Transcription factors （TFs） are important regulators of gene expression. To better understand TFencoding genes in maize （Zea mays L.）, a genome-wide TF prediction was performed using the updated B73 reference geno...Transcription factors （TFs） are important regulators of gene expression. To better understand TFencoding genes in maize （Zea mays L.）, a genome-wide TF prediction was performed using the updated B73 reference genome. A total of 2 298 TF genes were identified, which can be classified into 56 families. The largest family, known as the MYB superfamily, comprises 322 MYB and MYB-related TF genes. The expression patterns of 2014 （87.64%） TF genes were examined using RNA-seq data, which resulted in the identification of a subset of TFs that are specifically expressed in particular tissues （including root, shoot, leaf, ear, tassel and kernel）. Similarly, 98 kernel-specific TF genes were further analyzed, and it was observed that 29 of the kernel-specific genes were preferentially expressed in the early kernel developmental stage, while 69 of the genes were expressed in the late kernel developmental stage. Identification of these TFs, particularly the tissue-specific ones, provides important information for the understanding of development and transcriptional regulation of maize.展开更多
Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community.Here,we present RED（Rice Expression Database;http：//expression.ic4r.org）,an integrated dat...Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community.Here,we present RED（Rice Expression Database;http：//expression.ic4r.org）,an integrated database of rice gene expression profiles derived entirely from RNA-Seq data.RED features a comprehensive collection of 284 high-quality RNA-Seq experiments,integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments.Based on massive expression profiles,RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene（s） of interest.Besides,it provides user-friendly web interfaces for querying,browsing and visualizing expression profiles of concerned genes.Together,as a core resource in BIG Data Center,RED bears great utility for characterizing the function of rice genes and better understanding important biological processes and mechanisms underlying complex agronomic traits in rice.展开更多
Introduction:Multiple myeloma (MM) is a geriatric disease with onset at an average age of approximately 61 years.With the aging of the population,the incidence rate of MM is climbing.In the United States,the annual in...Introduction:Multiple myeloma (MM) is a geriatric disease with onset at an average age of approximately 61 years.With the aging of the population,the incidence rate of MM is climbing.In the United States,the annual incidence rate of MM is 2-5/100,000.Multiple myeloma accounts for approximately 1% of all tumor eases and slightly 】10% of cases with hematologic malignancy.Although an展开更多
Aristolochiae Fructus, a Chinese herbal medicine derived from the fruit of Aristolochia contorta Bge., contains nephrotoxic aristolochic acid analogues(AAAs). According to ancient medical texts, various medicinal part...Aristolochiae Fructus, a Chinese herbal medicine derived from the fruit of Aristolochia contorta Bge., contains nephrotoxic aristolochic acid analogues(AAAs). According to ancient medical texts, various medicinal parts of the fruit of A. contorta were ever used. In order to reveal which part could be safely and effectively used, it is necessary to analyze the chemical profiles of different medicinal parts. Herein we compared the chemical compositions and determined aristolochic acid I(AA-I) and aristolochic acid II(AA-II) in the four parts viz. outer pericarp, inner pericarp, septum, and seed. Ultra-high performance liquid chromatography equipped with quadrupole time-of-flight mass spectrometry(UHPLC-QTOF-MS) was applied for chemical profiling. Ultra-high performance liquid coupled with triple quadrupole mass spectrometry(UHPLC-Qq Q-MS) was employed to quantify AA-I and AA-II in different parts. It was found that the chemical compositions of the four parts varied both qualitatively and quantitatively. A total of 10 AAAs, including 5 aristolochic acids and 5 aristolactams, together with 3 alkaloids, were unambiguously or tentatively identified by UHPLC-QTOF-MS. The quantitatively analytical results obtained by UHPLC-Qq Q-MS showed that AA-I and AA-II exclusively accumulate in the seeds of A. contorta. These findings provide supporting data for the rational selection of medicinal parts.展开更多
Rice （Oryza sativa） is one of the most important staple food crops for more than half of the world＇s population. The demand is increasing for food security because of population growth and environmental challenges ...Rice （Oryza sativa） is one of the most important staple food crops for more than half of the world＇s population. The demand is increasing for food security because of population growth and environmental challenges triggered by climate changes. This scenario has led to more interest in developing crops with greater productivity and sustainability. The process of genetic transformation, a major tool for crop improvement, utilizes promoters as one of its key elements. Those promoters are generally divided into three types： constitutive, spatiotemporal, and condition-dependent. Tran- scriptional control of a constitutive promoter often leads to reduced plant growth, due to a negative effect of accumu- lated molecules during cellular functions or energy consump- tion. To maximize the effect of a transgene on transgenic plants, it is better to use condition-dependent or tissue- specific promoters. However, until now, those types have not been as widely applied in crop biotechnology. In this review, we introduce and discuss four groups of tissue-specific promoters （5o promoters in total） and six groups of condition-dependent promoters （27 promoters）. These pro- moters can be utilized to fine-tune desirable agronomic traits and develop crops with tolerance to various stresses, enhanced nutritional value, and advanced productivity.展开更多
PNZIP gene promoter has been cloned from Pharbitis nil by adaptor PCR, which con-forms to eukaryotic promoter characteristic. Primer extension analysis showed that the transcrip-tion start site was located 122 nucleot...PNZIP gene promoter has been cloned from Pharbitis nil by adaptor PCR, which con-forms to eukaryotic promoter characteristic. Primer extension analysis showed that the transcrip-tion start site was located 122 nucleotides upstream of the translation start site of PNZIP gene. According to the characteristic of PNZIP promoter, a series of deletions were purposely made by PCR. Five deletion fragments were fused to upstream of GUS gene and transferred into tobacco. Fluorometric GUS assay showed that five different length promoters all could specifically drive GUS gene expression in photosynthetic tissues and their activities decreased along with the gradual deletion of PNZIP promoter. In addition, the activity of full-length promoter was 9 times higher than that of CaMV 35S in leaf. PNZIP promoter may have two putative cis-elements, GAAATA and GATACT, which relate to gene expression in photosynthetic tissues. GATACT may determine the gene specific expression in photosynthetic tissues, while GAAATA, perhaps, as an enhancer, increases the intensity of gene expression.展开更多
Bidirectional promoters are relatively abundant in eukaryotic genomes, suggesting that they have an important biological significance. As yet, few of these promoters have been characterized in detail. Here, using a pr...Bidirectional promoters are relatively abundant in eukaryotic genomes, suggesting that they have an important biological significance. As yet, few of these promoters have been characterized in detail. Here, using a promoter：：GUS transgene approach has revealed that the intergenic region of Arabidopsis thaliana divergent genes At1g71850 and At1g71860 is an asymmetric bidirectional promoter, which exhibits an orientation-dependent expression profile. The strength of the forward promoter was greater than that of the reverse promoter, and their tissue specificities were not identical. Deletion analyses revealed that this bidirectional promoter could be divided into three functional regions. The basal level and tissue specificity of the promoter in the reverse orientation were regulated positively by region II and negatively by region III, whereas promoter activity in the forward orientation was regulated negatively by region II and positively by region I. Thus the 52-bp stretch of region II had a dual function, enhancing expression in the reverse orientation and suppressing it in the forward orientation. These results demonstrated that the activity of the At1g71850-At1g71860 bidirectional promoter was modulated by complex interactions between both positive and negative cis-acting elements. These findings will enhance our understanding of the regulatory mechanisms of plant bidirectional promoters.展开更多
Mdm2 and Mdm4 are negative regulators of the tumour suppressor p53; hence, this relationship is the focus of many cancerrelated studies. A multitude of experiments across various developmental stages have been conduct...Mdm2 and Mdm4 are negative regulators of the tumour suppressor p53; hence, this relationship is the focus of many cancerrelated studies. A multitude of experiments across various developmental stages have been conducted to explore the tissuespecific roles of these proteins in the mouse. When Mdm2 or Mdm4 are deleted in the germiine or specific tissues, they display different phenotypic defects, some of which lead to embryonic lethaLity. Mdm2 loss is often more deleterious than toss of its homotogue Mdm4. ALL tissues experience activation of p53 target genes upon toss of Mdm2 or Mdm4; however, the degree to which the p53 pathway is perturbed is highly tissue-specific and does not correlate to the severity of the morphological pheno- types. Therefore, a need for further understanding of how these proteins regulate p53 activity is warranted, as therapeutic targeting of the p53 pathway is rapidly evoLving and gaining attention in the field of cancer research. In this review, we discuss the tissue-specificity of Mdm proteins in regulating p53 and expose the need for investigation at the celt-specific level.展开更多
Owing to the prevalence of rotator cuff(RC)injuries and suboptimal healing outcome,rapid and functional regeneration of the tendon-bone interface(TBI)after RC repair continues to be a major clinical challenge.Given th...Owing to the prevalence of rotator cuff(RC)injuries and suboptimal healing outcome,rapid and functional regeneration of the tendon-bone interface(TBI)after RC repair continues to be a major clinical challenge.Given the essential role of the RC in shoulder movement,the engineering of biomimetic multi-tissue constructs presents an opportunity for complex TBI reconstruction after RC repair.Here,we propose a gradient cell-laden multi-tissue construct combined with compositional gradient TBI-specific bioinks via 3D cell-printing technology.In vitro studies demonstrated the capability of a gradient scaffold system in zone-specific inducibility and multi-tissue formation mimicking TBI.The regenerative performance of the gradient scaffold on RC regeneration was determined using a rat RC repair model.In particular,we adopted nondestructive,consecutive,and tissue-targeted near-infrared fluorescence imaging to visualize the direct anatomical change and the intricate RC regeneration progression in real time in vivo.Furthermore,the 3D cell-printed implant promotes effective restoration of shoulder locomotion function and accelerates TBI healing in vivo.In summary,this study identifies the therapeutic contribution of cell-printed constructs towards functional RC regeneration,demonstrating the translational potential of biomimetic gradient constructs for the clinical repair of multi-tissue interfaces.展开更多
Mesenchymal stem/progenitor cells (MSC/MPC) from a variety of tissue sources (bone marrow, adipose tissue, fat pads, synovial membranes, synovial fluid, skin, muscle and periosteal tissue) have been widely applied for...Mesenchymal stem/progenitor cells (MSC/MPC) from a variety of tissue sources (bone marrow, adipose tissue, fat pads, synovial membranes, synovial fluid, skin, muscle and periosteal tissue) have been widely applied for tissue engineering applications to generate replacements for injured or degenerated tissues. Alternatively, they have also been injected as free cells in an attempt to facilitate in vivo repair. Nearly all studies reported have used mixed cell populations of MSC/MPC, usually defined by cell surface phenotypes and/or functional ability to differentiate towards multiple cell lineages. Using more detailed cell surface phenotyping and limiting dilution approaches to isolate individual MSC/MPC clones have indicated that such mixed cell populations are very heterogeneous. In addition subsets of cells from different sources may have epigenetic modifications. While it is clear that MSC/MPC cells exhibit heterogeneity, the question of why this is the case has not been well addressed. This review will address some of these issues, as well as provide some insights into the implications when using such diverse cells for tissue engineering applications.展开更多
基金supported by the National Basic Research Program of China (973 Program: 2009CB118400)
文摘Transcription factors （TFs） are important regulators of gene expression. To better understand TFencoding genes in maize （Zea mays L.）, a genome-wide TF prediction was performed using the updated B73 reference genome. A total of 2 298 TF genes were identified, which can be classified into 56 families. The largest family, known as the MYB superfamily, comprises 322 MYB and MYB-related TF genes. The expression patterns of 2014 （87.64%） TF genes were examined using RNA-seq data, which resulted in the identification of a subset of TFs that are specifically expressed in particular tissues （including root, shoot, leaf, ear, tassel and kernel）. Similarly, 98 kernel-specific TF genes were further analyzed, and it was observed that 29 of the kernel-specific genes were preferentially expressed in the early kernel developmental stage, while 69 of the genes were expressed in the late kernel developmental stage. Identification of these TFs, particularly the tissue-specific ones, provides important information for the understanding of development and transcriptional regulation of maize.
基金supported by grants from Strategic Priority Research Program of the Chinese Academy of Sciences(No. XDA08020102 to Z.Z.and S.H.)International Partnership Program of the Chinese Academy of Sciences(No.153F11KYSB20160008)+3 种基金National Programs for High Technology Research and Development (863 ProgramNo.2015AA020108 to Z.Z.)National Natural Science Foundation of China(No.31100915 to LH.)the 100-Talent Program of Chinese Academy of Sciences(awarded to Z.Z.)
文摘Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community.Here,we present RED（Rice Expression Database;http：//expression.ic4r.org）,an integrated database of rice gene expression profiles derived entirely from RNA-Seq data.RED features a comprehensive collection of 284 high-quality RNA-Seq experiments,integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments.Based on massive expression profiles,RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene（s） of interest.Besides,it provides user-friendly web interfaces for querying,browsing and visualizing expression profiles of concerned genes.Together,as a core resource in BIG Data Center,RED bears great utility for characterizing the function of rice genes and better understanding important biological processes and mechanisms underlying complex agronomic traits in rice.
文摘Introduction:Multiple myeloma (MM) is a geriatric disease with onset at an average age of approximately 61 years.With the aging of the population,the incidence rate of MM is climbing.In the United States,the annual incidence rate of MM is 2-5/100,000.Multiple myeloma accounts for approximately 1% of all tumor eases and slightly 】10% of cases with hematologic malignancy.Although an
基金financially supported by the National Natural Science Foundation of China(No.81322051)the Project Funded by the Priority Academic Program Development(PAPD)of Jiangsu Higher Education Institutions and the Fundamental Research Funds for the Central Universities(No.G140026)
文摘Aristolochiae Fructus, a Chinese herbal medicine derived from the fruit of Aristolochia contorta Bge., contains nephrotoxic aristolochic acid analogues(AAAs). According to ancient medical texts, various medicinal parts of the fruit of A. contorta were ever used. In order to reveal which part could be safely and effectively used, it is necessary to analyze the chemical profiles of different medicinal parts. Herein we compared the chemical compositions and determined aristolochic acid I(AA-I) and aristolochic acid II(AA-II) in the four parts viz. outer pericarp, inner pericarp, septum, and seed. Ultra-high performance liquid chromatography equipped with quadrupole time-of-flight mass spectrometry(UHPLC-QTOF-MS) was applied for chemical profiling. Ultra-high performance liquid coupled with triple quadrupole mass spectrometry(UHPLC-Qq Q-MS) was employed to quantify AA-I and AA-II in different parts. It was found that the chemical compositions of the four parts varied both qualitatively and quantitatively. A total of 10 AAAs, including 5 aristolochic acids and 5 aristolactams, together with 3 alkaloids, were unambiguously or tentatively identified by UHPLC-QTOF-MS. The quantitatively analytical results obtained by UHPLC-Qq Q-MS showed that AA-I and AA-II exclusively accumulate in the seeds of A. contorta. These findings provide supporting data for the rational selection of medicinal parts.
基金supported by the Cooperative Research Program for Agriculture Science and Technology Development(Project title:Global identification and functional study of rice genes for enhancement of root development and nutrient use efficiency using genome information,project no.PJ01100401)
文摘Rice （Oryza sativa） is one of the most important staple food crops for more than half of the world＇s population. The demand is increasing for food security because of population growth and environmental challenges triggered by climate changes. This scenario has led to more interest in developing crops with greater productivity and sustainability. The process of genetic transformation, a major tool for crop improvement, utilizes promoters as one of its key elements. Those promoters are generally divided into three types： constitutive, spatiotemporal, and condition-dependent. Tran- scriptional control of a constitutive promoter often leads to reduced plant growth, due to a negative effect of accumu- lated molecules during cellular functions or energy consump- tion. To maximize the effect of a transgene on transgenic plants, it is better to use condition-dependent or tissue- specific promoters. However, until now, those types have not been as widely applied in crop biotechnology. In this review, we introduce and discuss four groups of tissue-specific promoters （5o promoters in total） and six groups of condition-dependent promoters （27 promoters）. These pro- moters can be utilized to fine-tune desirable agronomic traits and develop crops with tolerance to various stresses, enhanced nutritional value, and advanced productivity.
基金supported by the National Natural Science Foundation of China(Grant No.30270145)the“863”Projects(Grant No.2002AA224101)the National Special Program for Research and Industrialization of Transgenic Plants(Grant No.J99-A-038)in China.
文摘PNZIP gene promoter has been cloned from Pharbitis nil by adaptor PCR, which con-forms to eukaryotic promoter characteristic. Primer extension analysis showed that the transcrip-tion start site was located 122 nucleotides upstream of the translation start site of PNZIP gene. According to the characteristic of PNZIP promoter, a series of deletions were purposely made by PCR. Five deletion fragments were fused to upstream of GUS gene and transferred into tobacco. Fluorometric GUS assay showed that five different length promoters all could specifically drive GUS gene expression in photosynthetic tissues and their activities decreased along with the gradual deletion of PNZIP promoter. In addition, the activity of full-length promoter was 9 times higher than that of CaMV 35S in leaf. PNZIP promoter may have two putative cis-elements, GAAATA and GATACT, which relate to gene expression in photosynthetic tissues. GATACT may determine the gene specific expression in photosynthetic tissues, while GAAATA, perhaps, as an enhancer, increases the intensity of gene expression.
基金supported by grants from Shandong Provincial Natural Science Foundation (ZR2011CQ016 to Shijuan Liu)National Natural Science Foundation of China (31200196 to Shijuan Liu and 31170236 to Wei Zhang)
文摘Bidirectional promoters are relatively abundant in eukaryotic genomes, suggesting that they have an important biological significance. As yet, few of these promoters have been characterized in detail. Here, using a promoter：：GUS transgene approach has revealed that the intergenic region of Arabidopsis thaliana divergent genes At1g71850 and At1g71860 is an asymmetric bidirectional promoter, which exhibits an orientation-dependent expression profile. The strength of the forward promoter was greater than that of the reverse promoter, and their tissue specificities were not identical. Deletion analyses revealed that this bidirectional promoter could be divided into three functional regions. The basal level and tissue specificity of the promoter in the reverse orientation were regulated positively by region II and negatively by region III, whereas promoter activity in the forward orientation was regulated negatively by region II and positively by region I. Thus the 52-bp stretch of region II had a dual function, enhancing expression in the reverse orientation and suppressing it in the forward orientation. These results demonstrated that the activity of the At1g71850-At1g71860 bidirectional promoter was modulated by complex interactions between both positive and negative cis-acting elements. These findings will enhance our understanding of the regulatory mechanisms of plant bidirectional promoters.
文摘Mdm2 and Mdm4 are negative regulators of the tumour suppressor p53; hence, this relationship is the focus of many cancerrelated studies. A multitude of experiments across various developmental stages have been conducted to explore the tissuespecific roles of these proteins in the mouse. When Mdm2 or Mdm4 are deleted in the germiine or specific tissues, they display different phenotypic defects, some of which lead to embryonic lethaLity. Mdm2 loss is often more deleterious than toss of its homotogue Mdm4. ALL tissues experience activation of p53 target genes upon toss of Mdm2 or Mdm4; however, the degree to which the p53 pathway is perturbed is highly tissue-specific and does not correlate to the severity of the morphological pheno- types. Therefore, a need for further understanding of how these proteins regulate p53 activity is warranted, as therapeutic targeting of the p53 pathway is rapidly evoLving and gaining attention in the field of cancer research. In this review, we discuss the tissue-specificity of Mdm proteins in regulating p53 and expose the need for investigation at the celt-specific level.
基金supported by the National Research Foundation of Korea(NRF)grant funded by the Korean government(MSIP)(NRF-2020M3H4A1A02084827)(D.-W.C)and the U.S.NIH/NIBIB grants#R01EB022230(H.S.C.).
文摘Owing to the prevalence of rotator cuff(RC)injuries and suboptimal healing outcome,rapid and functional regeneration of the tendon-bone interface(TBI)after RC repair continues to be a major clinical challenge.Given the essential role of the RC in shoulder movement,the engineering of biomimetic multi-tissue constructs presents an opportunity for complex TBI reconstruction after RC repair.Here,we propose a gradient cell-laden multi-tissue construct combined with compositional gradient TBI-specific bioinks via 3D cell-printing technology.In vitro studies demonstrated the capability of a gradient scaffold system in zone-specific inducibility and multi-tissue formation mimicking TBI.The regenerative performance of the gradient scaffold on RC regeneration was determined using a rat RC repair model.In particular,we adopted nondestructive,consecutive,and tissue-targeted near-infrared fluorescence imaging to visualize the direct anatomical change and the intricate RC regeneration progression in real time in vivo.Furthermore,the 3D cell-printed implant promotes effective restoration of shoulder locomotion function and accelerates TBI healing in vivo.In summary,this study identifies the therapeutic contribution of cell-printed constructs towards functional RC regeneration,demonstrating the translational potential of biomimetic gradient constructs for the clinical repair of multi-tissue interfaces.
文摘Mesenchymal stem/progenitor cells (MSC/MPC) from a variety of tissue sources (bone marrow, adipose tissue, fat pads, synovial membranes, synovial fluid, skin, muscle and periosteal tissue) have been widely applied for tissue engineering applications to generate replacements for injured or degenerated tissues. Alternatively, they have also been injected as free cells in an attempt to facilitate in vivo repair. Nearly all studies reported have used mixed cell populations of MSC/MPC, usually defined by cell surface phenotypes and/or functional ability to differentiate towards multiple cell lineages. Using more detailed cell surface phenotyping and limiting dilution approaches to isolate individual MSC/MPC clones have indicated that such mixed cell populations are very heterogeneous. In addition subsets of cells from different sources may have epigenetic modifications. While it is clear that MSC/MPC cells exhibit heterogeneity, the question of why this is the case has not been well addressed. This review will address some of these issues, as well as provide some insights into the implications when using such diverse cells for tissue engineering applications.
