This study explores the integration path of ideological and political education in the course Design Thinking and Expression of environmental art design,aiming to enhance students’innovative thinking,social responsib...This study explores the integration path of ideological and political education in the course Design Thinking and Expression of environmental art design,aiming to enhance students’innovative thinking,social responsibility,and awareness of sustainable development.Based on the core philosophy of design thinking(people-oriented,problem-solving,and interdisciplinary collaboration)and the elements of ideological and political education in courses(moral education,cultural confidence,sustainable development,and social equity),the study proposes implementation paths for optimizing course objectives,adjusting course content,innovating teaching methods,and optimizing the evaluation system.Through project-based learning,situational teaching,and interdisciplinary collaboration,combined with practical cases such as historical district renewal,environmental design for rural revitalization,and green commercial space design,it has been verified that the effective integration of ideological and political elements in courses can enhance students’cultural identity,sense of social responsibility,and design innovation ability.This study provides theoretical support and practical demonstration for the ideological and political reform of environmental art design courses.In the future,interdisciplinary collaboration can be further deepened,social practice applications can be expanded,the evaluation system can be improved,and the systematic development of ideological and political courses can be promoted.展开更多
Objective To investigate integration and expression of adeno-associated virus (AAV) vectors in neuronal PC12 cells,the result of which can be applied in further gene therapy of diseases of the central nervous sys- tem...Objective To investigate integration and expression of adeno-associated virus (AAV) vectors in neuronal PC12 cells,the result of which can be applied in further gene therapy of diseases of the central nervous sys- tem. Methods Human neurotrophin-3(hNT3)genes were inserted into AAV vectors. Then the recombinat AAV plas- mids were encapsidated as recombinant virions. PCl2 cells were transfected with the virions and the positive cells were selected by G418. The transfection positive (hNT3 modified)PC12 cells were cultured for several generations and the cellular genomic DNA and total RNA were extracted. We investigated the integration locus or AAV vectors by South- ern blot and transcript situation or foreign genes by dot blot. Results The hybridization tests showed that AAV in- troduced foreign genes were stably integrated, but at random locus, and robustly transcribed in hNT3 modified PCl2 cells. Conclusion AAV vectors can serve as high efficiency vectors or target genes in neuronal PC12 cells.展开更多
Malolactic enzyme is the function enzyme which catalyses the reaction for L-malate converting to L-lactic during malolactic fermentation （MLF）. In this paper, researches concerning the malolactic enzyme gene mleA cl...Malolactic enzyme is the function enzyme which catalyses the reaction for L-malate converting to L-lactic during malolactic fermentation （MLF）. In this paper, researches concerning the malolactic enzyme gene mleA cloned from a patent strain Oenococcus oeni SD-2a screened in Chinese wine and integrated expressing in Saccharomyces cerevisiae were performed in order to carry out both alcoholic fermentation （AF） and malolactic fermentation （MLF） during winemaking, with a view to achieving a better control of MLF in enology. To construct the expression plasmid named pYILmleA, cloned mleA gene, PGK1 promoter, and ADH1 terminator were ligated and inserted into integrating vector YIp5. Yeast transformants were screened on SD/-Ura and identified by auxotrophic test, mating type test, and colony PCR. Target protein was detected by SDS-PAGE and the targeted gene integrated to the chromosome was detected by dot bloting hybridization. After the transformant was cultured in SD/-Ura adding glucose （10%） and L-malate （5 648 mg L-1） for 4 d, the culture supernatant was collected and L-malate and L-lactic acid contents were detected by HPLC. 1 278-1 312 mg L-1 L-lactic acids were detected, while the comparative drop rates of L-malate were 20.18-20.85%. L-malate and L-lactic contents of the transformants showed extra significant difference and significant difference with the control ones by t-test respectively. The result indicated that the functional expression was achieved in recombinants S. cerevisiae.展开更多
Phospholipase D(PLD)is an essential enzyme for the enzymatic phosphatidylserine synthesis and Bacillus subtilis is a potential microbial cell factory for the PLD production,but its widespread application in the food i...Phospholipase D(PLD)is an essential enzyme for the enzymatic phosphatidylserine synthesis and Bacillus subtilis is a potential microbial cell factory for the PLD production,but its widespread application in the food industry is limited by low expression levels and the use of antibiotics.In this study,a multi-copy recombinant strain BSPLD312 was constructed through screening genome location and the number of PLD expression cassettes.The enzyme activity of BS-PLD312 can reached 392.88 U/mL in the absence of antibiotics and inducers.Furthermore,a food grade reaction system within egg yolk was established and the phosphatidylserine content reached 35.13 g/L in egg yolk.This reaction system is applicable for synthesis of other PLs and regulating the composition of various phospholipids in egg yolk.The protocols established in this study shows great potential for application in industrial PLD production and expanded the practical application of PLD in food industry.展开更多
The wingless-related integration site(WNT)proteins are a family of secreted glycoproteins that are evolutionarily conserved and are believed to be involved in evolution in vertebrates and invertebrates.WNT signaling p...The wingless-related integration site(WNT)proteins are a family of secreted glycoproteins that are evolutionarily conserved and are believed to be involved in evolution in vertebrates and invertebrates.WNT signaling pathways may be associated with limb regeneration and development in crustaceans.However,the detail mechanisms remain unclear.Therefore,the distribution of WNT4 in the hepatopancreas,muscle,hemocyte,ganglion,heart,eyestalk,gill tissue,and diff erent larvae development stages of the swimming crab(Portunus trituberculatus)were characterized using immunofl uorescence,real-time PCR,and Western blotting.Signifi cant PtWNT4 expression was detected in heart and eyestalk.In addition,PtWNT4 was expressed in all larval stages of P.trituberculatus with a dynamic expression pattern,especially in the eyestalk and other organs in the carapace area.The injection of WNT4 dsRNA into regenerative limbs signifi cantly decreased PtWNT4 mRNA levels in the eyestalk,heart,and muscle,resulting in 1.9-fold,2.2-fold,and 2.7-fold decreases compared with those detected in the group injected with crab saline(P<0.05),respectively,indicating successful gene silencing.Overall,expression analysis on the WNT4 using RNAi provides an insight to its functional mechanism during limb regeneration in P.trituberculatus.The results not only demonstrated the requirement for WNT4 in limb regeneration of Crustaceans,but also suggested its ability to promote larval development at specifi c stages.展开更多
Colorectal cancers(CRCs) display a wide variety of genomic aberrations that may be either causally linked to their development and progression, or might serve as biomarkers for their presence. Recent advances in rapid...Colorectal cancers(CRCs) display a wide variety of genomic aberrations that may be either causally linked to their development and progression, or might serve as biomarkers for their presence. Recent advances in rapid high-throughput genetic and genomic analysis have helped to identify a plethora of alterations that can potentially serve as new cancer biomarkers, and thus help to improve CRC diagnosis, prognosis, and treatment. Each distinct data type(copy number variations, gene and micro RNAs expression, Cp G island methylation) provides an investigator with a different, partially independent, and complementary view of the entire genome. However, elucidation of gene function will require more information than can be provided by analyzing a single type of data. The integration of knowledge obtained from different sources is becoming increasingly essential for obtaining an interdisciplinary view of large amounts of information, and also for cross-validating experimental results. The integration of numerous types of genetic and genomic data derived from public sources, and via the use of ad-hoc bioinformatics tools and statistical methods facilitates the discovery and validation of novel, informative biomarkers. This combinatory approach will also enable researchers to more accurately and comprehensively understand the associations between different biologic pathways, mechanisms, and phenomena, and gain new insights into the etiology of CRC.展开更多
This paper explores how sculpture,as a medium,has transcended traditional boundaries and evolved into a diverse form of artistic expression that engages with both physical and social dimensions.Tracing the evolution f...This paper explores how sculpture,as a medium,has transcended traditional boundaries and evolved into a diverse form of artistic expression that engages with both physical and social dimensions.Tracing the evolution from traditional materials and techniques to modernist breaks and conceptual art,this study delves into key turning points,including the shift towards abstraction,the role of the readymade,and the influence of site-specificity.It also examines how contemporary sculpture serves as a dynamic platform for addressing social,cultural,and political issues,fostering public engagement and transforming public spaces.By analyzing these developments,this paper highlights sculpture’s growing role as a medium that not only reflects but also shapes societal narratives.展开更多
为构建综合能源系统安全域(integrated energy system security region,IESSR),该文提出一种基于多项式混沌展开(polynomial chaos expansion,PCE)的IESSR边界(IESR boundary,IESSRB)近似方法,借助该方法可得IESSRB的多项式逼近表达式...为构建综合能源系统安全域(integrated energy system security region,IESSR),该文提出一种基于多项式混沌展开(polynomial chaos expansion,PCE)的IESSR边界(IESR boundary,IESSRB)近似方法,借助该方法可得IESSRB的多项式逼近表达式。首先,根据IESSRB的边界拓扑特性,构建系统的IESSR边界点搜索优化模型;然后,根据PCE,对IESSR边界点搜索优化模型进行参数化处理,构建IESSRB搜索的参数化优化模型;进一步地,根据IESSRB搜索的参数化优化模型的KKT条件,将IESSRB的参数化优化模型转化为高维参数化非线性方程组;在此基础上,借助广义Galerkin投影构建关于近似IESSRB的多项式逼近系数的Galerkin投影方程组,通过求解该方程组可得IESSRB的多项式逼近系数,从而获得IESSRB的多项式逼近表达式;为进一步降低Galerkin投影方程组求解复杂度,提出多项式分段近似IESSRB方法,在提高IESSRB近似精度的同时,提升了IESSRB近似的计算效率;最后,通过IES E39-G20测试系统和IES E118-G96测试系统对所提方法进行分析、验证。结果表明,所提方法可实现IESSR的准确、有效构建。展开更多
The growing wealth of single-cell omics datasets presents unprecedented opportunities to uncover new insights into temporal gene dynamics during development.However,this relies on accessible,diverse time-series data a...The growing wealth of single-cell omics datasets presents unprecedented opportunities to uncover new insights into temporal gene dynamics during development.However,this relies on accessible,diverse time-series data and robust in-silico analysis methods—resources that are underutilized in current databases.Herein,we present TEDD 2.0(https://tedd.obg.cuhk.edu.hk/),an enhanced version of our Temporal Expression during Development Database,featuring advanced in-silico tools to characterize developmental lineages,investigate functional roles of temporally regulated genes,and compare developmental mechanisms across diverse species and life stages.This database integrates over 15 million cells from nine species,spanning 81 tissue-types and 42 time points,with three new analytical modules offered through an easy-to-use interface with dedicated cloud-based computational resources:(i)virtual gene knockout to assess transcriptomewide responses to gene perturbation and their functional consequences;(ii)cross-species integration which minimizes species and data batch effects to reveal evolutionarily conserved and divergent temporal gene expression patterns;and(iii)trajectory inference and marker gene analysis to infer developmental lineages and detect marker genes relevant in cell fates decisions.Overall,this database provides researchers with a powerful platform to explore the temporal expression patterns of target genes,decipher finer regulation of developmental mechanisms,and guide both research design and discovery across development.展开更多
The emergence of single-cell RNA sequencing(scRNA-seq)technology has revolutionized the study of cellular heterogeneity at the single-cell level.However,existing methods for identifying subpopulations of cells in scRN...The emergence of single-cell RNA sequencing(scRNA-seq)technology has revolutionized the study of cellular heterogeneity at the single-cell level.However,existing methods for identifying subpopulations of cells in scRNA-seq data mainly rely on gene expression features,neglecting the valuable genomic information present in the raw sequencing data.To address this limitation,we propose an end-to-end deep clustering model called scCluster,which integrates single-cell gene expression profiles and expressed variant features derived from the raw scRNA-seq data to stratify cell subpopulations in cancer tissues.scCluster employs a joint optimization strategy that combines a zero-inflated negative binomial model-based dual-modal autoencoder with deep embedding clustering in the pre-training phase.This allows both gene expression profiles and variant features to be encoded into the same latent embedding space.In the fine-tuning stage,scCluster further enhances the discriminability of the latent representations by integrating deep soft K-means clustering and cross-instance guided contrastive clustering techniques.Our extensive evaluations reveal that scCluster surpasses state-of-the-art methods in multiple real-world cancer scRNA-seq datasets.The results also indicate that incorporating the expressed variant features alongside gene expressions substantially enhances the stratification of cell subpopulations in cancer single-cell research.展开更多
Using a nuclear transplantation approach, the integration and expression of the green fluorescent protein (GFP) gene in the embryogenesis of transgenic loach (Misgurnus anguillicaudatus Cantor) have been studied. The ...Using a nuclear transplantation approach, the integration and expression of the green fluorescent protein (GFP) gene in the embryogenesis of transgenic loach (Misgurnus anguillicaudatus Cantor) have been studied. The GFP gene expression is first observed at the gastrula stage, which is consistent with the initiation of cell differentiation of fish embryos. The time course of the foreign gene expression is correlated with the regulatory sequences. The expression efficiency also depends on the gene configuration: the expression of pre-integrating circular plasmid at early embryos is higher than that of the linear plasmid. The integration of the GFP gene is first detected at the blastula stage and lasts for quite a long period. When two types of different plasmids are co-injected into fertilized eggs, the behavior of their integration and expression is not identical.展开更多
Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new op...Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new opportunity for investigating diagnosis,treatment,and prognosis of spinal cord injury.However,differentially expressed genes are not consistent among studies,and many key genes and signaling pathways have not yet been accurately studied.GSE5296 was retrieved from the Gene Expression Omnibus DataSet.Differentially expressed genes were obtained using R/Bioconductor software(expression changed at least two-fold;P < 0.05).Database for Annotation,Visualization and Integrated Discovery was used for functional annotation of differentially expressed genes and Animal Transcription Factor Database for predicting potential transcription factors.The resulting transcription regulatory protein interaction network was mapped to screen representative genes and investigate their diagnostic and therapeutic value for disease.In total,this study identified 109 genes that were upregulated and 30 that were downregulated at 0.5,4,and 24 hours,and 3,7,and 28 days after spinal cord injury.The number of downregulated genes was smaller than the number of upregulated genes at each time point.Database for Annotation,Visualization and Integrated Discovery analysis found that many inflammation-related pathways were upregulated in injured spinal cord.Additionally,expression levels of these inflammation-related genes were maintained for at least 28 days.Moreover,399 regulation modes and 77 nodes were shown in the protein-protein interaction network of upregulated differentially expressed genes.Among the 10 upregulated differentially expressed genes with the highest degrees of distribution,six genes were transcription factors.Among these transcription factors,ATF3 showed the greatest change.ATF3 was upregulated within 30 minutes,and its expression levels remained high at28 days after spinal cord injury.These key genes screened by bioinformatics tools can be used as biological markers to diagnose diseases and provide a reference for identifying therapeutic targets.展开更多
基金“Curriculum Ideological and Political Education”Demonstration Project of Chongqing University of Posts and Telecommunications:Design Thinking and Expression(Environmental Design)(XKCSZ2251)Construction and Practice of the Ability Training System for“Internet+”Design Talents to Serve Rural Revitalization(233231)。
文摘This study explores the integration path of ideological and political education in the course Design Thinking and Expression of environmental art design,aiming to enhance students’innovative thinking,social responsibility,and awareness of sustainable development.Based on the core philosophy of design thinking(people-oriented,problem-solving,and interdisciplinary collaboration)and the elements of ideological and political education in courses(moral education,cultural confidence,sustainable development,and social equity),the study proposes implementation paths for optimizing course objectives,adjusting course content,innovating teaching methods,and optimizing the evaluation system.Through project-based learning,situational teaching,and interdisciplinary collaboration,combined with practical cases such as historical district renewal,environmental design for rural revitalization,and green commercial space design,it has been verified that the effective integration of ideological and political elements in courses can enhance students’cultural identity,sense of social responsibility,and design innovation ability.This study provides theoretical support and practical demonstration for the ideological and political reform of environmental art design courses.In the future,interdisciplinary collaboration can be further deepened,social practice applications can be expanded,the evaluation system can be improved,and the systematic development of ideological and political courses can be promoted.
文摘Objective To investigate integration and expression of adeno-associated virus (AAV) vectors in neuronal PC12 cells,the result of which can be applied in further gene therapy of diseases of the central nervous sys- tem. Methods Human neurotrophin-3(hNT3)genes were inserted into AAV vectors. Then the recombinat AAV plas- mids were encapsidated as recombinant virions. PCl2 cells were transfected with the virions and the positive cells were selected by G418. The transfection positive (hNT3 modified)PC12 cells were cultured for several generations and the cellular genomic DNA and total RNA were extracted. We investigated the integration locus or AAV vectors by South- ern blot and transcript situation or foreign genes by dot blot. Results The hybridization tests showed that AAV in- troduced foreign genes were stably integrated, but at random locus, and robustly transcribed in hNT3 modified PCl2 cells. Conclusion AAV vectors can serve as high efficiency vectors or target genes in neuronal PC12 cells.
基金supported by the National High-Tech Research and Development Program of China (863 Program of China, 2007AA10Z314)andthe Earmarked Fund for Modern Agro-Industry Technology Research System, China (Z225020801)
文摘Malolactic enzyme is the function enzyme which catalyses the reaction for L-malate converting to L-lactic during malolactic fermentation （MLF）. In this paper, researches concerning the malolactic enzyme gene mleA cloned from a patent strain Oenococcus oeni SD-2a screened in Chinese wine and integrated expressing in Saccharomyces cerevisiae were performed in order to carry out both alcoholic fermentation （AF） and malolactic fermentation （MLF） during winemaking, with a view to achieving a better control of MLF in enology. To construct the expression plasmid named pYILmleA, cloned mleA gene, PGK1 promoter, and ADH1 terminator were ligated and inserted into integrating vector YIp5. Yeast transformants were screened on SD/-Ura and identified by auxotrophic test, mating type test, and colony PCR. Target protein was detected by SDS-PAGE and the targeted gene integrated to the chromosome was detected by dot bloting hybridization. After the transformant was cultured in SD/-Ura adding glucose （10%） and L-malate （5 648 mg L-1） for 4 d, the culture supernatant was collected and L-malate and L-lactic acid contents were detected by HPLC. 1 278-1 312 mg L-1 L-lactic acids were detected, while the comparative drop rates of L-malate were 20.18-20.85%. L-malate and L-lactic contents of the transformants showed extra significant difference and significant difference with the control ones by t-test respectively. The result indicated that the functional expression was achieved in recombinants S. cerevisiae.
基金supported by the National Key Research and Development Program of China(No.2023YFA0914500)the National Natural Science Foundation of China(No.32171261)the Taishan Industry Leading Talent of Shandong Province(No.tscx202211017).
文摘Phospholipase D(PLD)is an essential enzyme for the enzymatic phosphatidylserine synthesis and Bacillus subtilis is a potential microbial cell factory for the PLD production,but its widespread application in the food industry is limited by low expression levels and the use of antibiotics.In this study,a multi-copy recombinant strain BSPLD312 was constructed through screening genome location and the number of PLD expression cassettes.The enzyme activity of BS-PLD312 can reached 392.88 U/mL in the absence of antibiotics and inducers.Furthermore,a food grade reaction system within egg yolk was established and the phosphatidylserine content reached 35.13 g/L in egg yolk.This reaction system is applicable for synthesis of other PLs and regulating the composition of various phospholipids in egg yolk.The protocols established in this study shows great potential for application in industrial PLD production and expanded the practical application of PLD in food industry.
基金Supported by the National Natural Science Foundation of China(No.31602152)the Major Agriculture Program of Ningbo(No.2017C110007)the K.C.Wong Magana Fund in Ningbo University.The funding body had no role in the study design,experimental implementation,interpretation of data,or writing of the manuscript。
文摘The wingless-related integration site(WNT)proteins are a family of secreted glycoproteins that are evolutionarily conserved and are believed to be involved in evolution in vertebrates and invertebrates.WNT signaling pathways may be associated with limb regeneration and development in crustaceans.However,the detail mechanisms remain unclear.Therefore,the distribution of WNT4 in the hepatopancreas,muscle,hemocyte,ganglion,heart,eyestalk,gill tissue,and diff erent larvae development stages of the swimming crab(Portunus trituberculatus)were characterized using immunofl uorescence,real-time PCR,and Western blotting.Signifi cant PtWNT4 expression was detected in heart and eyestalk.In addition,PtWNT4 was expressed in all larval stages of P.trituberculatus with a dynamic expression pattern,especially in the eyestalk and other organs in the carapace area.The injection of WNT4 dsRNA into regenerative limbs signifi cantly decreased PtWNT4 mRNA levels in the eyestalk,heart,and muscle,resulting in 1.9-fold,2.2-fold,and 2.7-fold decreases compared with those detected in the group injected with crab saline(P<0.05),respectively,indicating successful gene silencing.Overall,expression analysis on the WNT4 using RNAi provides an insight to its functional mechanism during limb regeneration in P.trituberculatus.The results not only demonstrated the requirement for WNT4 in limb regeneration of Crustaceans,but also suggested its ability to promote larval development at specifi c stages.
基金Supported by Associazione Italiana per la Ricerca sul CancroGrants No.10529 and No.12162funds obtained throughan Italian law that allows taxpayers to allocate 0.5%share of theirincome tax contribution to a research institution of their choice
文摘Colorectal cancers(CRCs) display a wide variety of genomic aberrations that may be either causally linked to their development and progression, or might serve as biomarkers for their presence. Recent advances in rapid high-throughput genetic and genomic analysis have helped to identify a plethora of alterations that can potentially serve as new cancer biomarkers, and thus help to improve CRC diagnosis, prognosis, and treatment. Each distinct data type(copy number variations, gene and micro RNAs expression, Cp G island methylation) provides an investigator with a different, partially independent, and complementary view of the entire genome. However, elucidation of gene function will require more information than can be provided by analyzing a single type of data. The integration of knowledge obtained from different sources is becoming increasingly essential for obtaining an interdisciplinary view of large amounts of information, and also for cross-validating experimental results. The integration of numerous types of genetic and genomic data derived from public sources, and via the use of ad-hoc bioinformatics tools and statistical methods facilitates the discovery and validation of novel, informative biomarkers. This combinatory approach will also enable researchers to more accurately and comprehensively understand the associations between different biologic pathways, mechanisms, and phenomena, and gain new insights into the etiology of CRC.
文摘This paper explores how sculpture,as a medium,has transcended traditional boundaries and evolved into a diverse form of artistic expression that engages with both physical and social dimensions.Tracing the evolution from traditional materials and techniques to modernist breaks and conceptual art,this study delves into key turning points,including the shift towards abstraction,the role of the readymade,and the influence of site-specificity.It also examines how contemporary sculpture serves as a dynamic platform for addressing social,cultural,and political issues,fostering public engagement and transforming public spaces.By analyzing these developments,this paper highlights sculpture’s growing role as a medium that not only reflects but also shapes societal narratives.
文摘为构建综合能源系统安全域(integrated energy system security region,IESSR),该文提出一种基于多项式混沌展开(polynomial chaos expansion,PCE)的IESSR边界(IESR boundary,IESSRB)近似方法,借助该方法可得IESSRB的多项式逼近表达式。首先,根据IESSRB的边界拓扑特性,构建系统的IESSR边界点搜索优化模型;然后,根据PCE,对IESSR边界点搜索优化模型进行参数化处理,构建IESSRB搜索的参数化优化模型;进一步地,根据IESSRB搜索的参数化优化模型的KKT条件,将IESSRB的参数化优化模型转化为高维参数化非线性方程组;在此基础上,借助广义Galerkin投影构建关于近似IESSRB的多项式逼近系数的Galerkin投影方程组,通过求解该方程组可得IESSRB的多项式逼近系数,从而获得IESSRB的多项式逼近表达式;为进一步降低Galerkin投影方程组求解复杂度,提出多项式分段近似IESSRB方法,在提高IESSRB近似精度的同时,提升了IESSRB近似的计算效率;最后,通过IES E39-G20测试系统和IES E118-G96测试系统对所提方法进行分析、验证。结果表明,所提方法可实现IESSR的准确、有效构建。
基金supported by the Innovative and Technology Fund(PRP/042/22FX)the National Natural Science Foundation of China(32270678)+2 种基金the Guangdong Basic and Applied Basic Research Foundation(2023A1515030220)the General Research Fund(14117524)the Collaborative Research Fund(C4062-21GF)。
文摘The growing wealth of single-cell omics datasets presents unprecedented opportunities to uncover new insights into temporal gene dynamics during development.However,this relies on accessible,diverse time-series data and robust in-silico analysis methods—resources that are underutilized in current databases.Herein,we present TEDD 2.0(https://tedd.obg.cuhk.edu.hk/),an enhanced version of our Temporal Expression during Development Database,featuring advanced in-silico tools to characterize developmental lineages,investigate functional roles of temporally regulated genes,and compare developmental mechanisms across diverse species and life stages.This database integrates over 15 million cells from nine species,spanning 81 tissue-types and 42 time points,with three new analytical modules offered through an easy-to-use interface with dedicated cloud-based computational resources:(i)virtual gene knockout to assess transcriptomewide responses to gene perturbation and their functional consequences;(ii)cross-species integration which minimizes species and data batch effects to reveal evolutionarily conserved and divergent temporal gene expression patterns;and(iii)trajectory inference and marker gene analysis to infer developmental lineages and detect marker genes relevant in cell fates decisions.Overall,this database provides researchers with a powerful platform to explore the temporal expression patterns of target genes,decipher finer regulation of developmental mechanisms,and guide both research design and discovery across development.
基金supported by the National Natural Science Foun-dation of China(62402382 and 62102319)。
文摘The emergence of single-cell RNA sequencing(scRNA-seq)technology has revolutionized the study of cellular heterogeneity at the single-cell level.However,existing methods for identifying subpopulations of cells in scRNA-seq data mainly rely on gene expression features,neglecting the valuable genomic information present in the raw sequencing data.To address this limitation,we propose an end-to-end deep clustering model called scCluster,which integrates single-cell gene expression profiles and expressed variant features derived from the raw scRNA-seq data to stratify cell subpopulations in cancer tissues.scCluster employs a joint optimization strategy that combines a zero-inflated negative binomial model-based dual-modal autoencoder with deep embedding clustering in the pre-training phase.This allows both gene expression profiles and variant features to be encoded into the same latent embedding space.In the fine-tuning stage,scCluster further enhances the discriminability of the latent representations by integrating deep soft K-means clustering and cross-instance guided contrastive clustering techniques.Our extensive evaluations reveal that scCluster surpasses state-of-the-art methods in multiple real-world cancer scRNA-seq datasets.The results also indicate that incorporating the expressed variant features alongside gene expressions substantially enhances the stratification of cell subpopulations in cancer single-cell research.
文摘Using a nuclear transplantation approach, the integration and expression of the green fluorescent protein (GFP) gene in the embryogenesis of transgenic loach (Misgurnus anguillicaudatus Cantor) have been studied. The GFP gene expression is first observed at the gastrula stage, which is consistent with the initiation of cell differentiation of fish embryos. The time course of the foreign gene expression is correlated with the regulatory sequences. The expression efficiency also depends on the gene configuration: the expression of pre-integrating circular plasmid at early embryos is higher than that of the linear plasmid. The integration of the GFP gene is first detected at the blastula stage and lasts for quite a long period. When two types of different plasmids are co-injected into fertilized eggs, the behavior of their integration and expression is not identical.
基金supported by the Natural Science Foundation of Shaanxi Province of China,No.2018JQ8029(to LG)
文摘Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new opportunity for investigating diagnosis,treatment,and prognosis of spinal cord injury.However,differentially expressed genes are not consistent among studies,and many key genes and signaling pathways have not yet been accurately studied.GSE5296 was retrieved from the Gene Expression Omnibus DataSet.Differentially expressed genes were obtained using R/Bioconductor software(expression changed at least two-fold;P < 0.05).Database for Annotation,Visualization and Integrated Discovery was used for functional annotation of differentially expressed genes and Animal Transcription Factor Database for predicting potential transcription factors.The resulting transcription regulatory protein interaction network was mapped to screen representative genes and investigate their diagnostic and therapeutic value for disease.In total,this study identified 109 genes that were upregulated and 30 that were downregulated at 0.5,4,and 24 hours,and 3,7,and 28 days after spinal cord injury.The number of downregulated genes was smaller than the number of upregulated genes at each time point.Database for Annotation,Visualization and Integrated Discovery analysis found that many inflammation-related pathways were upregulated in injured spinal cord.Additionally,expression levels of these inflammation-related genes were maintained for at least 28 days.Moreover,399 regulation modes and 77 nodes were shown in the protein-protein interaction network of upregulated differentially expressed genes.Among the 10 upregulated differentially expressed genes with the highest degrees of distribution,six genes were transcription factors.Among these transcription factors,ATF3 showed the greatest change.ATF3 was upregulated within 30 minutes,and its expression levels remained high at28 days after spinal cord injury.These key genes screened by bioinformatics tools can be used as biological markers to diagnose diseases and provide a reference for identifying therapeutic targets.
