AIM:To identify the genes induced and regulated by the MYC protein in generating tumors from liver stem cells.METHODS:In this study,we have used an immortal porcine liver stem cell line,PICM-19,to study the role of c-...AIM:To identify the genes induced and regulated by the MYC protein in generating tumors from liver stem cells.METHODS:In this study,we have used an immortal porcine liver stem cell line,PICM-19,to study the role of c-MYC in hepatocarcinogenesis.PICM-19 cells were converted into cancer cells(PICM-19-CSCs)by overexpressing human MYC.To identify MYC-driven differential gene expression,transcriptome sequencing was carried out by RNA sequencing,and genes identified by this method were validated using real-time PCR.In vivo tumorigenicity studies were then conducted by injecting PICM-19-CSCs into the flanks of immunodeficient mice.RESULTS:Our results showed that MYC-overexpressing PICM-19 stem cells formed tumors in immunodeficient mice demonstrating that a single oncogene was sufficient to convert them into cancer cells(PICM-19-CSCs).By using comparative bioinformatics analyses,we have determined that>1000 genes were differentially expressed between PICM-19 and PICM-19-CSCs.Gene ontology analysis further showed that the MYCinduced,altered gene expression was primarily associated with various cellular processes,such as metabolism,cell adhesion,growth and proliferation,cell cycle,inflammation and tumorigenesis.Interestingly,six genes expressed by PICM-19 cells(CDO1,C22orf39,DKK2,ENPEP,GPX6,SRPX2)were completely silenced after MYC-induction in PICM-19-CSCs,suggesting that the absence of these genes may be critical for inducingtumorigenesis.CONCLUSION:MYC-driven genes may serve as promising candidates for the development of hepatocellular carcinoma therapeutics that would not have deleterious effects on other cell types in the liver.展开更多
We propose a quantum-mechanical Brayton engine model that works between two superposed states,employing a single particle confined in an arbitrary power-law trap as the working substance. Applying the superposition pr...We propose a quantum-mechanical Brayton engine model that works between two superposed states,employing a single particle confined in an arbitrary power-law trap as the working substance. Applying the superposition principle,we obtain the explicit expressions of the power and efficiency,and find that the efficiency at maximum power is bounded from above by the function: η+= θ/(θ+1),with θ being a potential-dependent exponent.展开更多
The development of genomic sequencing technology,from conventional techniques to state-of-the-art inventions,has greatly improved our understanding of genetic material.This review examines important advancements in se...The development of genomic sequencing technology,from conventional techniques to state-of-the-art inventions,has greatly improved our understanding of genetic material.This review examines important advancements in sequencing techniques and how they have revolutionized genomics research.Highthroughput capabilities made possible by next-generation sequencing(NGS)have enabled quick and affordable genomic analysis.Digital gene expression profiling was made possible by methods such as serial analysis of gene expression(SAGE),whereas long-read capabilities without amplification were analyzed by single-molecule sequencing,as demonstrated by Oxford Nanopore’s nanopore-based sequencing and PacBio’s single-molecule real-time(SMRT)technology.Synthetic long-read sequencing is one example of a hybrid technique that enhances genome assembly.New techniques,such as epigenetic sequencing,have revealed that DNA alterations are essential for gene control,and spatial transcriptomics has connected gene expression to tissue-specific patterns.Target analysis and knowledge of microbial ecosystems were further enhanced via the use of sophisticated techniques,including metagenomics and CRISPRCas9-based sequencing.When combined,these techniques allow researchers to examine microbial communities,transcriptome diversity,genomic structure,and epigenetic changes with new clarity.For example,single-cell sequencing has shown molecular heterogeneity between cells,and long-read sequencing has revealed intricate isoform variants.Personalized medicine has advanced owing to spatial transcriptomics,which targets gene expression in specific organs.Digital sequencing has also improved the sensitivity of mutation identification,transforming the diagnosis of the disease.The convergence of sequencing technologies has ushered in a new era of genomic studies,opening the door to groundbreaking findings in ecology,biology,and medicine.Future developments will improve knowledge of human genetics by further improving sequencing accuracy,affordability,and applicability.展开更多
There are now more than 300000 RNA sequencing samples available,stemming from thousands of exper-iments capturing gene expression in organs,tissues,developmental stages,and experimental treatments for hundreds of plan...There are now more than 300000 RNA sequencing samples available,stemming from thousands of exper-iments capturing gene expression in organs,tissues,developmental stages,and experimental treatments for hundreds of plant species.The expression data have great value,as they can be re-analyzed by others to ask and answer questions that go beyond the aims of the study that generated the data.Because gene expression provides essential clues to where and when a gene is active,the data provide powerful tools for predicting gene function,and comparative analyses allow us to study plant evolution from a new perspective.This review describes how we can gain new knowledge from gene expression profiles,expres-sion specificities,co-expression networks,differential gene expression,and experiment correlation.We also introduce and demonstrate databases that provide user-friendly access to these tools.展开更多
基金Supported by Departmental funds to Dr.Aravalli RN
文摘AIM:To identify the genes induced and regulated by the MYC protein in generating tumors from liver stem cells.METHODS:In this study,we have used an immortal porcine liver stem cell line,PICM-19,to study the role of c-MYC in hepatocarcinogenesis.PICM-19 cells were converted into cancer cells(PICM-19-CSCs)by overexpressing human MYC.To identify MYC-driven differential gene expression,transcriptome sequencing was carried out by RNA sequencing,and genes identified by this method were validated using real-time PCR.In vivo tumorigenicity studies were then conducted by injecting PICM-19-CSCs into the flanks of immunodeficient mice.RESULTS:Our results showed that MYC-overexpressing PICM-19 stem cells formed tumors in immunodeficient mice demonstrating that a single oncogene was sufficient to convert them into cancer cells(PICM-19-CSCs).By using comparative bioinformatics analyses,we have determined that>1000 genes were differentially expressed between PICM-19 and PICM-19-CSCs.Gene ontology analysis further showed that the MYCinduced,altered gene expression was primarily associated with various cellular processes,such as metabolism,cell adhesion,growth and proliferation,cell cycle,inflammation and tumorigenesis.Interestingly,six genes expressed by PICM-19 cells(CDO1,C22orf39,DKK2,ENPEP,GPX6,SRPX2)were completely silenced after MYC-induction in PICM-19-CSCs,suggesting that the absence of these genes may be critical for inducingtumorigenesis.CONCLUSION:MYC-driven genes may serve as promising candidates for the development of hepatocellular carcinoma therapeutics that would not have deleterious effects on other cell types in the liver.
基金Supported by the National Natural Science Foundation of China under Grant Nos.1150509111265010+1 种基金and 11365015the Jiangxi Provincial Natural Science Foundation under Grant No.20132BAB212009
文摘We propose a quantum-mechanical Brayton engine model that works between two superposed states,employing a single particle confined in an arbitrary power-law trap as the working substance. Applying the superposition principle,we obtain the explicit expressions of the power and efficiency,and find that the efficiency at maximum power is bounded from above by the function: η+= θ/(θ+1),with θ being a potential-dependent exponent.
文摘The development of genomic sequencing technology,from conventional techniques to state-of-the-art inventions,has greatly improved our understanding of genetic material.This review examines important advancements in sequencing techniques and how they have revolutionized genomics research.Highthroughput capabilities made possible by next-generation sequencing(NGS)have enabled quick and affordable genomic analysis.Digital gene expression profiling was made possible by methods such as serial analysis of gene expression(SAGE),whereas long-read capabilities without amplification were analyzed by single-molecule sequencing,as demonstrated by Oxford Nanopore’s nanopore-based sequencing and PacBio’s single-molecule real-time(SMRT)technology.Synthetic long-read sequencing is one example of a hybrid technique that enhances genome assembly.New techniques,such as epigenetic sequencing,have revealed that DNA alterations are essential for gene control,and spatial transcriptomics has connected gene expression to tissue-specific patterns.Target analysis and knowledge of microbial ecosystems were further enhanced via the use of sophisticated techniques,including metagenomics and CRISPRCas9-based sequencing.When combined,these techniques allow researchers to examine microbial communities,transcriptome diversity,genomic structure,and epigenetic changes with new clarity.For example,single-cell sequencing has shown molecular heterogeneity between cells,and long-read sequencing has revealed intricate isoform variants.Personalized medicine has advanced owing to spatial transcriptomics,which targets gene expression in specific organs.Digital sequencing has also improved the sensitivity of mutation identification,transforming the diagnosis of the disease.The convergence of sequencing technologies has ushered in a new era of genomic studies,opening the door to groundbreaking findings in ecology,biology,and medicine.Future developments will improve knowledge of human genetics by further improving sequencing accuracy,affordability,and applicability.
基金supported by a Singapore Ministry of Education tier-two grant(MOE2018-T2-2-053)a Singapore Food Agency grant(SFS_RND_SUFP_001_05).
文摘There are now more than 300000 RNA sequencing samples available,stemming from thousands of exper-iments capturing gene expression in organs,tissues,developmental stages,and experimental treatments for hundreds of plant species.The expression data have great value,as they can be re-analyzed by others to ask and answer questions that go beyond the aims of the study that generated the data.Because gene expression provides essential clues to where and when a gene is active,the data provide powerful tools for predicting gene function,and comparative analyses allow us to study plant evolution from a new perspective.This review describes how we can gain new knowledge from gene expression profiles,expres-sion specificities,co-expression networks,differential gene expression,and experiment correlation.We also introduce and demonstrate databases that provide user-friendly access to these tools.
