Cotton fibers elongate rapidly after initiation of elongation, eventually leading to the deposit of a large amount of cellulose. To reveal features of cotton fiber cells at the fast elongation and the secondary cell w...Cotton fibers elongate rapidly after initiation of elongation, eventually leading to the deposit of a large amount of cellulose. To reveal features of cotton fiber cells at the fast elongation and the secondary cell wall synthesis stages, we compared the respective transcriptomes and metabolite profiles. Comparative analysis of transcriptomes by cDNA array identified 633 genes that were differentially regulated during fiber development. Principal component analysis （PCA） using expressed genes as variables divided fiber samples into four groups, which are diagnostic of developmental stages. Similar grouping results are also found if we use non-polar or polar metabolites as variables for PCA of developing fibers. Auxin signaling, wall-loosening and lipid metabolism are highly active during fiber elongation, whereas cellulose biosynthesis is predominant and many other metabolic pathways are downregulated at the secondary cell wall synthesis stage. Transcript and metabolite profiles and enzyme activities are consistent in demonstrating a specialization process of cotton fiber development toward cellulose synthesis. These data demonstrate that cotton fiber cell at a certain stage has its own unique feature, and developmental stages of cotton fiber cells can be distinguished by their transcript and metabolite profiles. During the secondary cell wall synthesis stage, metabolic pathways are streamed into cellulose synthesis.展开更多
Research has shown that the hypomagnetic field(HMF)can affect embryo development,cell proliferation,learning and memory,and in vitro tubulin assembly.In the present study,we aimed to elucidate the molecular mechanism ...Research has shown that the hypomagnetic field(HMF)can affect embryo development,cell proliferation,learning and memory,and in vitro tubulin assembly.In the present study,we aimed to elucidate the molecular mechanism by which the HMF exerts its effect,by comparing the transcriptome profiles of human neuroblastoma cells exposed to either the HMF or the geomagnetic field.A total of 2464 differentially expressed genes(DEGs)were identified,216 of which were up-regulated and2248 of which were down-regulated after exposure to the HMF.These DEGs were found to be significantly clustered into several key processes,namely macromolecule localization,protein transport,RNA processing,and brain function.Seventeen DEGs were verified by real-time quantitative PCR,and the expression levels of nine of these DEGs were measured every 6 h.Most notably,MAPK1 and CRY2,showed significant up-and down-regulation,respectively,during the first 6 h of HMF exposure,which suggests involvement of the MAPK pathway and cryptochrome in the early bio-HMF response.Our results provide insights into the molecular mechanisms underlying the observed biological effects of the HMF.展开更多
Peripheral nerve injury may trigger changes in mRNA levels in the spinal cord.Finding key mRNAs is important for improving repair after nerve injury.This study aimed to investigate changes in mRNAs in the spinal cord ...Peripheral nerve injury may trigger changes in mRNA levels in the spinal cord.Finding key mRNAs is important for improving repair after nerve injury.This study aimed to investigate changes in mRNAs in the spinal cord following sciatic nerve injury by transcriptomic analysis.The left sciatic nerve denervation model was established in C57 BL/6 mice.The left L4–6 spinal cord segment was obtained at 0,1,2,4 and 8 weeks after severing the sciatic nerve.mRNA expression profiles were generated by RNA sequencing.The sequencing results of spinal cord mRNA at 1,2,4,and 8 weeks after severing the sciatic nerve were compared with those at 0 weeks by bioinformatic analysis.We identified 1915 differentially expressed mRNAs in the spinal cord,of which 4,1909,and 2 were differentially expressed at 1,4,and 8 weeks after sciatic nerve injury,respectively.Sequencing results indicated that the number of differentially expressed mRNAs in the spinal cord was highest at 4 weeks after sciatic nerve injury.These mRNAs were associated with the cellular response to lipid,ATP metabolism,energy coupled proton transmembrane transport,nuclear transcription factor complex,vacuolar proton-transporting V-type ATPase complex,inner mitochondrial membrane protein complex,tau protein binding,NADH dehydrogenase activity and hydrogen ion transmembrane transporter activity.Of these mRNAs,Sgk1,Neurturin and Gpnmb took part in cell growth and development.Pathway analysis showed that these mRNAs were mainly involved in aldosterone-regulated sodium reabsorption,oxidative phosphorylation and collecting duct acid secretion.Functional assessment indicated that these mRNAs were associated with inflammation and cell morphology development.Our findings show that the number and type of spinal cord mRNAs involved in changes at different time points after peripheral nerve injury were different.The number of differentially expressed mRNAs in the spinal cord was highest at 4 weeks after sciatic nerve injury.These results provide reference data for finding new target展开更多
Chimeric antigen receptor (CAR) T cell therapy has exhibited dramatic anti-tumor effi-cacy in clinical trials. In this study,we reported the transcriptome profiles of bone marrow cells in four B cell acute lymphoblast...Chimeric antigen receptor (CAR) T cell therapy has exhibited dramatic anti-tumor effi-cacy in clinical trials. In this study,we reported the transcriptome profiles of bone marrow cells in four B cell acute lymphoblastic leukemia (B-ALL) patients before and after CD19-specific CAR-T therapy. CD19-CAR-T therapy remarkably reduced the number of leukemia cells,and three patients achieved bone marrow remission (minimal residual disease negative). The efficacy of CD19-CAR-T therapy on B-ALL was positively correlated with the abundance of CAR and immune cell subpopulations,e.g.,CD8+T cells and natural killer (NK) cells,in the bone marrow. Additionally,CD19-CAR-T therapy mainly influenced the expression of genes linked to cell cycle and immune response pathways,including the NK cell mediated cytotoxicity and NOD-like recep-tor signaling pathways. The regulatory network analyses revealed that microRNAs (e.g.,miR-148a-3p and miR-375),acting as oncogenes or tumor suppressors,could regulate the crosstalk between the genes encoding transcription factors (TFs,e.g.,JUN and FOS) and histones (e.g.,HIST1H4A and HIST2H4A) involved in CD19-CAR-T therapy. Furthermore,many long non-coding RNAs showed a high degree of co-expression with TFs or histones (e.g.,FOS and HIST1H4B) and were associated with immune processes. These transcriptome analyses provided important clues for fur-ther understanding the gene expression and related mechanisms underlying the efficacy of CAR-T immunotherapy.展开更多
【目的】基于沟眶象属Eucryptorrhynchus两近缘种沟眶象E.scrobiculatus和臭椿沟眶象E.brandti不同虫态的转录组数据进行气味受体(odorant receptor,OR)基因的鉴定及表达特征分析,补充两种象甲的气味受体信息,为之后的功能研究提供理论...【目的】基于沟眶象属Eucryptorrhynchus两近缘种沟眶象E.scrobiculatus和臭椿沟眶象E.brandti不同虫态的转录组数据进行气味受体(odorant receptor,OR)基因的鉴定及表达特征分析,补充两种象甲的气味受体信息,为之后的功能研究提供理论依据。【方法】从沟眶象(幼虫、蛹和成虫)和臭椿沟眶象(卵、幼虫、蛹和成虫)不同虫态转录组数据库中筛选OR基因序列;基于两种象甲触角转录组数据,对两种象甲筛选得到的ORs进行种间和种内的序列比对;利用最大似然法对两种象甲新鉴定的ORs进行系统发育分析;根据两种象甲不同虫态转录组数据中OR基因的FPKM(fragments per kilobase per million mapped fragments)值对新鉴定的OR基因进行表达丰度分析;利用qPCR检测新鉴定的OR基因在沟眶象和臭椿沟眶象不同发育阶段和成虫不同组织中的表达谱。【结果】从沟眶象和臭椿沟眶象不同虫态转录组数据库中分别鉴定出6和4个OR基因,都具有完整的开放阅读框。根据与触角转录组数据的序列比对结果,从沟眶象和臭椿沟眶象分别新鉴定出4个(EscrOR50-53)和2个(EbraOR46-47)OR基因;在两象甲种间发现了一对可能的同源基因EscrOR53和EbraOR45。系统发育树显示,6个新鉴定的OR蛋白分属于鞘翅目OR亚家族2B和7。结合不同虫态转录组的FPKM数据及qPCR检测的时空表达谱得知,沟眶象3个和臭椿沟眶象2个新鉴定到的OR基因均在成虫的非嗅觉组织中高表达,且在卵、幼虫或蛹期也有表达。【结论】本研究明确了沟眶象和臭椿沟眶象不同虫态转录组中的气味受体基因及其时空表达谱,并且发现两种象甲的生殖器官中可能存在非嗅觉的功能性的ORs,提示其可能在发育的早期阶段就已发挥功能。展开更多
The unicellular green alga Dunaliella salina is well adapted to salt stress and contains compounds（including β-carotene and vitamins） with potential commercial value.A large transcriptome database of D.salina durin...The unicellular green alga Dunaliella salina is well adapted to salt stress and contains compounds（including β-carotene and vitamins） with potential commercial value.A large transcriptome database of D.salina during the adjustment, exponential and stationary growth phases was generated using a high throughput sequencing platform.We characterized the metabolic processes in D.salina with a focus on valuable metabolites, with the aim of manipulating D.salina to achieve greater economic value in large-scale production through a bioengineering strategy.Gene expression profiles under salt stress verified using quantitative polymerase chain reaction（qPCR） implied that salt can regulate the expression of key genes.This study generated a substantial fraction of D.salina transcriptional sequences for the entire growth cycle, providing a basis for the discovery of novel genes.This first full-scale transcriptome study of D.salina establishes a foundation for further comparative genomic studies.展开更多
文摘Cotton fibers elongate rapidly after initiation of elongation, eventually leading to the deposit of a large amount of cellulose. To reveal features of cotton fiber cells at the fast elongation and the secondary cell wall synthesis stages, we compared the respective transcriptomes and metabolite profiles. Comparative analysis of transcriptomes by cDNA array identified 633 genes that were differentially regulated during fiber development. Principal component analysis （PCA） using expressed genes as variables divided fiber samples into four groups, which are diagnostic of developmental stages. Similar grouping results are also found if we use non-polar or polar metabolites as variables for PCA of developing fibers. Auxin signaling, wall-loosening and lipid metabolism are highly active during fiber elongation, whereas cellulose biosynthesis is predominant and many other metabolic pathways are downregulated at the secondary cell wall synthesis stage. Transcript and metabolite profiles and enzyme activities are consistent in demonstrating a specialization process of cotton fiber development toward cellulose synthesis. These data demonstrate that cotton fiber cell at a certain stage has its own unique feature, and developmental stages of cotton fiber cells can be distinguished by their transcript and metabolite profiles. During the secondary cell wall synthesis stage, metabolic pathways are streamed into cellulose synthesis.
基金supported by the Queensland-Chinese Academy of Sciences(QCAS)Biotechnology Fund(GJHZ1131)the Project of Chinese Academy of Sciences for the Development of Major Scientific Research Equipment(YZ201148)+1 种基金the National Natural Science Foundation of China(31200628)the External Cooperation Program of Bureau of International Cooperation,Chinese Academy of Sciences(GJHZ201302)
文摘Research has shown that the hypomagnetic field(HMF)can affect embryo development,cell proliferation,learning and memory,and in vitro tubulin assembly.In the present study,we aimed to elucidate the molecular mechanism by which the HMF exerts its effect,by comparing the transcriptome profiles of human neuroblastoma cells exposed to either the HMF or the geomagnetic field.A total of 2464 differentially expressed genes(DEGs)were identified,216 of which were up-regulated and2248 of which were down-regulated after exposure to the HMF.These DEGs were found to be significantly clustered into several key processes,namely macromolecule localization,protein transport,RNA processing,and brain function.Seventeen DEGs were verified by real-time quantitative PCR,and the expression levels of nine of these DEGs were measured every 6 h.Most notably,MAPK1 and CRY2,showed significant up-and down-regulation,respectively,during the first 6 h of HMF exposure,which suggests involvement of the MAPK pathway and cryptochrome in the early bio-HMF response.Our results provide insights into the molecular mechanisms underlying the observed biological effects of the HMF.
基金supported by the National Natural Science Foundation of China,No.81671215(to XFY),No.31571002(to BGJ)the Natural Science Foundation of Beijing of China,No.7192215(to XFY)
文摘Peripheral nerve injury may trigger changes in mRNA levels in the spinal cord.Finding key mRNAs is important for improving repair after nerve injury.This study aimed to investigate changes in mRNAs in the spinal cord following sciatic nerve injury by transcriptomic analysis.The left sciatic nerve denervation model was established in C57 BL/6 mice.The left L4–6 spinal cord segment was obtained at 0,1,2,4 and 8 weeks after severing the sciatic nerve.mRNA expression profiles were generated by RNA sequencing.The sequencing results of spinal cord mRNA at 1,2,4,and 8 weeks after severing the sciatic nerve were compared with those at 0 weeks by bioinformatic analysis.We identified 1915 differentially expressed mRNAs in the spinal cord,of which 4,1909,and 2 were differentially expressed at 1,4,and 8 weeks after sciatic nerve injury,respectively.Sequencing results indicated that the number of differentially expressed mRNAs in the spinal cord was highest at 4 weeks after sciatic nerve injury.These mRNAs were associated with the cellular response to lipid,ATP metabolism,energy coupled proton transmembrane transport,nuclear transcription factor complex,vacuolar proton-transporting V-type ATPase complex,inner mitochondrial membrane protein complex,tau protein binding,NADH dehydrogenase activity and hydrogen ion transmembrane transporter activity.Of these mRNAs,Sgk1,Neurturin and Gpnmb took part in cell growth and development.Pathway analysis showed that these mRNAs were mainly involved in aldosterone-regulated sodium reabsorption,oxidative phosphorylation and collecting duct acid secretion.Functional assessment indicated that these mRNAs were associated with inflammation and cell morphology development.Our findings show that the number and type of spinal cord mRNAs involved in changes at different time points after peripheral nerve injury were different.The number of differentially expressed mRNAs in the spinal cord was highest at 4 weeks after sciatic nerve injury.These results provide reference data for finding new target
基金the National Natural Science Foundation of China (Grant Nos. 31822030, 31801113, and 31771458)the National Key R&D Program of China (Grant No. 2017YFA0700403)China Postdoctoral Science Foundation (Grant No. 2018M632830)
文摘Chimeric antigen receptor (CAR) T cell therapy has exhibited dramatic anti-tumor effi-cacy in clinical trials. In this study,we reported the transcriptome profiles of bone marrow cells in four B cell acute lymphoblastic leukemia (B-ALL) patients before and after CD19-specific CAR-T therapy. CD19-CAR-T therapy remarkably reduced the number of leukemia cells,and three patients achieved bone marrow remission (minimal residual disease negative). The efficacy of CD19-CAR-T therapy on B-ALL was positively correlated with the abundance of CAR and immune cell subpopulations,e.g.,CD8+T cells and natural killer (NK) cells,in the bone marrow. Additionally,CD19-CAR-T therapy mainly influenced the expression of genes linked to cell cycle and immune response pathways,including the NK cell mediated cytotoxicity and NOD-like recep-tor signaling pathways. The regulatory network analyses revealed that microRNAs (e.g.,miR-148a-3p and miR-375),acting as oncogenes or tumor suppressors,could regulate the crosstalk between the genes encoding transcription factors (TFs,e.g.,JUN and FOS) and histones (e.g.,HIST1H4A and HIST2H4A) involved in CD19-CAR-T therapy. Furthermore,many long non-coding RNAs showed a high degree of co-expression with TFs or histones (e.g.,FOS and HIST1H4B) and were associated with immune processes. These transcriptome analyses provided important clues for fur-ther understanding the gene expression and related mechanisms underlying the efficacy of CAR-T immunotherapy.
文摘【目的】基于沟眶象属Eucryptorrhynchus两近缘种沟眶象E.scrobiculatus和臭椿沟眶象E.brandti不同虫态的转录组数据进行气味受体(odorant receptor,OR)基因的鉴定及表达特征分析,补充两种象甲的气味受体信息,为之后的功能研究提供理论依据。【方法】从沟眶象(幼虫、蛹和成虫)和臭椿沟眶象(卵、幼虫、蛹和成虫)不同虫态转录组数据库中筛选OR基因序列;基于两种象甲触角转录组数据,对两种象甲筛选得到的ORs进行种间和种内的序列比对;利用最大似然法对两种象甲新鉴定的ORs进行系统发育分析;根据两种象甲不同虫态转录组数据中OR基因的FPKM(fragments per kilobase per million mapped fragments)值对新鉴定的OR基因进行表达丰度分析;利用qPCR检测新鉴定的OR基因在沟眶象和臭椿沟眶象不同发育阶段和成虫不同组织中的表达谱。【结果】从沟眶象和臭椿沟眶象不同虫态转录组数据库中分别鉴定出6和4个OR基因,都具有完整的开放阅读框。根据与触角转录组数据的序列比对结果,从沟眶象和臭椿沟眶象分别新鉴定出4个(EscrOR50-53)和2个(EbraOR46-47)OR基因;在两象甲种间发现了一对可能的同源基因EscrOR53和EbraOR45。系统发育树显示,6个新鉴定的OR蛋白分属于鞘翅目OR亚家族2B和7。结合不同虫态转录组的FPKM数据及qPCR检测的时空表达谱得知,沟眶象3个和臭椿沟眶象2个新鉴定到的OR基因均在成虫的非嗅觉组织中高表达,且在卵、幼虫或蛹期也有表达。【结论】本研究明确了沟眶象和臭椿沟眶象不同虫态转录组中的气味受体基因及其时空表达谱,并且发现两种象甲的生殖器官中可能存在非嗅觉的功能性的ORs,提示其可能在发育的早期阶段就已发挥功能。
基金Project supported by the National High-Tech R&D Program(863)of China(No.2007AA09Z449)
文摘The unicellular green alga Dunaliella salina is well adapted to salt stress and contains compounds（including β-carotene and vitamins） with potential commercial value.A large transcriptome database of D.salina during the adjustment, exponential and stationary growth phases was generated using a high throughput sequencing platform.We characterized the metabolic processes in D.salina with a focus on valuable metabolites, with the aim of manipulating D.salina to achieve greater economic value in large-scale production through a bioengineering strategy.Gene expression profiles under salt stress verified using quantitative polymerase chain reaction（qPCR） implied that salt can regulate the expression of key genes.This study generated a substantial fraction of D.salina transcriptional sequences for the entire growth cycle, providing a basis for the discovery of novel genes.This first full-scale transcriptome study of D.salina establishes a foundation for further comparative genomic studies.
