 day after SCI was the important period of ferroptosis progression.Bioinformatics analysis identified the following top ten hub ferroptosis genes in the subgroup at 1 day after SCI:STAT3,JUN,TLR4,ATF3,HMOX1,MAPK1,MAPK9,PTGS2,VEGFA,and RELA.Real-time polymerase chain reaction on rat spinal cord tissue confirmed that STAT3,JUN,TLR4,ATF3,HMOX1,PTGS2,and RELA mRNA levels were up-regulated and VEGFA,MAPK1 and MAPK9 mRNA levels were down-regulated.Ten potential compounds were predicted using the DSigDB database as potential drugs or molecules targeting ferroptosis to repair SCI.We also constructed a ferroptosis-related mRNA-miRNA-lncRNA network in SCI that included 66 lncRNAs,10 miRNAs,and 12 genes.Our results help further the understanding of the mechanism underlying ferroptosis in SCI.展开更多
BACKGROUND Hepatocellular carcinoma(HCC)is a common malignant gastrointestinal tumor.There are currently few clinical diagnostic and prognostic markers for HCC.LncRNA cancer susceptibility candidate 9(CASC9)is a long-...BACKGROUND Hepatocellular carcinoma(HCC)is a common malignant gastrointestinal tumor.There are currently few clinical diagnostic and prognostic markers for HCC.LncRNA cancer susceptibility candidate 9(CASC9)is a long-chain non-coding RNA discovered in recent years,and previous studies have found that lncRNA CASC9 participates in the occurrence and development of HCC,but its clinical value remains unclear.AIM To determine the expression of lncRNA CASC9 in HCC and its diagnostic and prognostic value.METHODS Data on CASC9 expression in patients with HCC were collected from the Cancer Genome Atlas(TCGA)database to analyze the relationship between CASC9 and patient survival.A total of 80 HCC patients treated in The First Affiliated Hospital of Guangxi Medical University from May 2012 to January 2014 were enrolled in the patient group,and 50 healthy subjects were enrolled in the control group during the same period.CASC9 expression in the two groups was determined using quantitative real-time polymerase chain reaction,and its diagnostic and prognostic value was analyzed based on the CASC9 data and pathological data in these HCC patients.The relationship between CASC9 and patient survival was assessed during the 5-year follow-up period.RESULTS Analysis of data from TCGA database revealed that control samples showed significantly lower CASC9 expression than carcinoma tissue samples(P<0.001);the low CASC9 expression group had a higher survival rate than the high CASC9 expression group(P=0.011),and the patient group showed significantly increased expression of serum CASC9,with the area under the curve(AUC)of 0.933.CASC9 expression was related to tumor size,combined hepatitis,tumor,node,metastasis(TNM)staging,lymph node metastasis,differentiation and alpha fetoprotein,and the high CASC9 expression group showed lower 1-year,3-year and 5-year survival rates than the low CASC9 expression group(all aP<0.05).Multivariate Cox regression analysis revealed that TNM staging,lymph node metastasis,differentiation,alpha fetoprotein and展开更多
Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacteri...Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft(partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.展开更多
Plastids communicate their developmental and physiological status to the nucleus via retrograde signaling,allowing nuclear gene expression to be adjusted appropriately.Signaling during plastid biogenesis and responses...Plastids communicate their developmental and physiological status to the nucleus via retrograde signaling,allowing nuclear gene expression to be adjusted appropriately.Signaling during plastid biogenesis and responses of mature chloroplasts to environmental changes are designated“biogenic”and“operational”controls,respectively.A prominent example of the investigation of biogenic signaling is the screen for gun(genomes uncoupled)mutants.Although the first five gun mutants were identified 30 years ago,the functions of GUN proteins in retrograde signaling remain controversial,and that of GUN1 is hotly disputed.Here,we provide background information and critically discuss recently proposed concepts that address GUN-related signaling and some novel gun mutants.Moreover,considering heme as a candidate in retrograde signaling,we revisit the spatial organization of heme biosynthesis and export from plastids.Although this review focuses on GUN pathways,we also highlight recent progress in the identification and elucidation of chloroplast-derived signals that regulate the acclimation response in green algae and plants.Here,stress-induced accumulation of unfolded/misassembled chloroplast proteins evokes a chloroplast-specific unfolded protein response,which leads to changes in the expression levels of nucleus-encoded chaperones and proteases to restore plastid protein homeostasis.We also address the importance of chloroplast-derived signals for activation of flavonoid biosynthesis leading to production of anthocyanins during stress acclimation through sucrose non-fermenting 1-related protein kinase 1.Finally,a framework for identification and quantification of intercompartmental signaling cascades at the proteomic and metabolomic levels is provided,and we discuss future directions of dissection of organelle-nucleus communication.展开更多
While the peripheral nervous system has regenerative ability,restoration of sufficient function remains a challenge.Vimentin has been shown to be localized in axonal growth fronts and associated with nerve regeneratio...While the peripheral nervous system has regenerative ability,restoration of sufficient function remains a challenge.Vimentin has been shown to be localized in axonal growth fronts and associated with nerve regeneration,including myelination,neuroplasticity,kinase signaling in nerve axoplasm,and cell migration;however,the mechanisms regulating its expression within Schwann cell（SC） remain unexplored.The aim of this study was to profile the spatial and temporal expression profile of micro RNA（mi RNA） in a regenerating rat sciatic nerve after transection,and explore the potential role of mi R-138-5 p targeting vimentin in SC proliferation and migration.A rat sciatic nerve transection model,utilizing a polyethylene nerve guide,was used to investigate mi RNA expression at 7,14,30,60,and 90 days during nerve regeneration.Relative levels of mi RNA expression were determined using microarray analysis and subsequently validated with quantitative real-time polymerase chain reaction.In vitro assays were conducted with cultured Schwann cells transfected with mi RNA mimics and assessed for migratory and proliferative potential.The top seven dysregulated mi RNAs reported in this study have been implicated in cell migration elsewhere,and GO and KEGG analyses predicted activities essential to wound healing.Transfection of one of these,mi RNA-138-5 p,into SCs reduced cell migration and proliferation.mi R-138-5 p has been shown to directly target vimentin in cancer cells,and the luciferase assay performed here in rat Schwann cells confirmed it.These results detail a role of mi R-138-5 p in rat peripheral nerve regeneration and expand on reports of it as an important regulator in the peripheral nervous system.展开更多
The exact mechanisms associated with secondary brain damage following traumatic brain injury(TBI)remain unclear;therefore,identifying the critical molecular mechanisms involved in TBI is essential.The m RNA expression...The exact mechanisms associated with secondary brain damage following traumatic brain injury(TBI)remain unclear;therefore,identifying the critical molecular mechanisms involved in TBI is essential.The m RNA expression microarray GSE2871 was downloaded from the Gene Expression Omnibus(GEO)repository.GSE2871 comprises a total of 31 cerebral cortex samples,including two post-TBI time points.The microarray features eight control and seven TBI samples,from 4 hours post-TBI,and eight control and eight TBI samples from 24 hours post-TBI.In this bioinformatics-based study,109 and 66 differentially expressed genes(DEGs)were identified in a Sprague-Dawley(SD)rat TBI model,4 and 24 hours post-TBI,respectively.Functional enrichment analysis showed that the identified DEGs were significantly enriched in several terms,such as positive regulation of nuclear factor-κB transcription factor activity,mitogen-activated protein kinase signaling pathway,negative regulation of apoptotic process,and tumor necrosis factor signaling pathway.Moreover,the hub genes with high connectivity degrees were primarily related to inflammatory mediators.To validate the top five hub genes,a rat model of TBI was established using the weight-drop method,and real-time quantitative polymerase chain reaction analysis of the cerebral cortex was performed.The results showed that compared with control rats,Tnf-α,c-Myc,Spp1,Cxcl10,Ptprc,Egf,Mmp9,and Lcn2 were upregulated,and Fn1 was downregulated in TBI rats.Among these hub genes,Fn1,c-Myc,and Ptprc may represent novel biomarkers or therapeutic targets for TBI.These identified pathways and key genes may provide insights into the molecular mechanisms of TBI and provide potential treatment targets for patients with TBI.This study was approved by the Experimental Animal Ethics Committee of the First Affiliated Hospital of Nanchang University,China(approval No.003)in January 2016.展开更多
MATLAB software and optimal complete subgraph algorithm were used to extract and reveal the microsatellite distribution features in the complete genomes of the tobacco vein clearing virus （NC-003 378.1） from the NCB...MATLAB software and optimal complete subgraph algorithm were used to extract and reveal the microsatellite distribution features in the complete genomes of the tobacco vein clearing virus （NC-003 378.1） from the NCBI database.The results showed that the repetitions number and their location of the N-base group has been extracted and displayed.The largest repetitions of N-base group in the complete genomes of the tobacco vein clearing virus was decreased as the exponential function with the increasing of N.The method used in this study could be applied to the extraction and revealing of the microsatellite distribution features in the complete genomes of other viruses,thereby provided a basis for the research of the structure and the law of function,inheritance and variation by the using of the microsatellite distribution features.展开更多
The ecology and evolutionary biology of insect-plant associations has real- ized extensive attention, especially during the past 60 years. The classifications （categorical designations） of continuous variation in bi...The ecology and evolutionary biology of insect-plant associations has real- ized extensive attention, especially during the past 60 years. The classifications （categorical designations） of continuous variation in biodiversity, ranging from global patterns （e.g., lat- itudinal gradients in species richness/diversity and degree of herbivore feeding specialization） to localized insect-plant associations that span the biospectrum from polyphenisms, polymorphisms, biotypes, demes, host races, to cryptic species, remain academically contentious. Semantic and biosystematic （taxonomical） disagreements sometimes detract from more important ecological and evolutionary processes that drive diversification, the dynamics of gene flow and local extinctions. This review addresses several aspects of insect specialization, host-associated divergence and ecological （including ＂hybrid＂） speciation, with special reference to the climate warming impacts on species borders of hybridiz- ing swallowtail butterflies （Papilionidae）. Interspecific hybrid introgression may result in collapse of multi-species communities or increase species numbers via homoploid hybrid speciation. We may see diverging, merging, or emerging genotypes across hybrid zones, all part of the ongoing processes of evolution. Molecular analyses of genetic mosaics and genomic dynamics with ＂divergence hitchhiking＂, combined with ecological, ethological and physiological studies of＂species porosity＂, have already begun to unveil some answers for some important ecological/evolutionary questions. （i） How rapidly can host-associated divergence lead to new species （and why doesn＇t it always do so, e.g., resulting in ＂incom- plete＂ speciation）？ （ii） How might ＂speciation genes＂ function, and how/where would we find them？ （iii） Can oscillations from specialists to generalists and back to specialists help explain global diversity in herbivorous insects？ （iv） How could recombinant interspecific hybridization l展开更多
A DNA barcode is a short segment of sequence that is able to distinguish species. A barcode must ideally contain enough variation to distinguish every individual species and be easily obtained. Fungi of Nectriaceae ar...A DNA barcode is a short segment of sequence that is able to distinguish species. A barcode must ideally contain enough variation to distinguish every individual species and be easily obtained. Fungi of Nectriaceae are economically important and show high species diversity. To establish a standard DNA barcode for this group of fungi, the genomes of Neurospora crassa and 30 other filamentous fungi were compared. The expect value was treated as a criterion to recognize homologous sequences. Four candidate markers, Hsp90, AAC, CDC48, and EF3, were tested for their feasibility as barcodes in the identification of 34 well-established species belonging to 13 genera of Nectriaceae. Two hundred and fifteen sequences were analyzed. Intraand inter-specific variations and the success rate of PCR amplification and sequencing were considered as important criteria for estimation of the candidate markers. Ultimately, the partial EF3 gene met the requirements for a good DNA barcode: No overlap was found between the intra-and inter-specific pairwise distances. The smallest inter-specific distance of EF3 gene was 3.19%, while the largest intra-specific distance was 1.79%. In addition, there was a high success rate in PCR and sequencing for this gene (96.3%). CDC48 showed sufficiently high sequence variation among species, but the PCR and sequencing success rate was 84% using a single pair of primers. Although the Hsp90 and AAC genes had higher PCR and sequencing success rates (96.3% and 97.5%, respectively), overlapping occurred between the intraand inter-specific variations, which could lead to misidentification. Therefore, we propose the EF3 gene as a possible DNA barcode for the nectriaceous fungi.展开更多
Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study ...Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae.The cp genomes,vary-ing in size from 153,366 to 159,895 bp,followed the typical quadripartite organization consisting of a large single-copy(LSC)region(84,545 to 87,883 bp),a small single-copy(SSC)region(18,174 to 19,259 bp),and a pair of inverted repeat(IR)regions(25,310 to 26,396 bp).These genomes contained 132–138 annotated genes,including 87 to 93 protein-coding genes(PCGs),37 tRNA genes,and 8 rRNA genes using MISA software,52 to 121 simple sequence repeat(SSR)loci were identified.D.arbuscular contained the least of SSRs and did not have hexanotides,A.lineata contained the richest SSRs.Long terminal repeats(LTRs)were primarily composed of palindromic and forward repeat sequences,meanwhile,The richest LTRs were found in Argentina lineata.Except for Argentina lineata,Fragariastrum eriocarpum,and Prunus trichostoma,which varied in gene type and position on both sides of the boundary,the remaining species were found to be mostly conserved according to IR boundary analysis.The examination of the Ka/Ks ratio revealed that only the infA gene had a value greater than 1,indicating that this gene was primarily subjected to positive selection during evolution.Additionally,9 hotspots of variation were identified in the LSC and SSC regions.Phylogenetic analysis confirmed the scientific validity of the genus Prunus L.sensu lato(s.l.)within the Rosaceae family.The separation of the three genera Argentina Hill,Fragariastrum Heist.ex Fabr.and Dasiphora Raf.from Potentilla L.may be a more scientific classification.These results offer fresh perspectives on the taxonomy of the Rosaceae.展开更多
Following in the footsteps of traditional developmental genetics, research over the last 15 years has shown that innate immunity against bacteria and fungi is governed largely by two NF-κB signal transduction pathway...Following in the footsteps of traditional developmental genetics, research over the last 15 years has shown that innate immunity against bacteria and fungi is governed largely by two NF-κB signal transduction pathways, Toll and IMD. Antiviral immunity appears to stem from RNA interference, whereas resistance against parasitoids is conferred by Toll signaling. The identification of these post-transcriptional regulatory mechanisms and the annotation of most Drosophila immunity genes have derived from functional genomic studies using ＂model＂ pathogens, intact animals and cell lines. The D. melanogaster host has thus provided the core information that can be used to study responses to natural microbial and metazoan pathogens as they become identified, as well as to test ideas of selection and evolutionary change. These analyses are of general importance to understanding mechanisms of other insect host-pathogen interactions and determinants of variation in host resistance.展开更多
基金Supported by the National Natural Science Foundation of China,No.U1504815 and No.U1504808
文摘BACKGROUND Pancreatic cancer is a highly invasive malignant tumor. Expression levels of the autophagy-related protein microtubule-associated protein 1 A/1 B-light chain 3(LC3) and perineural invasion(PNI) are closely related to its occurrence and development. Our previous results showed that the high expression of LC3 was positively correlated with PNI in the patients with pancreatic cancer. In this study, we further searched for differential genes involved in autophagy of pancreatic cancer by gene expression profiling and analyzed their biological functions in pancreatic cancer, which provides a theoretical basis for elucidating the pathophysiological mechanism of autophagy in pancreatic cancer and PNI.AIM To identify differentially expressed genes involved in pancreatic cancer autophagy and explore the pathogenesis at the molecular level.METHODS Two sets of gene expression profiles of pancreatic cancer/normal tissue(GSE16515 and GSE15471) were collected from the Gene Expression Omnibus.Significance analysis of microarrays algorithm was used to screen differentially expressed genes related to pancreatic cancer. Gene Ontology(GO) analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis were used to analyze the functional enrichment of the differentially expressed genes. Protein interaction data containing only differentially expressed genes was downloaded from String database and screened. Module mining was carried out by Cytoscape software and ClusterOne plug-in. The interaction relationship between the modules was analyzed and the pivot nodes between the functional modules were determined according to the information of the functional modules and the data of reliable protein interaction network.RESULTS Based on the above two data sets of pancreatic tissue total gene expression, 6098 and 12928 differentially expressed genes were obtained by analysis of genes with higher phenotypic correlation. After extracting the intersection of the two differential gene sets, 4870 genes were determined. GO a
基金supported by National Key Research and Development Project of Stem Cell and Transformation Research,No.2019YFA0112100Tianjin Key Research and Development Plan,Key Projects for Science and Technology Support,No.19YFZCSY00660(both to SQF)。
文摘Ferroptosis plays a key role in aggravating the progression of spinal cord injury(SCI),but the specific mechanism remains unknown.In this study,we constructed a rat model of T10 SCI using a modified Allen method.We identified 48,44,and 27 ferroptosis genes that were differentially expressed at 1,3,and 7 days after SCI induction.Compared with the sham group and other SCI subgroups,the subgroup at 1 day after SCI showed increased expression of the ferroptosis marker acyl-CoA synthetase long-chain family member 4 and the oxidative stress marker malondialdehyde in the injured spinal cord while glutathione in the injured spinal cord was lower.These findings with our bioinformatics results suggested that 1 day after SCI was the important period of ferroptosis progression.Bioinformatics analysis identified the following top ten hub ferroptosis genes in the subgroup at 1 day after SCI:STAT3,JUN,TLR4,ATF3,HMOX1,MAPK1,MAPK9,PTGS2,VEGFA,and RELA.Real-time polymerase chain reaction on rat spinal cord tissue confirmed that STAT3,JUN,TLR4,ATF3,HMOX1,PTGS2,and RELA mRNA levels were up-regulated and VEGFA,MAPK1 and MAPK9 mRNA levels were down-regulated.Ten potential compounds were predicted using the DSigDB database as potential drugs or molecules targeting ferroptosis to repair SCI.We also constructed a ferroptosis-related mRNA-miRNA-lncRNA network in SCI that included 66 lncRNAs,10 miRNAs,and 12 genes.Our results help further the understanding of the mechanism underlying ferroptosis in SCI.
文摘BACKGROUND Hepatocellular carcinoma(HCC)is a common malignant gastrointestinal tumor.There are currently few clinical diagnostic and prognostic markers for HCC.LncRNA cancer susceptibility candidate 9(CASC9)is a long-chain non-coding RNA discovered in recent years,and previous studies have found that lncRNA CASC9 participates in the occurrence and development of HCC,but its clinical value remains unclear.AIM To determine the expression of lncRNA CASC9 in HCC and its diagnostic and prognostic value.METHODS Data on CASC9 expression in patients with HCC were collected from the Cancer Genome Atlas(TCGA)database to analyze the relationship between CASC9 and patient survival.A total of 80 HCC patients treated in The First Affiliated Hospital of Guangxi Medical University from May 2012 to January 2014 were enrolled in the patient group,and 50 healthy subjects were enrolled in the control group during the same period.CASC9 expression in the two groups was determined using quantitative real-time polymerase chain reaction,and its diagnostic and prognostic value was analyzed based on the CASC9 data and pathological data in these HCC patients.The relationship between CASC9 and patient survival was assessed during the 5-year follow-up period.RESULTS Analysis of data from TCGA database revealed that control samples showed significantly lower CASC9 expression than carcinoma tissue samples(P<0.001);the low CASC9 expression group had a higher survival rate than the high CASC9 expression group(P=0.011),and the patient group showed significantly increased expression of serum CASC9,with the area under the curve(AUC)of 0.933.CASC9 expression was related to tumor size,combined hepatitis,tumor,node,metastasis(TNM)staging,lymph node metastasis,differentiation and alpha fetoprotein,and the high CASC9 expression group showed lower 1-year,3-year and 5-year survival rates than the low CASC9 expression group(all aP<0.05).Multivariate Cox regression analysis revealed that TNM staging,lymph node metastasis,differentiation,alpha fetoprotein and
基金Supported by Coordenao de Aperfeioamento de Pessoal de Nível Superior(CAPES)in Brazil,processes BEX 12954-12-8 and 11517-12-3,to Barbosa EGV and Aburjaile FF
文摘Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft(partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.
基金supported by the Deutsche Forschungsgemeinschaft(TRR175,project C01 to T.K.,project C02 to M.S.,project C04 to B.G.,project C05 to K.K.and D.L.,project C06 to A.S.R.,and project D03 to T.N.).
文摘Plastids communicate their developmental and physiological status to the nucleus via retrograde signaling,allowing nuclear gene expression to be adjusted appropriately.Signaling during plastid biogenesis and responses of mature chloroplasts to environmental changes are designated“biogenic”and“operational”controls,respectively.A prominent example of the investigation of biogenic signaling is the screen for gun(genomes uncoupled)mutants.Although the first five gun mutants were identified 30 years ago,the functions of GUN proteins in retrograde signaling remain controversial,and that of GUN1 is hotly disputed.Here,we provide background information and critically discuss recently proposed concepts that address GUN-related signaling and some novel gun mutants.Moreover,considering heme as a candidate in retrograde signaling,we revisit the spatial organization of heme biosynthesis and export from plastids.Although this review focuses on GUN pathways,we also highlight recent progress in the identification and elucidation of chloroplast-derived signals that regulate the acclimation response in green algae and plants.Here,stress-induced accumulation of unfolded/misassembled chloroplast proteins evokes a chloroplast-specific unfolded protein response,which leads to changes in the expression levels of nucleus-encoded chaperones and proteases to restore plastid protein homeostasis.We also address the importance of chloroplast-derived signals for activation of flavonoid biosynthesis leading to production of anthocyanins during stress acclimation through sucrose non-fermenting 1-related protein kinase 1.Finally,a framework for identification and quantification of intercompartmental signaling cascades at the proteomic and metabolomic levels is provided,and we discuss future directions of dissection of organelle-nucleus communication.
文摘While the peripheral nervous system has regenerative ability,restoration of sufficient function remains a challenge.Vimentin has been shown to be localized in axonal growth fronts and associated with nerve regeneration,including myelination,neuroplasticity,kinase signaling in nerve axoplasm,and cell migration;however,the mechanisms regulating its expression within Schwann cell（SC） remain unexplored.The aim of this study was to profile the spatial and temporal expression profile of micro RNA（mi RNA） in a regenerating rat sciatic nerve after transection,and explore the potential role of mi R-138-5 p targeting vimentin in SC proliferation and migration.A rat sciatic nerve transection model,utilizing a polyethylene nerve guide,was used to investigate mi RNA expression at 7,14,30,60,and 90 days during nerve regeneration.Relative levels of mi RNA expression were determined using microarray analysis and subsequently validated with quantitative real-time polymerase chain reaction.In vitro assays were conducted with cultured Schwann cells transfected with mi RNA mimics and assessed for migratory and proliferative potential.The top seven dysregulated mi RNAs reported in this study have been implicated in cell migration elsewhere,and GO and KEGG analyses predicted activities essential to wound healing.Transfection of one of these,mi RNA-138-5 p,into SCs reduced cell migration and proliferation.mi R-138-5 p has been shown to directly target vimentin in cancer cells,and the luciferase assay performed here in rat Schwann cells confirmed it.These results detail a role of mi R-138-5 p in rat peripheral nerve regeneration and expand on reports of it as an important regulator in the peripheral nervous system.
基金supported by the National Natural Science Foundation of China,Nos.81860409(to ZF),81660382(to ZF)Graduate Students Innovation Fund Project in Jiangxi Province of China,No.YC2019-B036(to YLT)。
文摘The exact mechanisms associated with secondary brain damage following traumatic brain injury(TBI)remain unclear;therefore,identifying the critical molecular mechanisms involved in TBI is essential.The m RNA expression microarray GSE2871 was downloaded from the Gene Expression Omnibus(GEO)repository.GSE2871 comprises a total of 31 cerebral cortex samples,including two post-TBI time points.The microarray features eight control and seven TBI samples,from 4 hours post-TBI,and eight control and eight TBI samples from 24 hours post-TBI.In this bioinformatics-based study,109 and 66 differentially expressed genes(DEGs)were identified in a Sprague-Dawley(SD)rat TBI model,4 and 24 hours post-TBI,respectively.Functional enrichment analysis showed that the identified DEGs were significantly enriched in several terms,such as positive regulation of nuclear factor-κB transcription factor activity,mitogen-activated protein kinase signaling pathway,negative regulation of apoptotic process,and tumor necrosis factor signaling pathway.Moreover,the hub genes with high connectivity degrees were primarily related to inflammatory mediators.To validate the top five hub genes,a rat model of TBI was established using the weight-drop method,and real-time quantitative polymerase chain reaction analysis of the cerebral cortex was performed.The results showed that compared with control rats,Tnf-α,c-Myc,Spp1,Cxcl10,Ptprc,Egf,Mmp9,and Lcn2 were upregulated,and Fn1 was downregulated in TBI rats.Among these hub genes,Fn1,c-Myc,and Ptprc may represent novel biomarkers or therapeutic targets for TBI.These identified pathways and key genes may provide insights into the molecular mechanisms of TBI and provide potential treatment targets for patients with TBI.This study was approved by the Experimental Animal Ethics Committee of the First Affiliated Hospital of Nanchang University,China(approval No.003)in January 2016.
基金Supported by the Eleventh Five-year Development Planning Project for Instructional Science in Hubei Province (2006B131)~~
文摘MATLAB software and optimal complete subgraph algorithm were used to extract and reveal the microsatellite distribution features in the complete genomes of the tobacco vein clearing virus （NC-003 378.1） from the NCBI database.The results showed that the repetitions number and their location of the N-base group has been extracted and displayed.The largest repetitions of N-base group in the complete genomes of the tobacco vein clearing virus was decreased as the exponential function with the increasing of N.The method used in this study could be applied to the extraction and revealing of the microsatellite distribution features in the complete genomes of other viruses,thereby provided a basis for the research of the structure and the law of function,inheritance and variation by the using of the microsatellite distribution features.
基金This review reflects decades of personally treasured friendships and assistance from colleagues in the insectplant interactions field of study. The Papilionidae research from our laboratory was supported by such academic synergism and also in part by the National Science Foundation （DEB-9201122 DEB-9510044+1 种基金 DEB 0716683 DEB 0918879） and the Michigan Agricultural Experiment Station （Project # 01644）. I wish to thank all laboratory members and friends for their enthusiasm and assistance over the years, and most recently, Matthew Aardema, Rodrigo Mercader and Gabe Ording. Special thanks are extended to one particularly helpful reviewer.
文摘The ecology and evolutionary biology of insect-plant associations has real- ized extensive attention, especially during the past 60 years. The classifications （categorical designations） of continuous variation in biodiversity, ranging from global patterns （e.g., lat- itudinal gradients in species richness/diversity and degree of herbivore feeding specialization） to localized insect-plant associations that span the biospectrum from polyphenisms, polymorphisms, biotypes, demes, host races, to cryptic species, remain academically contentious. Semantic and biosystematic （taxonomical） disagreements sometimes detract from more important ecological and evolutionary processes that drive diversification, the dynamics of gene flow and local extinctions. This review addresses several aspects of insect specialization, host-associated divergence and ecological （including ＂hybrid＂） speciation, with special reference to the climate warming impacts on species borders of hybridiz- ing swallowtail butterflies （Papilionidae）. Interspecific hybrid introgression may result in collapse of multi-species communities or increase species numbers via homoploid hybrid speciation. We may see diverging, merging, or emerging genotypes across hybrid zones, all part of the ongoing processes of evolution. Molecular analyses of genetic mosaics and genomic dynamics with ＂divergence hitchhiking＂, combined with ecological, ethological and physiological studies of＂species porosity＂, have already begun to unveil some answers for some important ecological/evolutionary questions. （i） How rapidly can host-associated divergence lead to new species （and why doesn＇t it always do so, e.g., resulting in ＂incom- plete＂ speciation）？ （ii） How might ＂speciation genes＂ function, and how/where would we find them？ （iii） Can oscillations from specialists to generalists and back to specialists help explain global diversity in herbivorous insects？ （iv） How could recombinant interspecific hybridization l
基金supported by the National Natural Science Foundation of China (Grant No. 31070015)the Special Project for Fundamental Research (Grant No. 2006FY120100) from Ministry of Science and Technology of Chinathe Knowledge Innovation Program of Chinese Academy of Sciences (Grant No. KSCX2-EW-J-6)
文摘A DNA barcode is a short segment of sequence that is able to distinguish species. A barcode must ideally contain enough variation to distinguish every individual species and be easily obtained. Fungi of Nectriaceae are economically important and show high species diversity. To establish a standard DNA barcode for this group of fungi, the genomes of Neurospora crassa and 30 other filamentous fungi were compared. The expect value was treated as a criterion to recognize homologous sequences. Four candidate markers, Hsp90, AAC, CDC48, and EF3, were tested for their feasibility as barcodes in the identification of 34 well-established species belonging to 13 genera of Nectriaceae. Two hundred and fifteen sequences were analyzed. Intraand inter-specific variations and the success rate of PCR amplification and sequencing were considered as important criteria for estimation of the candidate markers. Ultimately, the partial EF3 gene met the requirements for a good DNA barcode: No overlap was found between the intra-and inter-specific pairwise distances. The smallest inter-specific distance of EF3 gene was 3.19%, while the largest intra-specific distance was 1.79%. In addition, there was a high success rate in PCR and sequencing for this gene (96.3%). CDC48 showed sufficiently high sequence variation among species, but the PCR and sequencing success rate was 84% using a single pair of primers. Although the Hsp90 and AAC genes had higher PCR and sequencing success rates (96.3% and 97.5%, respectively), overlapping occurred between the intraand inter-specific variations, which could lead to misidentification. Therefore, we propose the EF3 gene as a possible DNA barcode for the nectriaceous fungi.
基金funded by the Jiangxi Provincial Natural Science Foundation,Grant Number 20232BAB216119.
文摘Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae.The cp genomes,vary-ing in size from 153,366 to 159,895 bp,followed the typical quadripartite organization consisting of a large single-copy(LSC)region(84,545 to 87,883 bp),a small single-copy(SSC)region(18,174 to 19,259 bp),and a pair of inverted repeat(IR)regions(25,310 to 26,396 bp).These genomes contained 132–138 annotated genes,including 87 to 93 protein-coding genes(PCGs),37 tRNA genes,and 8 rRNA genes using MISA software,52 to 121 simple sequence repeat(SSR)loci were identified.D.arbuscular contained the least of SSRs and did not have hexanotides,A.lineata contained the richest SSRs.Long terminal repeats(LTRs)were primarily composed of palindromic and forward repeat sequences,meanwhile,The richest LTRs were found in Argentina lineata.Except for Argentina lineata,Fragariastrum eriocarpum,and Prunus trichostoma,which varied in gene type and position on both sides of the boundary,the remaining species were found to be mostly conserved according to IR boundary analysis.The examination of the Ka/Ks ratio revealed that only the infA gene had a value greater than 1,indicating that this gene was primarily subjected to positive selection during evolution.Additionally,9 hotspots of variation were identified in the LSC and SSC regions.Phylogenetic analysis confirmed the scientific validity of the genus Prunus L.sensu lato(s.l.)within the Rosaceae family.The separation of the three genera Argentina Hill,Fragariastrum Heist.ex Fabr.and Dasiphora Raf.from Potentilla L.may be a more scientific classification.These results offer fresh perspectives on the taxonomy of the Rosaceae.
文摘Following in the footsteps of traditional developmental genetics, research over the last 15 years has shown that innate immunity against bacteria and fungi is governed largely by two NF-κB signal transduction pathways, Toll and IMD. Antiviral immunity appears to stem from RNA interference, whereas resistance against parasitoids is conferred by Toll signaling. The identification of these post-transcriptional regulatory mechanisms and the annotation of most Drosophila immunity genes have derived from functional genomic studies using ＂model＂ pathogens, intact animals and cell lines. The D. melanogaster host has thus provided the core information that can be used to study responses to natural microbial and metazoan pathogens as they become identified, as well as to test ideas of selection and evolutionary change. These analyses are of general importance to understanding mechanisms of other insect host-pathogen interactions and determinants of variation in host resistance.
