Objective: The aim of this study was to establish reproducible two-dimensional electrophoretic assay used for profiling and identification of differentially expressed proteins in human stage I lung adenocarcinoma and...Objective: The aim of this study was to establish reproducible two-dimensional electrophoretic assay used for profiling and identification of differentially expressed proteins in human stage I lung adenocarcinoma and paired normal tumor-adjacent tissue. Methods: The proteins from 12 human stage I lung adenocarcinoma tissues and normal tumor-adjacent tissues were separated using isoelectric focusing electrophoresis (the first dimension) and the subsequent homogeneous SDS-polyacrylamide gel electrophoresis (SDS-PAGE) (the second dimension). The differentially expressed proteins were determined with PDQuest image analysis software, and identified using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and database searching. Results: The well-reproducible 2-DE gel patterns of human stage I lung adenocarcinoma and normal tumor-adjacent tissues were profiled and 26 differentially expressed proteins uncovered. Nine of these 26 protein spots were cut out from the preparation gels and determined with MALDI-TOF-MS. Searching against the protein database, four candidate proteins were identified. They were 60S acidic ribosomal protein P2, Cathepsin B1, Apolipoprotein A-I precursor, and La 4.1 protein. Conclusion: In this study, high reproducible 2-DE gel protein images of human stage I lung adenocarcinoma and paired normal tumor-adjacent tissues were achieved successfully, and 4 differentially expressed proteins were revealed. These data will be helpful for screen of early biomarker and study of molecular mechanisms of human lung adenocarcinoma.展开更多
In the 21st Century of the increasing living standards, the social demand for talents with various aspects of ability is becoming higher and higher. The families, study and society of generations after 70s and 80s pay...In the 21st Century of the increasing living standards, the social demand for talents with various aspects of ability is becoming higher and higher. The families, study and society of generations after 70s and 80s pay more attention to cultivating their own children's comprehensive development. Juvenile moral education is an important part of the contemporary juvenile education. Juvenile moral education is worthy of being paid attention to. On one hand, it is because the juvenile education is in the most basic and critical stage of the whole education stage, which is in the stage of the biggest influence of education development; on the other hand, it is because the young people are active and curious by nature, which will cause the difficulty of moral education to increase in the education process. Various countries and regions in the world have their own unique cultures and adjustments,and these different cultures affect the residents of different countries and regions with different living habits, ways of thinking and behaviors; thus forming different cultural differences. This paper, by taking the juvenile moral education between China and America as the research object, aims at analyzing the Chinese and Western cultural difference in juvenile moral education representation and transmission, aiming at from point to area,promoting the communication and development of juvenile moral education.展开更多
The authors investigate the comparative classification performance of the two groups linear classification techniques. They compared the Fisher linear classification analysis, its robust version based on the minimum c...The authors investigate the comparative classification performance of the two groups linear classification techniques. They compared the Fisher linear classification analysis, its robust version based on the minimum covariance determinant with the Filter linear classification rule and the linear combination linear classification technique. These procedures are investigated using laboratory reared aedes albopictus mosquito data set and simulated data set generated based on heteroscedastic covariance matrices with various proportion of contamination. The evaluation procedure is based on the effect of contamination on the mean probabilities of correct classification obtain for each technique. The comparative analysis revealed that the robust Fisher linear classification rule and the linear combination linear classification rule are robust and comparable than the other procedures.展开更多
Although the effects of arbuscular mycorrhizal fungi(AMF)on host plants have been well documented,whether the effects of AMF on parental generations affect offspring performance is not fully clear.We conducted a commo...Although the effects of arbuscular mycorrhizal fungi(AMF)on host plants have been well documented,whether the effects of AMF on parental generations affect offspring performance is not fully clear.We conducted a common garden experiment to determine whether AMF status of host plants(Medicago truncatula)affects phenotype and transcriptome expression of their offspring.Seeds from four type parental treatments(low-phosphorus(P)soil without AMF,low-P soil with AMF,high-P soil without AMF and high-P soil with AMF)were grown under low-P(LPS)and normal-P soil(OHS)conditions.The fowering pattern of LP offspring was similar to their parents,such that plants with AMF fowered earlier than those without AMF under OHS condition but were opposite under LPS condition.The transcriptome differential analysis showed that some differential transcripts(45 for parental plants growing under low-P condition and 3 for parental plants growing under high-P condition)expression patterns between offspring were comparable,and that only affected by parental AMF status regardless of the P environment that offspring was grown.Others(146 for parental plants growing under low-P condition and 2 for parental plants growing under high-P condition),however,were affected both by the parental AMF status and the offspring P environment.In addition,the number of differential transcripts between offspring whose parental plants grew under high-P condition was far less than under low-P condition.These results indicate that AMF may not only affect the current generation of host plants but also affect the offspring especially when their parents have experienced a stressful environment.展开更多
Prostate cancer is a common malignancy among men in Western countries. Recently the morbidity and mortality of prostate cancer increase dramatically in several oriental countries including China. Rapidly evolving tech...Prostate cancer is a common malignancy among men in Western countries. Recently the morbidity and mortality of prostate cancer increase dramatically in several oriental countries including China. Rapidly evolving technology in molecular biology such as high-throughput sequencing and integrative analysis of genomic and transcriptomic landscapes have enabled the identification of key oncogenic events for prostate cancer initiation, progression and resistance to hormonal therapy. These surging data of prostate cancer genome also provide insights on ethnic variation and the differences in histological subtype of this disease. In this review, differences in the incidence of prostate cancer and the prevalence of main genetic alterations between Asian and Western populations are discussed. We also review the recent findings on the mechanisms underlying neuroendocrine differentiation of prostate cancer and the development of small cell neuroendocrine carcinoma after androgen deprivation therapy.展开更多
Objective: To find new protein biomarkers for the detection and evaluation of liver injury and to analyze the relationship between such proteins and disease progression in concanavalin A (Con A)-induced hepatitis. ...Objective: To find new protein biomarkers for the detection and evaluation of liver injury and to analyze the relationship between such proteins and disease progression in concanavalin A (Con A)-induced hepatitis. Methods: Twenty-five mice were randomly divided into five groups: an untreated group, a control group injected with phosphate buffered saline (PBS), and groups with Con A-induced hepatitis evaluated at 1, 3 and 6 h. Two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) were used to identify differences in protein expression among groups. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to verify the results. Results: In mice with Con A-induced hepatitis, expression levels of four proteins were increased: RIKEN, fructose bisphosphatase 1 (fbp1), ketohexokinase (khk), and Chain A of class pi glutathione S-transferase. Changes in fbpl and khk were confirmed by qRT-PCR. Conclusion: Levels of two proteins, fbp1 and khk, are clearly up-regulated in mice with Con A-induced hepatitis.展开更多
An organ unique to mammals, the mammary gland develops 90% of its mass after birth and experiences the pregnancy-lactation-involution cycle (PL cycle) during reproduction. To understand mammogenesis at the transcrip...An organ unique to mammals, the mammary gland develops 90% of its mass after birth and experiences the pregnancy-lactation-involution cycle (PL cycle) during reproduction. To understand mammogenesis at the transcriptomic level and using a ribo-minus RNA-seq protocol, we acquired greater than 50 million reads each for the mouse mammary gland during pregnancy (day 12 of pregnancy), lactation (day 14 of lactation), and involution (day 7 of involution). The pregnancy-, lacta- tion- and involution-related sequencing reads were assembled into 17344, 10160, and 13739 protein-coding transcripts and 1803, 828, and 1288 non-coding RNAs (ncRNAs), respectively. Differentially expressed genes (DEGs) were defined in the three samples, which comprised 4843 DEGs (749 up-regulated and 4094 down-regulated) from pregnancy to lactation and 4926 DEGs (4706 up-regulated and 220 down-regulated) from lactation to involution. Besides the obvious and substantive up- and down-regulation of the DEGs, we observe that lysosomal enzymes were highly expressed and that their expression coin- cided with milk secretion. Further analysis of transcription factors such as Trpsl, Gtf2i, Tcf712, Nuprl, Vdr, Rbl, and Aebpl, and ncRNAs such as mir-125b, Let7, mir-146a, and mir-15 has enabled us to identify key regulators in mammary gland de- velopment and the PL cycle.展开更多
RNA-Seq technology is becoming widely used in various transcriptomics studies;however,analyzing and interpreting the RNA-Seq data face serious challenges.With the development of high-throughput sequencing technologies...RNA-Seq technology is becoming widely used in various transcriptomics studies;however,analyzing and interpreting the RNA-Seq data face serious challenges.With the development of high-throughput sequencing technologies,the sequencing cost is dropping dramatically with the sequencing output increasing sharply.However,the sequencing reads are still short in length and contain various sequencing errors.Moreover,the intricate transcriptome is always more complicated than we expect.These challenges proffer the urgent need of efficient bioinformatics algorithms to effectively handle the large amount of transcriptome sequencing data and carry out diverse related studies.This review summarizes a number of frequently-used applications of transcriptome sequencing and their related analyzing strategies,including short read mapping,exon-exon splice junction detection,gene or isoform expression quantification,differential expression analysis and transcriptome reconstruction.展开更多
Uncertainty characterization has become increasingly recognized as an integral component in thematic mapping based on remotely sensed imagery, and descriptors such as percent correctly classified pixels (PCC) and Kapp...Uncertainty characterization has become increasingly recognized as an integral component in thematic mapping based on remotely sensed imagery, and descriptors such as percent correctly classified pixels (PCC) and Kappa coefficients of agreement have been devised as thematic accuracy metrics. However, such spatially averaged measures about accuracy neither offer hints about spatial variation in misclassification, nor are useful for quantifying error margins in derivatives, such as the areal extents of different land cover types and the land cover change statistics. Such limitations originate from the deficiency that spatial dependency is not accommodated in the conventional methods for error analysis. Geostatistics provides a good framework for uncertainty characterization in land cover information. Methods for predicting and propagating misclassification will be described on the basis of indicator samples and covariates, such as spectrally derived posteriori probabilities. An experiment using simulated datasets was carried out to quantify the error in land cover change derived from postclassification comparison. It was found that significant biases result from applying joint probability rules assuming temporal independence between misclassifications across time, thus emphasizing the need for the stochastic simulation in error modeling. Further investigations, incorporating indicators and probabilistic data for mapping and propagating misclassification, are anticipated.展开更多
基金Supported by a grant from the National Natural Sciences Foundation of China (No.30571552)
文摘Objective: The aim of this study was to establish reproducible two-dimensional electrophoretic assay used for profiling and identification of differentially expressed proteins in human stage I lung adenocarcinoma and paired normal tumor-adjacent tissue. Methods: The proteins from 12 human stage I lung adenocarcinoma tissues and normal tumor-adjacent tissues were separated using isoelectric focusing electrophoresis (the first dimension) and the subsequent homogeneous SDS-polyacrylamide gel electrophoresis (SDS-PAGE) (the second dimension). The differentially expressed proteins were determined with PDQuest image analysis software, and identified using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and database searching. Results: The well-reproducible 2-DE gel patterns of human stage I lung adenocarcinoma and normal tumor-adjacent tissues were profiled and 26 differentially expressed proteins uncovered. Nine of these 26 protein spots were cut out from the preparation gels and determined with MALDI-TOF-MS. Searching against the protein database, four candidate proteins were identified. They were 60S acidic ribosomal protein P2, Cathepsin B1, Apolipoprotein A-I precursor, and La 4.1 protein. Conclusion: In this study, high reproducible 2-DE gel protein images of human stage I lung adenocarcinoma and paired normal tumor-adjacent tissues were achieved successfully, and 4 differentially expressed proteins were revealed. These data will be helpful for screen of early biomarker and study of molecular mechanisms of human lung adenocarcinoma.
文摘In the 21st Century of the increasing living standards, the social demand for talents with various aspects of ability is becoming higher and higher. The families, study and society of generations after 70s and 80s pay more attention to cultivating their own children's comprehensive development. Juvenile moral education is an important part of the contemporary juvenile education. Juvenile moral education is worthy of being paid attention to. On one hand, it is because the juvenile education is in the most basic and critical stage of the whole education stage, which is in the stage of the biggest influence of education development; on the other hand, it is because the young people are active and curious by nature, which will cause the difficulty of moral education to increase in the education process. Various countries and regions in the world have their own unique cultures and adjustments,and these different cultures affect the residents of different countries and regions with different living habits, ways of thinking and behaviors; thus forming different cultural differences. This paper, by taking the juvenile moral education between China and America as the research object, aims at analyzing the Chinese and Western cultural difference in juvenile moral education representation and transmission, aiming at from point to area,promoting the communication and development of juvenile moral education.
文摘The authors investigate the comparative classification performance of the two groups linear classification techniques. They compared the Fisher linear classification analysis, its robust version based on the minimum covariance determinant with the Filter linear classification rule and the linear combination linear classification technique. These procedures are investigated using laboratory reared aedes albopictus mosquito data set and simulated data set generated based on heteroscedastic covariance matrices with various proportion of contamination. The evaluation procedure is based on the effect of contamination on the mean probabilities of correct classification obtain for each technique. The comparative analysis revealed that the robust Fisher linear classification rule and the linear combination linear classification rule are robust and comparable than the other procedures.
基金supported by the National Natural Science Foundation of China(31470483,31570411)the Postdoctoral Science Foundation of China(2021M693732)the Postdoctoral Science Foundation of Chongqing,China(cstc2021jcyj-bshX0165)。
文摘Although the effects of arbuscular mycorrhizal fungi(AMF)on host plants have been well documented,whether the effects of AMF on parental generations affect offspring performance is not fully clear.We conducted a common garden experiment to determine whether AMF status of host plants(Medicago truncatula)affects phenotype and transcriptome expression of their offspring.Seeds from four type parental treatments(low-phosphorus(P)soil without AMF,low-P soil with AMF,high-P soil without AMF and high-P soil with AMF)were grown under low-P(LPS)and normal-P soil(OHS)conditions.The fowering pattern of LP offspring was similar to their parents,such that plants with AMF fowered earlier than those without AMF under OHS condition but were opposite under LPS condition.The transcriptome differential analysis showed that some differential transcripts(45 for parental plants growing under low-P condition and 3 for parental plants growing under high-P condition)expression patterns between offspring were comparable,and that only affected by parental AMF status regardless of the P environment that offspring was grown.Others(146 for parental plants growing under low-P condition and 2 for parental plants growing under high-P condition),however,were affected both by the parental AMF status and the offspring P environment.In addition,the number of differential transcripts between offspring whose parental plants grew under high-P condition was far less than under low-P condition.These results indicate that AMF may not only affect the current generation of host plants but also affect the offspring especially when their parents have experienced a stressful environment.
基金supported by the Prostate Cancer Foundationthe Broad Stem Cell Research Center at University of California, Los Angeles+5 种基金supported by the Department of Defense Prostate Cancer Research Program W81XWH-11-1-0227 (PI: Jiaoti Huang)W81XWH-12-1-0206 (PI: Lily Wu)UCLA SPORE in prostate cancer (PI: Robert Reiter)NCI 1R01CA158627 (PI: Leonard Marks)Stand-up-to-Cancer Dream Team Award (PI: Small and Witte)Prostate Cancer Foundation Honorable A. David Mazzone Special Challenge Award (PI: Robert Reiter)
文摘Prostate cancer is a common malignancy among men in Western countries. Recently the morbidity and mortality of prostate cancer increase dramatically in several oriental countries including China. Rapidly evolving technology in molecular biology such as high-throughput sequencing and integrative analysis of genomic and transcriptomic landscapes have enabled the identification of key oncogenic events for prostate cancer initiation, progression and resistance to hormonal therapy. These surging data of prostate cancer genome also provide insights on ethnic variation and the differences in histological subtype of this disease. In this review, differences in the incidence of prostate cancer and the prevalence of main genetic alterations between Asian and Western populations are discussed. We also review the recent findings on the mechanisms underlying neuroendocrine differentiation of prostate cancer and the development of small cell neuroendocrine carcinoma after androgen deprivation therapy.
基金Project (No.20082X10002-007) supported by the National Natural Science Foundation of China
文摘Objective: To find new protein biomarkers for the detection and evaluation of liver injury and to analyze the relationship between such proteins and disease progression in concanavalin A (Con A)-induced hepatitis. Methods: Twenty-five mice were randomly divided into five groups: an untreated group, a control group injected with phosphate buffered saline (PBS), and groups with Con A-induced hepatitis evaluated at 1, 3 and 6 h. Two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) were used to identify differences in protein expression among groups. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to verify the results. Results: In mice with Con A-induced hepatitis, expression levels of four proteins were increased: RIKEN, fructose bisphosphatase 1 (fbp1), ketohexokinase (khk), and Chain A of class pi glutathione S-transferase. Changes in fbpl and khk were confirmed by qRT-PCR. Conclusion: Levels of two proteins, fbp1 and khk, are clearly up-regulated in mice with Con A-induced hepatitis.
基金supported by grant from Ministry of Science and Technology of China (2011CB944100,2011CB944101)
文摘An organ unique to mammals, the mammary gland develops 90% of its mass after birth and experiences the pregnancy-lactation-involution cycle (PL cycle) during reproduction. To understand mammogenesis at the transcriptomic level and using a ribo-minus RNA-seq protocol, we acquired greater than 50 million reads each for the mouse mammary gland during pregnancy (day 12 of pregnancy), lactation (day 14 of lactation), and involution (day 7 of involution). The pregnancy-, lacta- tion- and involution-related sequencing reads were assembled into 17344, 10160, and 13739 protein-coding transcripts and 1803, 828, and 1288 non-coding RNAs (ncRNAs), respectively. Differentially expressed genes (DEGs) were defined in the three samples, which comprised 4843 DEGs (749 up-regulated and 4094 down-regulated) from pregnancy to lactation and 4926 DEGs (4706 up-regulated and 220 down-regulated) from lactation to involution. Besides the obvious and substantive up- and down-regulation of the DEGs, we observe that lysosomal enzymes were highly expressed and that their expression coin- cided with milk secretion. Further analysis of transcription factors such as Trpsl, Gtf2i, Tcf712, Nuprl, Vdr, Rbl, and Aebpl, and ncRNAs such as mir-125b, Let7, mir-146a, and mir-15 has enabled us to identify key regulators in mammary gland de- velopment and the PL cycle.
基金supported by the National Basic Research Program of China (Grant Nos. 2010CB945401, 2007CB108800)National Natural Science Foundation of China (Grant Nos. 30870575,31071162,31000590)Science and Technology Commission of Shanghai Municipality (Grant No. 11DZ2260300)
文摘RNA-Seq technology is becoming widely used in various transcriptomics studies;however,analyzing and interpreting the RNA-Seq data face serious challenges.With the development of high-throughput sequencing technologies,the sequencing cost is dropping dramatically with the sequencing output increasing sharply.However,the sequencing reads are still short in length and contain various sequencing errors.Moreover,the intricate transcriptome is always more complicated than we expect.These challenges proffer the urgent need of efficient bioinformatics algorithms to effectively handle the large amount of transcriptome sequencing data and carry out diverse related studies.This review summarizes a number of frequently-used applications of transcriptome sequencing and their related analyzing strategies,including short read mapping,exon-exon splice junction detection,gene or isoform expression quantification,differential expression analysis and transcriptome reconstruction.
基金Supported by the National 973 Program of China (No. 2006CB701302)the Hubei Department of Science and Technology (No. 2007ABA276)
文摘Uncertainty characterization has become increasingly recognized as an integral component in thematic mapping based on remotely sensed imagery, and descriptors such as percent correctly classified pixels (PCC) and Kappa coefficients of agreement have been devised as thematic accuracy metrics. However, such spatially averaged measures about accuracy neither offer hints about spatial variation in misclassification, nor are useful for quantifying error margins in derivatives, such as the areal extents of different land cover types and the land cover change statistics. Such limitations originate from the deficiency that spatial dependency is not accommodated in the conventional methods for error analysis. Geostatistics provides a good framework for uncertainty characterization in land cover information. Methods for predicting and propagating misclassification will be described on the basis of indicator samples and covariates, such as spectrally derived posteriori probabilities. An experiment using simulated datasets was carried out to quantify the error in land cover change derived from postclassification comparison. It was found that significant biases result from applying joint probability rules assuming temporal independence between misclassifications across time, thus emphasizing the need for the stochastic simulation in error modeling. Further investigations, incorporating indicators and probabilistic data for mapping and propagating misclassification, are anticipated.