F-box proteins are components of the SCF （SkpA-Cullin 1-F-box） E3 ligase complexes, acting as the specificity-determinants in targeting substrate proteins for ubiquitination and degradation. In humans, at least 22 o...F-box proteins are components of the SCF （SkpA-Cullin 1-F-box） E3 ligase complexes, acting as the specificity-determinants in targeting substrate proteins for ubiquitination and degradation. In humans, at least 22 out of 75 F-box proteins have experimentally documented substrates, whereas in Drosophila 12 F-box proteins have been characterized with known substrates. To systematically investigate the genetic and molecular functions of F-box proteins in Drosophila, we performed a survey of the literature and databases. We identified 45 Drosophila genes that encode proteins containing at least one F-box domain. We collected publically available RNAi lines against these genes and used them in a tissue-specific RNAi-based phenotypic screen. Here, we present our systematic phenotypic dataset from the eye, the wing and the notum. This dataset is the first of its kind and represents a useful resource for future studies of the molecular and genetic functions of F-box genes in Drosophila. Our results show that, as expected, F-box genes in Drosophila have regulatory roles in a diverse array of processes including cell proliferation, cell growth, signal transduction, and cellular and animal survival.展开更多
Objective Cytokine responses to activation of innate immunity differ between individuals,yet the genomic and tissue-specific transcriptomic determinants of inflammatory responsiveness are not well understood. We hypot...Objective Cytokine responses to activation of innate immunity differ between individuals,yet the genomic and tissue-specific transcriptomic determinants of inflammatory responsiveness are not well understood. We hypothesized that tissue-specific mRNA and long intergenic non-coding RNA (lincRNA) induction differs between individuals with divergent evoked inflammatory responses.展开更多
Surgical resection,chemotherapy,and radiation are the standard therapeutic modalities for treating cancer.These approaches are intended to target the more mature and rapidly dividing cancer cells.However,they spare th...Surgical resection,chemotherapy,and radiation are the standard therapeutic modalities for treating cancer.These approaches are intended to target the more mature and rapidly dividing cancer cells.However,they spare the relatively quiescent and intrinsically resistant cancer stem cells(CSCs)subpopulation residing within the tumor tissue.Thus,a temporary eradication is achieved and the tumor bulk tends to revert supported by CSCs'resistant features.Based on their unique expression profile,the identification,isolation,and selective targeting of CSCs hold great promise for challenging treatment failure and reducing the risk of cancer recurrence.Yet,targeting CSCs is limited mainly by the irrelevance of the utilized cancer models.A new era of targeted and personalized anti-cancer therapies has been developed with cancer patient-derived organoids(PDOs)as a tool for establishing pre-clinical tumor models.Herein,we discuss the updated and presently available tissue-specific CSC markers in five highly occurring solid tumors.Additionally,we highlight the advantage and relevance of the threedimensional PDOs culture model as a platform for modeling cancer,evaluating the efficacy of CSC-based therapeutics,and predicting drug response in cancer patients.展开更多
Introduction:Although many studies have shown the vast potential of circulating tumor cells(CTCs)detection in cancer diagnosis and prognosis,our understanding of their clinical significance is still far from complete....Introduction:Although many studies have shown the vast potential of circulating tumor cells(CTCs)detection in cancer diagnosis and prognosis,our understanding of their clinical significance is still far from complete.A major obstacle arises from the lack of well-established tumor or tissue-specific markers to detect CTCs by immunocytochemical staining after immunomagnetic enrichment(IE).Methods:We have established the utility of cytokeratin 20(CK20),a gastrointestinal tract specific marker,for the specific detection and identification of colorectal cancer(CRC)CTCs.This breakthrough was successfully validated in spike-in experiments using CRC cell line models followed by a pilot study which recruited 32 metastatic CRC patients,25 benign colorectal diseases patients and 27 normal subjects.Results:CK20-positive CTCs were detected in 90%metastatic CRC patients but not in benign colorectal diseases patients and normal subjects using this refined assay.Conclusions:These impressive results have laid the foundation for further development of CK20-positive CTCs as a promising marker in diagnosis,prognostication and treatment monitoring of metastatic CRC.展开更多
We are deeply interested in the recent findings onβ-arrestin 2.Liu et al demonstrated thatβ-arrestin 2 knockout provides significant protection in diabetic nephropathy,underscoring its potential as a promising thera...We are deeply interested in the recent findings onβ-arrestin 2.Liu et al demonstrated thatβ-arrestin 2 knockout provides significant protection in diabetic nephropathy,underscoring its potential as a promising therapeutic target for diabetic nephropathy treatment.Furthermore,the role ofβ-arrestin 2 in metabolic regulation is equally critical,particularly in insulin signaling,hepatic glucose production,and adipose tissue function.Althoughβ-arrestin 2 plays a distinct role in metabolism and kidney protection,its tissue-specific regulation opens up valuable avenues for developing targeted therapeutic strategies centered onβ-arrestin 2.展开更多
To investigate the tissue-specificities of isozymes and the genetic structureof wild spotted halibut ( Verasper variegatus) population, horizontal starch gel electrophoresiswas performed on 45 individuals collected in...To investigate the tissue-specificities of isozymes and the genetic structureof wild spotted halibut ( Verasper variegatus) population, horizontal starch gel electrophoresiswas performed on 45 individuals collected in part of the Yellow Sea. The performances of 17 isozymesin 8 kinds of tissues or organs were screened preliminarily in a TC-7.0 buffer system. The resultsshowed that the screened isozymes displayed remarkable tissue-specificities. Finally, 14 enzymes(AAT, ADH, EST, OPI, G3PDH, IDHP, LAP, LDH, MDH, MPI, PGDH, PGM, SDH and SOD) and 4 kinds of tissues(eye, skeleton muscle, liver and heart) were selected for genetic analysis. Fourteen isozymes areencoded by 20 loci, and 9 of them are polymorphic. The polymorphic loci are AAT-1~*, GPI-2~*,G3PDH~*, IDHP-1~*, LDH~*, MPI~*, PGM-1~*. PGM-2~* and SDH~*, and the proportion of polymorphic lociis 0.4500 (P_(0.99)) ? The mean values of observed and expected heterozygosities are 0.0278and 0.0265, respectively and the average effective number of alleles is 1.0675.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 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
The development of epigenetic maps, such as the ENCODE project in humans, provides resources for gene regulation studies and a reference for research of disease-related regulatory elements. However,epigenetic informat...The development of epigenetic maps, such as the ENCODE project in humans, provides resources for gene regulation studies and a reference for research of disease-related regulatory elements. However,epigenetic information, such as a bird-specific chromatin accessibility atlas, is currently lacking for the thousands of bird species currently described.The major genomic difference between birds and mammals is their shorter introns and intergenic distances, which seriously hinders the use of humans and mice as a reference for studying the function of important regulatory regions in birds. In this study, using chicken as a model bird species, we systematically compiled a chicken chromatin accessibility atlas using 53 Assay of Transposase Accessible Chromatin sequencing(ATAC-seq)samples across 11 tissues. An average of 50 ?796open chromatin regions were identified per sample,cumulatively accounting for 20.36% of the chicken genome. Tissue specificity was largely reflected by differences in intergenic and intronic peaks, with specific functional regulation achieved by two mechanisms: recruitment of several sequence-specific transcription factors and direct regulation of adjacent functional genes. By integrating data from genome-wide association studies, our results suggest that chicken body weight is driven by different regulatory variants active in growth-relevant tissues. We propose CAB39L(active in the duodenum), RCBTB1(muscle and liver), and novel long non-coding RNA ENSGALG00000053256(bone) as candidate genes regulating chicken body weight. Overall, this study demonstrates the value of epigenetic data in fine-mapping functional variants and provides a compendium of resources for further research on the epigenetics and evolution of birds and mammals.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
Tissue-specific knockout technology enables the analysis of the gene function in specific tissues in adult mammals.However,conventional strategy for producing tissue-specific knockout mice is a time- and labor-consumi...Tissue-specific knockout technology enables the analysis of the gene function in specific tissues in adult mammals.However,conventional strategy for producing tissue-specific knockout mice is a time- and labor-consuming process,restricting rapid study of the gene function in vivo.CRISPR-Cas9 system from bacteria is a simple and efficient gene-editing technique,which has enabled rapid generation of gene knockout lines in mouse by direct injection of CRISPR-Cas9 into zygotes.Here,we demonstrate CRISPR-Cas9-mediated spermatogenic cell-specific disruption of Scp3 gene in testes in one step.We first generated transgenic mice by pronuclear injection of a plasmid containing Hspa2 promoter driving Cas9 expression and showed Cas9 specific expression in spermatogenic cells.We then produced transgenic mice carrying Hspa2 promoter driven Cas9 and constitutive expressed sgRNA targeting Scp3 gene.Male founders were infertile due to developmental arrest of spermatogenic cells while female founders could produce progeny normally.Consistently,male progeny from female founders were infertile and females could transmit the transgenes to the next generation.Our study establishes a CRISPR-Cas9-based one-step strategy to analyze the gene function in adult tissues by a temporal-spatial pattern.展开更多
Rice varieties having high Fe concentration in the endospermic region can be used as a good source for Fe deficit population.In this study,303 Oryza sativa varieties and 1 Oryza rufipogon accession were assessed for s...Rice varieties having high Fe concentration in the endospermic region can be used as a good source for Fe deficit population.In this study,303 Oryza sativa varieties and 1 Oryza rufipogon accession were assessed for spatial Fe accumulation in grains by Prussian blue staining method.Spatial ferritin protein distribution in grains was visualized by immunohistochemistry,and ferritin expression was assessed in selected rice varieties using semi-quantitative reverse transcription PCR.Three popular rice varieties,namely Sarjoo 52,Madhukar and Jalmagna,and the O.rufipogon variety showed Fe in all the regions of grains,and the highest Fe concentration was observed in the embryo region.Some high-yielding varieties like Swarna,Swarna Sub 1,CSR13 and NDRR359 had lower Fe concentration in the embryo region.The highest Fe concentration was detected in O.rufipogon(49.8μg/g),followed by Sarjoo 52(26.1μg/g)and Madhukar(25.7μg/g).Phytic acid concentration was the minimum in O.rufipogon(5.75 mg/g)followed by Sarjoo 52(5.83 mg/g).Western blot and semi-quantitative reverse transcription PCR showed higher expression of ferritin gene in O.rufipogon,Sarjoo 52 and Madhukar.In conclusion,O.rufipogon and Sarjoo 52 had higher Fe concentration in the embryo regions as well as endosperm and aleurone layer,whereas the other varieties had lower Fe concentration in the endosperm.Sarjoo 52 could be used as a donor in the rice breeding program for the generation of new varieties with elevated grain Fe concentration.展开更多
The transcription activity of ectogenic human carcinoembryonic antigen （CEA） promoter in lung adenocarcinoma cells A549 was investigated for the further gene-targeting therapy. The reporter gene green fluorescent pr...The transcription activity of ectogenic human carcinoembryonic antigen （CEA） promoter in lung adenocarcinoma cells A549 was investigated for the further gene-targeting therapy. The reporter gene green fluorescent protein （GFP） driven by CEA promoter and human cytomegalovirus （CMV） promoter were relatively constructed and named plasmid pCEA-EGFP and pCMV-GFP respectively. The intensity of fluorescence was detected by fluorescence microscope and flow cytometry analysis after the pCEA-GFP and pSNAV-GFP plasmids were transfected into A549 cells through liposome respectively. The results showed （4,08±0.63） % of the A549 cells transfected with pCEA-AFP plasmid expressed, significantly lower than that of the A549 cells transfected with pCMV-GFP [（43.27±3.54） %]. It was suggested that ectogenic human CEA promoter in lung adenocarcinoma cells A549 was weakly expressed. The distinct specificity of CEA promoter in CEA high expression cells was regarded as a tool in selective gene therapy, but the transcription activity of ectogenic human CEA promoter was needed to increase in the future.展开更多
Establishing the hepatoma cell-specific expression of human interferon gene mediated by retroviral vectors. Methods: Human interferon-β complementary DNA (IFN-β cDNA) was inserted into polylinker site of pMNSM retro...Establishing the hepatoma cell-specific expression of human interferon gene mediated by retroviral vectors. Methods: Human interferon-β complementary DNA (IFN-β cDNA) was inserted into polylinker site of pMNSM retroviral vector to construct recombinant retroviral vector pMNSIFNB, where the transcription of IFN-β gene was driven by SV40 early region promoter, and MNAIFNB, where the transcription of IFN-β gene was driven by SV40 early region promoter regulated by α-fetoprotein enhancer. The retroviral constructs were respectively introduced into PA317 amphotropic packaging cells by means of lipofectamine mediated gene transfer procedure. The plasmids transfection efficiency was among (4-25)ｘ103 colonies/μg DNA/106 PA317 cells. The retrovirus infection efficiency was among (4. 5-500)ｘ104 Colony Forming Units (CFU)/ml. The recombinant retroviruses were used to infect human hepatoma cells, renal cell carcinoma cells and melanoma cell lines in the presence of 4 μg/ml polybrene. Results: Dot hybridization of total RNA from the neomycin resistant colonies and interferon expression assay indicated that human α-fetoprotein enhancer induced efficient and specific transcription and expression of IFN-β gene driven by the promoter of different origin in human hepatoma cells by which α-fetoprotein was highly produced. Conclusion: Cis-active element of α-fetoprotein gene can drive IFN-β gene specifically expressed in human hepatoma cells, which presents some valuable materials for the hepatoma-specific immune gene therapy.展开更多
The promoter is a cis-acting element in regulating gene expression. A promoterless plasmid containing UidA gene was transformed into tritordeum by barmbadment. Histochemical analysis of various tissues in transgenic t...The promoter is a cis-acting element in regulating gene expression. A promoterless plasmid containing UidA gene was transformed into tritordeum by barmbadment. Histochemical analysis of various tissues in transgenic tritordeum was carried to examine tissue-specific expression of GUS(beta-glucuronidase) activity. The pollen-specific promoter was trapped and identified successfully in a transformant line. PCR(polymerase chain reaction) method was used to isolate this pollen-specific promoter. By sequencing and analyzing the amplified fragment from PCR, a part of UidA gene and a flanking sequence were obtained. Some essential elements of plant promoters were found in the sequence. To determine the function of it, the cloned fragment was fused with UidA gene, then cloned and transformed into Triticum durum. The transgenic plant transformed by this vector showed GUS expression only in pollen. Therefore a pollen-specific promoter was isolated successfully.展开更多
The cis-regulatory elements of promoters regulate temporal and spatial expression of genes. DNA inethylation, histone methylation and histone acetylation are the main types of epigenetic modifications, which play impo...The cis-regulatory elements of promoters regulate temporal and spatial expression of genes. DNA inethylation, histone methylation and histone acetylation are the main types of epigenetic modifications, which play important roles in plant growth and development. DNA methylation could seilenco transposons, affect gene imprinting and gene expression. In this study, we found that granule bound starch synthase 1 （GBSSI） gene is expressed specifically in wheat endosperm rath- er than in the embryo. We also analyzed the cis-elements within this promoter region and found some seed-specific elements. In order to confirm the tissue specifici- ty, we cloned 4k bp sequences upstream of GBSS1 gene to link to vector with GUS and this construct was transferred to tobacco by Agrobacterium mediated transfor- marion. The results showed that wheat GBSS1 promoter mediated the seed-specific expression of GUS gene, hut not mediated expression in embryo. In addition, we found that GBSSI promoter is methylated in wheat embryo and de-methylated in wheat endosperm. Our study might provide the molecular basis for specific expres- sion of GBSSI gene.展开更多
Pearl millet(Pennisetum glaucum)is a major staple food in arid and semi-arid regions of sub-Saharan Africa,India,and South Asia.However,how epigenetic mechanisms regulate tissue-specific gene expression in this crop r...Pearl millet(Pennisetum glaucum)is a major staple food in arid and semi-arid regions of sub-Saharan Africa,India,and South Asia.However,how epigenetic mechanisms regulate tissue-specific gene expression in this crop remains poorly understood.In this study,we profiled multiple epigenetic features in the young panicles and roots of pearl millet using RNA-seq,ATAC-seq,whole-genome bisulfite sequencing,and ChIP-seq(H3K4me3 and H3K36me3).We identified thousands of genes that were differentially expressed between these two tissues.Root-specific genes were enriched for plant hormone signaling,oxidative phosphorylation,and stress responses.Analysis of chromatin accessibility revealed that root-specific accessible chromatin regions(ACRs)were enriched in binding motifs for stress-responsive transcription factors(e.g.,NAC,WRKY),whereas ACRs in young panicles were enriched in motifs for developmental regulators(e.g.,AP2/ERF).DNA methylation profiling revealed 25,141 tissue-specific differentially methylated regions,with CHH methylation—rather than CG or CHG methylation—showing the strongest tissue specificity.Promoters of root-specific genes had higher levels of CHH methylation compared to those of young panicle–specific genes,suggesting that the roles of CHH methylation in regulating transcription might be tissue dependent.Notably,promoter-associated H3K4me3 marked panicle-specific genes,whereas root-specific expression was primarily linked to chromatin accessibility,suggesting a transcription factor–mediated regulatory mechanism.Together,our findings highlight the distinct epigenetic frameworks governing tissue-specific gene expression in pearl millet and provide valuable insights for advancing the genetic improvement of this crop.展开更多
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 （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
A promoter of the PNZIP （Pharbitis nil leucine zipper） gene （1.459 kb） was cloned from Pharbitis nil and fused to the GUS（^-glucuronidase） and Bacillus thuringiensis endotoxin （Cry9C） genes. Several transgenic...A promoter of the PNZIP （Pharbitis nil leucine zipper） gene （1.459 kb） was cloned from Pharbitis nil and fused to the GUS（^-glucuronidase） and Bacillus thuringiensis endotoxin （Cry9C） genes. Several transgenic PNZIP：：GUS and PNZIP：：Cry9C cotton lines were developed by Agrobacterium-mediated transformation. Strong GUS staining was detected in the green tissues of the transgenic PNZIP：：GUS cotton plants. In contrast, GUS staining in the reproductive structures such as petals, anther, and immature seeds of PNZIP：：GUS cotton was very faint. Two transgenic PNZIP：：Cry9C lines and one trans- genic cauliflower mosaic virus （CaMV） 35S：：Cry9C line were selected for enzyme-linked immunosorbent assay （ELISA） and insect bioassays. Expression of the Cry9C protein in the 35S：：Cry9C line maintained a high level in most tissues ranging from 24.6 to 45.5 ~tg g-I fresh weight. In green tissues such as the leaves, boll rinds, and bracts of the PNZIP：：Cry9C line, the Cry9C protein accumulated up to 50.2, 39.7, and 48.3 jag g-a fresh weight respectively. In contrast, seeds of the PNZIP：：Cry9C line （PZ1.3） accumulated only 0.26 ~ag g-~ fresh weight of the Cry9C protein, which was 100 times lower than that recorded for the seeds of the CaMV 35S：：Cry9C line. The insect bioassay showed that the transgenic PNZIP：：Cry9C cotton plant exhibited strong resistance to both the cotton bollworm and the pink bollworm. The PNZIP promoter could effectively drive Bt toxin ex- pression in green tissues of cotton and lower accumulated levels of the Bt protein in seeds. These features should allay public concerns about the safety of transgenic foods. We propose the future utility of PNZIP as an economical, environmentally friendly promoter in cotton biotechnology.展开更多
基金financially supported by the National Basic Research Program of China(973 Program)(No.2009CB918702)the National Natural Science Foundation of China(Nos.31071087 and 31100889)
文摘F-box proteins are components of the SCF （SkpA-Cullin 1-F-box） E3 ligase complexes, acting as the specificity-determinants in targeting substrate proteins for ubiquitination and degradation. In humans, at least 22 out of 75 F-box proteins have experimentally documented substrates, whereas in Drosophila 12 F-box proteins have been characterized with known substrates. To systematically investigate the genetic and molecular functions of F-box proteins in Drosophila, we performed a survey of the literature and databases. We identified 45 Drosophila genes that encode proteins containing at least one F-box domain. We collected publically available RNAi lines against these genes and used them in a tissue-specific RNAi-based phenotypic screen. Here, we present our systematic phenotypic dataset from the eye, the wing and the notum. This dataset is the first of its kind and represents a useful resource for future studies of the molecular and genetic functions of F-box genes in Drosophila. Our results show that, as expected, F-box genes in Drosophila have regulatory roles in a diverse array of processes including cell proliferation, cell growth, signal transduction, and cellular and animal survival.
文摘Objective Cytokine responses to activation of innate immunity differ between individuals,yet the genomic and tissue-specific transcriptomic determinants of inflammatory responsiveness are not well understood. We hypothesized that tissue-specific mRNA and long intergenic non-coding RNA (lincRNA) induction differs between individuals with divergent evoked inflammatory responses.
文摘Surgical resection,chemotherapy,and radiation are the standard therapeutic modalities for treating cancer.These approaches are intended to target the more mature and rapidly dividing cancer cells.However,they spare the relatively quiescent and intrinsically resistant cancer stem cells(CSCs)subpopulation residing within the tumor tissue.Thus,a temporary eradication is achieved and the tumor bulk tends to revert supported by CSCs'resistant features.Based on their unique expression profile,the identification,isolation,and selective targeting of CSCs hold great promise for challenging treatment failure and reducing the risk of cancer recurrence.Yet,targeting CSCs is limited mainly by the irrelevance of the utilized cancer models.A new era of targeted and personalized anti-cancer therapies has been developed with cancer patient-derived organoids(PDOs)as a tool for establishing pre-clinical tumor models.Herein,we discuss the updated and presently available tissue-specific CSC markers in five highly occurring solid tumors.Additionally,we highlight the advantage and relevance of the threedimensional PDOs culture model as a platform for modeling cancer,evaluating the efficacy of CSC-based therapeutics,and predicting drug response in cancer patients.
文摘Introduction:Although many studies have shown the vast potential of circulating tumor cells(CTCs)detection in cancer diagnosis and prognosis,our understanding of their clinical significance is still far from complete.A major obstacle arises from the lack of well-established tumor or tissue-specific markers to detect CTCs by immunocytochemical staining after immunomagnetic enrichment(IE).Methods:We have established the utility of cytokeratin 20(CK20),a gastrointestinal tract specific marker,for the specific detection and identification of colorectal cancer(CRC)CTCs.This breakthrough was successfully validated in spike-in experiments using CRC cell line models followed by a pilot study which recruited 32 metastatic CRC patients,25 benign colorectal diseases patients and 27 normal subjects.Results:CK20-positive CTCs were detected in 90%metastatic CRC patients but not in benign colorectal diseases patients and normal subjects using this refined assay.Conclusions:These impressive results have laid the foundation for further development of CK20-positive CTCs as a promising marker in diagnosis,prognostication and treatment monitoring of metastatic CRC.
基金Supported by National Natural Science Foundation of China,No.82471616,No.82170418,and No.82271618Natural Science Foundation of Hubei Province,No.2022CFA015+2 种基金Central Guiding Local Science and Technology Development Project,No.2022BGE237Key Research and Development Program of Hubei Province,No.2022BCE001,and No.2023BCB139Hubei Provincial Health Commission Project,No.WJ2023M151。
文摘We are deeply interested in the recent findings onβ-arrestin 2.Liu et al demonstrated thatβ-arrestin 2 knockout provides significant protection in diabetic nephropathy,underscoring its potential as a promising therapeutic target for diabetic nephropathy treatment.Furthermore,the role ofβ-arrestin 2 in metabolic regulation is equally critical,particularly in insulin signaling,hepatic glucose production,and adipose tissue function.Althoughβ-arrestin 2 plays a distinct role in metabolism and kidney protection,its tissue-specific regulation opens up valuable avenues for developing targeted therapeutic strategies centered onβ-arrestin 2.
文摘To investigate the tissue-specificities of isozymes and the genetic structureof wild spotted halibut ( Verasper variegatus) population, horizontal starch gel electrophoresiswas performed on 45 individuals collected in part of the Yellow Sea. The performances of 17 isozymesin 8 kinds of tissues or organs were screened preliminarily in a TC-7.0 buffer system. The resultsshowed that the screened isozymes displayed remarkable tissue-specificities. Finally, 14 enzymes(AAT, ADH, EST, OPI, G3PDH, IDHP, LAP, LDH, MDH, MPI, PGDH, PGM, SDH and SOD) and 4 kinds of tissues(eye, skeleton muscle, liver and heart) were selected for genetic analysis. Fourteen isozymes areencoded by 20 loci, and 9 of them are polymorphic. The polymorphic loci are AAT-1~*, GPI-2~*,G3PDH~*, IDHP-1~*, LDH~*, MPI~*, PGM-1~*. PGM-2~* and SDH~*, and the proportion of polymorphic lociis 0.4500 (P_(0.99)) ? The mean values of observed and expected heterozygosities are 0.0278and 0.0265, respectively and the average effective number of alleles is 1.0675.
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 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.
基金supported by the National Natural Science Foundation of China(U2002205,32272862)。
文摘The development of epigenetic maps, such as the ENCODE project in humans, provides resources for gene regulation studies and a reference for research of disease-related regulatory elements. However,epigenetic information, such as a bird-specific chromatin accessibility atlas, is currently lacking for the thousands of bird species currently described.The major genomic difference between birds and mammals is their shorter introns and intergenic distances, which seriously hinders the use of humans and mice as a reference for studying the function of important regulatory regions in birds. In this study, using chicken as a model bird species, we systematically compiled a chicken chromatin accessibility atlas using 53 Assay of Transposase Accessible Chromatin sequencing(ATAC-seq)samples across 11 tissues. An average of 50 ?796open chromatin regions were identified per sample,cumulatively accounting for 20.36% of the chicken genome. Tissue specificity was largely reflected by differences in intergenic and intronic peaks, with specific functional regulation achieved by two mechanisms: recruitment of several sequence-specific transcription factors and direct regulation of adjacent functional genes. By integrating data from genome-wide association studies, our results suggest that chicken body weight is driven by different regulatory variants active in growth-relevant tissues. We propose CAB39L(active in the duodenum), RCBTB1(muscle and liver), and novel long non-coding RNA ENSGALG00000053256(bone) as candidate genes regulating chicken body weight. Overall, this study demonstrates the value of epigenetic data in fine-mapping functional variants and provides a compendium of resources for further research on the epigenetics and evolution of birds and mammals.
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.
基金supported by the grants from the Ministry of Science and Technology of China(Nos.2014CB964803 and 2015AA020307)the National Natural Science Foundation of China(Nos.91319310,31225017 and 31530048)the Chinese Academy of Sciences(No.XDA01010403)
文摘Tissue-specific knockout technology enables the analysis of the gene function in specific tissues in adult mammals.However,conventional strategy for producing tissue-specific knockout mice is a time- and labor-consuming process,restricting rapid study of the gene function in vivo.CRISPR-Cas9 system from bacteria is a simple and efficient gene-editing technique,which has enabled rapid generation of gene knockout lines in mouse by direct injection of CRISPR-Cas9 into zygotes.Here,we demonstrate CRISPR-Cas9-mediated spermatogenic cell-specific disruption of Scp3 gene in testes in one step.We first generated transgenic mice by pronuclear injection of a plasmid containing Hspa2 promoter driving Cas9 expression and showed Cas9 specific expression in spermatogenic cells.We then produced transgenic mice carrying Hspa2 promoter driven Cas9 and constitutive expressed sgRNA targeting Scp3 gene.Male founders were infertile due to developmental arrest of spermatogenic cells while female founders could produce progeny normally.Consistently,male progeny from female founders were infertile and females could transmit the transgenes to the next generation.Our study establishes a CRISPR-Cas9-based one-step strategy to analyze the gene function in adult tissues by a temporal-spatial pattern.
基金supported by the Department of Biotechnology,New Delhi,India.
文摘Rice varieties having high Fe concentration in the endospermic region can be used as a good source for Fe deficit population.In this study,303 Oryza sativa varieties and 1 Oryza rufipogon accession were assessed for spatial Fe accumulation in grains by Prussian blue staining method.Spatial ferritin protein distribution in grains was visualized by immunohistochemistry,and ferritin expression was assessed in selected rice varieties using semi-quantitative reverse transcription PCR.Three popular rice varieties,namely Sarjoo 52,Madhukar and Jalmagna,and the O.rufipogon variety showed Fe in all the regions of grains,and the highest Fe concentration was observed in the embryo region.Some high-yielding varieties like Swarna,Swarna Sub 1,CSR13 and NDRR359 had lower Fe concentration in the embryo region.The highest Fe concentration was detected in O.rufipogon(49.8μg/g),followed by Sarjoo 52(26.1μg/g)and Madhukar(25.7μg/g).Phytic acid concentration was the minimum in O.rufipogon(5.75 mg/g)followed by Sarjoo 52(5.83 mg/g).Western blot and semi-quantitative reverse transcription PCR showed higher expression of ferritin gene in O.rufipogon,Sarjoo 52 and Madhukar.In conclusion,O.rufipogon and Sarjoo 52 had higher Fe concentration in the embryo regions as well as endosperm and aleurone layer,whereas the other varieties had lower Fe concentration in the endosperm.Sarjoo 52 could be used as a donor in the rice breeding program for the generation of new varieties with elevated grain Fe concentration.
基金This project was supported by a grant from Hubei Provincial Natural Sciences of China (No. 2003ABA144)
文摘The transcription activity of ectogenic human carcinoembryonic antigen （CEA） promoter in lung adenocarcinoma cells A549 was investigated for the further gene-targeting therapy. The reporter gene green fluorescent protein （GFP） driven by CEA promoter and human cytomegalovirus （CMV） promoter were relatively constructed and named plasmid pCEA-EGFP and pCMV-GFP respectively. The intensity of fluorescence was detected by fluorescence microscope and flow cytometry analysis after the pCEA-GFP and pSNAV-GFP plasmids were transfected into A549 cells through liposome respectively. The results showed （4,08±0.63） % of the A549 cells transfected with pCEA-AFP plasmid expressed, significantly lower than that of the A549 cells transfected with pCMV-GFP [（43.27±3.54） %]. It was suggested that ectogenic human CEA promoter in lung adenocarcinoma cells A549 was weakly expressed. The distinct specificity of CEA promoter in CEA high expression cells was regarded as a tool in selective gene therapy, but the transcription activity of ectogenic human CEA promoter was needed to increase in the future.
文摘Establishing the hepatoma cell-specific expression of human interferon gene mediated by retroviral vectors. Methods: Human interferon-β complementary DNA (IFN-β cDNA) was inserted into polylinker site of pMNSM retroviral vector to construct recombinant retroviral vector pMNSIFNB, where the transcription of IFN-β gene was driven by SV40 early region promoter, and MNAIFNB, where the transcription of IFN-β gene was driven by SV40 early region promoter regulated by α-fetoprotein enhancer. The retroviral constructs were respectively introduced into PA317 amphotropic packaging cells by means of lipofectamine mediated gene transfer procedure. The plasmids transfection efficiency was among (4-25)ｘ103 colonies/μg DNA/106 PA317 cells. The retrovirus infection efficiency was among (4. 5-500)ｘ104 Colony Forming Units (CFU)/ml. The recombinant retroviruses were used to infect human hepatoma cells, renal cell carcinoma cells and melanoma cell lines in the presence of 4 μg/ml polybrene. Results: Dot hybridization of total RNA from the neomycin resistant colonies and interferon expression assay indicated that human α-fetoprotein enhancer induced efficient and specific transcription and expression of IFN-β gene driven by the promoter of different origin in human hepatoma cells by which α-fetoprotein was highly produced. Conclusion: Cis-active element of α-fetoprotein gene can drive IFN-β gene specifically expressed in human hepatoma cells, which presents some valuable materials for the hepatoma-specific immune gene therapy.
基金NSFC foundation,Guangdong Province and China Education Ministry joint production-education-research funding Program ( No. 2009B090300198)the Fundamental Research Funds for the Central Universities,HUST( No. M2009060)PhD dissertation Foundation of Huazhong University of Science & Technology
文摘The promoter is a cis-acting element in regulating gene expression. A promoterless plasmid containing UidA gene was transformed into tritordeum by barmbadment. Histochemical analysis of various tissues in transgenic tritordeum was carried to examine tissue-specific expression of GUS(beta-glucuronidase) activity. The pollen-specific promoter was trapped and identified successfully in a transformant line. PCR(polymerase chain reaction) method was used to isolate this pollen-specific promoter. By sequencing and analyzing the amplified fragment from PCR, a part of UidA gene and a flanking sequence were obtained. Some essential elements of plant promoters were found in the sequence. To determine the function of it, the cloned fragment was fused with UidA gene, then cloned and transformed into Triticum durum. The transgenic plant transformed by this vector showed GUS expression only in pollen. Therefore a pollen-specific promoter was isolated successfully.
基金Supported by Agricultural Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences(CXGC2016D01)
文摘The cis-regulatory elements of promoters regulate temporal and spatial expression of genes. DNA inethylation, histone methylation and histone acetylation are the main types of epigenetic modifications, which play important roles in plant growth and development. DNA methylation could seilenco transposons, affect gene imprinting and gene expression. In this study, we found that granule bound starch synthase 1 （GBSSI） gene is expressed specifically in wheat endosperm rath- er than in the embryo. We also analyzed the cis-elements within this promoter region and found some seed-specific elements. In order to confirm the tissue specifici- ty, we cloned 4k bp sequences upstream of GBSS1 gene to link to vector with GUS and this construct was transferred to tobacco by Agrobacterium mediated transfor- marion. The results showed that wheat GBSS1 promoter mediated the seed-specific expression of GUS gene, hut not mediated expression in embryo. In addition, we found that GBSSI promoter is methylated in wheat embryo and de-methylated in wheat endosperm. Our study might provide the molecular basis for specific expres- sion of GBSSI gene.
基金supported by the National Key Research and Development Program of China(2024YFC3407200,2023YFF1000800)the National Natural Science Foundation of China(32170554,32370582)+2 种基金the Natural Science Foundation of Fujian(2023J01486)the“Chu Ying”young talent project of Fujian,and funding for High-level Overseas Personnel(Ministry of Human Resources and Social Security)the Department of Science and Technology of Xizang Autonomous Region(No.XZ202501ZY0021).
文摘Pearl millet(Pennisetum glaucum)is a major staple food in arid and semi-arid regions of sub-Saharan Africa,India,and South Asia.However,how epigenetic mechanisms regulate tissue-specific gene expression in this crop remains poorly understood.In this study,we profiled multiple epigenetic features in the young panicles and roots of pearl millet using RNA-seq,ATAC-seq,whole-genome bisulfite sequencing,and ChIP-seq(H3K4me3 and H3K36me3).We identified thousands of genes that were differentially expressed between these two tissues.Root-specific genes were enriched for plant hormone signaling,oxidative phosphorylation,and stress responses.Analysis of chromatin accessibility revealed that root-specific accessible chromatin regions(ACRs)were enriched in binding motifs for stress-responsive transcription factors(e.g.,NAC,WRKY),whereas ACRs in young panicles were enriched in motifs for developmental regulators(e.g.,AP2/ERF).DNA methylation profiling revealed 25,141 tissue-specific differentially methylated regions,with CHH methylation—rather than CG or CHG methylation—showing the strongest tissue specificity.Promoters of root-specific genes had higher levels of CHH methylation compared to those of young panicle–specific genes,suggesting that the roles of CHH methylation in regulating transcription might be tissue dependent.Notably,promoter-associated H3K4me3 marked panicle-specific genes,whereas root-specific expression was primarily linked to chromatin accessibility,suggesting a transcription factor–mediated regulatory mechanism.Together,our findings highlight the distinct epigenetic frameworks governing tissue-specific gene expression in pearl millet and provide valuable insights for advancing the genetic improvement of this crop.
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 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the National Natural Science Foundation of China (31171592, 31371673)Fundamental Research Funds for the Central Universities (2013PY064)
文摘A promoter of the PNZIP （Pharbitis nil leucine zipper） gene （1.459 kb） was cloned from Pharbitis nil and fused to the GUS（^-glucuronidase） and Bacillus thuringiensis endotoxin （Cry9C） genes. Several transgenic PNZIP：：GUS and PNZIP：：Cry9C cotton lines were developed by Agrobacterium-mediated transformation. Strong GUS staining was detected in the green tissues of the transgenic PNZIP：：GUS cotton plants. In contrast, GUS staining in the reproductive structures such as petals, anther, and immature seeds of PNZIP：：GUS cotton was very faint. Two transgenic PNZIP：：Cry9C lines and one trans- genic cauliflower mosaic virus （CaMV） 35S：：Cry9C line were selected for enzyme-linked immunosorbent assay （ELISA） and insect bioassays. Expression of the Cry9C protein in the 35S：：Cry9C line maintained a high level in most tissues ranging from 24.6 to 45.5 ~tg g-I fresh weight. In green tissues such as the leaves, boll rinds, and bracts of the PNZIP：：Cry9C line, the Cry9C protein accumulated up to 50.2, 39.7, and 48.3 jag g-a fresh weight respectively. In contrast, seeds of the PNZIP：：Cry9C line （PZ1.3） accumulated only 0.26 ~ag g-~ fresh weight of the Cry9C protein, which was 100 times lower than that recorded for the seeds of the CaMV 35S：：Cry9C line. The insect bioassay showed that the transgenic PNZIP：：Cry9C cotton plant exhibited strong resistance to both the cotton bollworm and the pink bollworm. The PNZIP promoter could effectively drive Bt toxin ex- pression in green tissues of cotton and lower accumulated levels of the Bt protein in seeds. These features should allay public concerns about the safety of transgenic foods. We propose the future utility of PNZIP as an economical, environmentally friendly promoter in cotton biotechnology.
