AIM： TO investigate the protein profile of human hepatocarcinoma cell line SMMC-7721, to analyze the specific functions of abundant expressed proteins in the processes of hepatocarcinoma genesis, growth and metastasi...AIM： TO investigate the protein profile of human hepatocarcinoma cell line SMMC-7721, to analyze the specific functions of abundant expressed proteins in the processes of hepatocarcinoma genesis, growth and metastasis, to identify the hepatocarcinoma-specific biomarkers for the early prediction in diagnosis, and to explore the new drug targets for liver cancer therapy. METHODS： Total proteins from human hepatocarcinoma cell line SMMC-7721 were separated by two-dimensional electrophoresis （2DE）. The silver-stained gel was analyzed by 2DE software Image Master 2D Elite. Interesting protein spots were identified by peptide mass fingerprinting based on matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry （MALDI-TOF-MS） and database searching. RESULTS： We obtained protein profile of human hepatocarcinoma cell line SMMC-7721. Among the twenty-one successfully identified proteins, mitofilin, endoplasmic reticulum protein ERp29, ubiquinol-cytochrome C reductase complex core protein I, peroxisomal enoyl CoA hydratase, peroxiredoxin-4 and probable 3-oxoacid CoA transferase 1 precursor were the six novel proteins identified in human hepatocarcinoma cells or tissues. Specific functions of the identified heat-shock proteins were analyzed in detail, and the results suggested that these proteins might promote tumorigenesis via inhibiting cell death induced by several cancer-related stresses or via inhibiting apoptosis at multiple points in the apoptotic signal pathway. Other identified chaperones and cancer-related proteins were also analyzed.CONCLUSION： Based on the protein profile of SMMC-7721 cells, functional analysis suggests that the identified chaperones and cancer-related proteins have their own pathways to contribute to the tumorigenesis, tumor growth and metastasis of liver cancer. Furthermore, proteomic analysis is indicated to be feasible in the cancer study.展开更多
This paper reported firstly successful cloning of lycopene ε-cyclase （lbLCYe） gene from sweetpotato, lpomoea batatas （L.） Lam. Using rapid amplification of cDNA ends （RACE）, lbLCYe gene was cloned from sweetpot...This paper reported firstly successful cloning of lycopene ε-cyclase （lbLCYe） gene from sweetpotato, lpomoea batatas （L.） Lam. Using rapid amplification of cDNA ends （RACE）, lbLCYe gene was cloned from sweetpotato cv. Nongdafu 14 with high carotenoid content. The 1 805 bp cDNA sequence oflbLCYe gene contained a 1236 bp open reading frame （ORF） encoding a 411 amino acids polypeptide with a molecular weight of 47 kDa and an isoelectric point （pI） of 6.95. IbLCYe protein contained one potential lycopene ε-cyclase domain and one potential FAD （flavinadenine dinucleotide）/NAD（P） （nicotinamide adenine dinucleotide phosphate）-binding domain, indicating that this protein shares the typical characteristics of LCYe proteins. The gDNA oflbLCYe gene was 4 029 bp and deduced to contain 5 introns and 6 exons. Real-time quantitative PCR analysis revealed that the expression level of IbLCYe gene was significantly higher in the storage roots of Nongdafu 14 than those in the leaves and stems. Transgenic tobacco （cv. Wisconsin 38） expressing [bLCYe gene accumulated significantly more ^-carotene compared to the untransformed control plants. These results showed that lbLCYe gene has an important function for the accumulation of carotenoids of sweetpotato.展开更多
An EMS(ethy methanesulfonate)-induced lethal etiolated(le)mutant obtained from the rice variety Zhongjian 100 was characterized by lethal etiolated phenotypes,with significantly reduced levels of chlorophyll a,chlorop...An EMS(ethy methanesulfonate)-induced lethal etiolated(le)mutant obtained from the rice variety Zhongjian 100 was characterized by lethal etiolated phenotypes,with significantly reduced levels of chlorophyll a,chlorophyll b,total chlorophyll,and carotenoids.Additionally,the mutant displayed a significantly decreased number of chloroplast grana,along with irregular and less-stacked grana lamellae.The le mutant showed markedly diminished root length,root surface area,and root volume compared with the wild type.It also exhibited significantly lower catalase activity and total protein content,while peroxidase activity was significantly higher.Using the map-based cloning method,we successfully mapped the LE gene to a 48-kb interval between markers RM16107 and RM16110 on rice chromosome 3.A mutation(from T to C)was identified at nucleotide position 692 bp of LOC_Os03g59640(ChlD),resulting in a change from leucine to proline.By crossing HM133(a pale green mutant with a single-base substitution of A for G in exon 10 of ChlD subunit)with a heterozygous line of le(LEle),we obtained two plant lines heterozygous at both the LE and HM133 loci.Among 15 transgenic plants,3 complementation lines displayed normal leaf color with significantly higher total chlorophyll,chlorophyll a,and chlorophyll b contents.The mutation in le led to a lethal etiolated phenotype,which has not been observed in other ChlD mutants.The mutation in the AAA+domain of ChlD disrupted the interaction of ChlDle with ChlI as demonstrated by a yeast two-hybrid assay,leading to the loss of ChlD function and hindering chlorophyll synthesis and chloroplast development.Consequently,this disruption is responsible for the lethal etiolated phenotype in the mutant.展开更多
Fiber cell initiation is a complex process involving many pathways,including phytohormones and components for transcriptional and posttranscriptional regulation.Here we report expression
The width of rice leaves determines the size of the photosynthetic area.Optimizing rice leaf width can improve the photosynthetic rate,thereby increasing rice yield.In this study,a genome-wide association study(GWAS)w...The width of rice leaves determines the size of the photosynthetic area.Optimizing rice leaf width can improve the photosynthetic rate,thereby increasing rice yield.In this study,a genome-wide association study(GWAS)was conducted by 225 rice germplasm resources to explore the genetic basis of rice flag leaf width(FLW).We identified nine QTLs associated with FLW(qFLWs),with phenotypic contribution rates ranging from 3.17%to 14.37%.Near-isogenic lines(NILs)were developed for fine-mapping of qFLW11,and the function of FLW11 was further verified.We narrowed down q FLW11 to an 87-kb interval,which contains five genes.展开更多
The SKP1 gene is an important component of the SCF(SKP1-Cullin1-F-box)complex and serves as a bridge connecting the F-box and Cullin1genes(F-box-SKP1-Cullin1).The pattern of S-RNase being ubiquitously labelled by the ...The SKP1 gene is an important component of the SCF(SKP1-Cullin1-F-box)complex and serves as a bridge connecting the F-box and Cullin1genes(F-box-SKP1-Cullin1).The pattern of S-RNase being ubiquitously labelled by the SCF complex and degraded by the 26S protease accounts for the bulk of the available self-incompatibility studies.In this study,15 ClSKP1s from the‘Xiangshui'lemon genome and ubiquitome exist in the same SKP1 conserved domain(CD)as SKP1s in other species.The q PCR results showed that SKP1-6 and SKP1-14 have tissue expression patterns specific for expression in pollen.In addition,SKP1-6 and SKP1-14 in the stigma,style and ovary were significantly upregulated after self-pollination compared to those after cross-pollination.A subcellular location showed that SKP1-6 and SKP1-14 were located in the nucleus.In addition,yeast two-hybrid(Y2H)assays,bimolecular fluorescence complementation(BiFC)and luciferase complementation imaging(LCI)assays showed that SKP1-6 interacted with F-box1,F-box33,F-box34,F-box17,F-box19,Cullin1-2 and 26S proteasome subunit 4 homolog A(26S PS4HA).SKP1-14 interacted with F-box17,F-box19,F-box35,Cullin1-2 and 26S PS4HA.The interaction of Cullin1-2 and the F-box with SKP1 as a bridge was verified by a yeast three-hybrid experiment.The ability of S3-RNase to inhibit pollen and pollen tube growth and development was assessed using in vitro pollen co-culture experiments with recombinant S3-RNase proteins.Overall,this study provides important experimental evidence and theoretical basis for understanding the mechanism of self-incompatibility in plants by revealing the key role of the SCF complex in‘Xiangshui'lemon,which is bridged by ClSKP1-6,in self-incompatibility.The results of this study are of great significance for the future indepth exploration of the molecular mechanism of the SCF complex and its wide application in the self-incompatibility of plants.展开更多
BACKGROUND ATP-binding cassette subfamily B member 4(ABCB4)deficiency is associated with cholestatic liver disease primarily because of missense mutations,and many variants remain unidentified.Here,we validate the pat...BACKGROUND ATP-binding cassette subfamily B member 4(ABCB4)deficiency is associated with cholestatic liver disease primarily because of missense mutations,and many variants remain unidentified.Here,we validate the pathogenicity and mechanism of ABCB4 variants in clinical and in vitro trials,hypothesizing that these variants are responsible for impaired biliary function and contribute to the development of cholestatic liver diseases.AIM To clarify the functional features and pathogenicity of ABCB4 variants.METHODS Clinical data were collected from five patients with cholestatic liver disease that was initially not detected by routine examinations.Later,whole-exome sequencing confirmed ABCB4 variants and the patients were treated from January 2017 to December 2023.Pathogenic mechanisms were analyzed using bioinformatics tools,and a cell model in vitro was established to investigate ABCB4 mRNA expression,multidrug resistance protein 3(MDR3)expression,cellular localization,and phosphatidylcholine secretion.Results were compared using Student's t-tests.RESULTS Five missense variants(c.1757T>A,c.1865G>A,c.2362C>T,c.2777C>T and c.3250C>T),one intron variant(c.537-32G>T),and one synonymous(c.C504T)variant were identified.Three of the five patients had various degrees of cholestasis,two presented with liver cirrhosis,and all had elevated gamma-glutamyl transferase.Three of the four patients who underwent a liver biopsy had bile duct dilation,and one had gallstones.Two of the four patients had normal and reduced MDR3 immunohistochemical levels.Bioinformatic analysis indicated that these variants were likely pathogenic except c.C504T variant.None of the missense variants influenced subcellular MDR3 Localization in vitro.However,the c.1865G>A variant significantly decreased ABCB4 mRNA values,and all missense variants down-regulated phosphatidylcholine secretion.CONCLUSION This study uncovered new ABCB4 variants and emphasized the pathogenic potential of specific variants.The findings from five patients provided insight into the pathogenic mechanisms underlying ABCB4-related diseases.展开更多
[Objectives]This study was conducted to comprehensively understand the changes in gene expression of plants under environmental stress during different growth and development stages.[Methods]The effects of continuous ...[Objectives]This study was conducted to comprehensively understand the changes in gene expression of plants under environmental stress during different growth and development stages.[Methods]The effects of continuous cropping on the roots and leaves of Polygonatum sibiricum were investigated using transcriptome sequencing.Normally-grown first crop P.sibiricum was used as the control group,while continuous cropping plants served as the treatment group.Transcriptomic differences in roots and leaves under different conditions were compared.[Results]The leaf materials of first crop and continuous cropping P.sibiricum(CCLZ vs FCLZ)showed 21916 differentially expressed genes(DEGs),while the root materials of first crop and continuous cropping P.sibiricum(CCRZ vs FCRZ)exhibited 12726 DEGs(the lowest DEG count)(12726).Among them,1896 DEGs were common.GO enrichment analysis revealed that DEGs were mainly enriched in metabolism,cell wall degradation,and pathogen defense.KEGG enrichment analysis indicated that DEGs in CCLZ vs FCLZ and CCRZ vs FCRZ primarily affected hormone signal transduction and pathogen interaction pathways.[Conclusions]This study preliminarily elucidate the regulatory mechanisms in the roots and leaves of continuous cropping P.sibiricum at the molecular level,providing reference for research on its adaptation to continuous cropping.展开更多
Temperature plays a crucial role in shaping microbial ecosystems during anaerobic digestion.However,the specific microbial communities and their functions across a wide temperature range still remain elusive.This stud...Temperature plays a crucial role in shaping microbial ecosystems during anaerobic digestion.However,the specific microbial communities and their functions across a wide temperature range still remain elusive.This study employed a genome-centric metagenomic approach to explore microbial metabolic pathways and synergistic networks at temperatures of 35,44,53,55,and 65℃.A total of 84 metagenome assembled genomes(MAGs)were assembled,with over 65%of these MAGs corresponding to novel bacterial and archaeal species(including Firmicutes,Chloroflexota,Bacteroidia and Methanobacteriota),greatly enhancing our current comprehension anaerobic digestion process.Notably,functional annotation identified that 44_bin.2(Methanothrix_A sp.001602645)harbors enzymes associated with hydrogenotrophic metabolism.Additionally,this microorganism exhibited diverse metabolic capabilities at 44℃,a temperature commonly employed in industrial practice yet less explored in bench studies.Consequently,it implies a promising potential for conducting anaerobic digestion at a moderate thermophilic temperature,as opposed to the conventional mesophilic range.The microorganism exhibited a variety of metabolic capabilities at 44℃,a temperature frequently employed in industrial applications but underexplored in laboratory investigations.The findings suggest that anaerobic digestion carried out at moderate thermophilic temperatures may have a higher potential for methane production.展开更多
Objective Humans are exposed to complex mixtures of environmental chemicals and other factors that can affect their health.Analysis of these mixture exposures presents several key challenges for environmental epidemio...Objective Humans are exposed to complex mixtures of environmental chemicals and other factors that can affect their health.Analysis of these mixture exposures presents several key challenges for environmental epidemiology and risk assessment,including high dimensionality,correlated exposure,and subtle individual effects.Methods We proposed a novel statistical approach,the generalized functional linear model(GFLM),to analyze the health effects of exposure mixtures.GFLM treats the effect of mixture exposures as a smooth function by reordering exposures based on specific mechanisms and capturing internal correlations to provide a meaningful estimation and interpretation.The robustness and efficiency was evaluated under various scenarios through extensive simulation studies.Results We applied the GFLM to two datasets from the National Health and Nutrition Examination Survey(NHANES).In the first application,we examined the effects of 37 nutrients on BMI(2011–2016 cycles).The GFLM identified a significant mixture effect,with fiber and fat emerging as the nutrients with the greatest negative and positive effects on BMI,respectively.For the second application,we investigated the association between four pre-and perfluoroalkyl substances(PFAS)and gout risk(2007–2018 cycles).Unlike traditional methods,the GFLM indicated no significant association,demonstrating its robustness to multicollinearity.Conclusion GFLM framework is a powerful tool for mixture exposure analysis,offering improved handling of correlated exposures and interpretable results.It demonstrates robust performance across various scenarios and real-world applications,advancing our understanding of complex environmental exposures and their health impacts on environmental epidemiology and toxicology.展开更多
In this paper,a standardized analysis method is established for identifying meat quality-related genes in Ordos finewool sheep using transcriptome sequencing data.A meticulously standardized approach is utilized to in...In this paper,a standardized analysis method is established for identifying meat quality-related genes in Ordos finewool sheep using transcriptome sequencing data.A meticulously standardized approach is utilized to investigate the genetic determinants of meat quality in Ordos fine-wool sheep through transcriptome sequencing analysis.Muscle samples from the longissimus dorsi of one-year-old sheep are collected under controlled conditions,and key texture properties—hardness,elasticity,and chewiness—are measured to categorize samples into high-and low-textural-value groups.Genes significantly associated with meat quality traits are identified through standardized RNA extraction,high-throughput sequencing,and differential gene expression analysis.Functional enrichment analysis reveals their involvement in biological processes such as extracellular matrix organization and metabolic pathways.The findings underscore the pivotal role of standardization in meat quality research,laying a solid scientific foundation for future research on meat quality improvement and molecular breeding.展开更多
Four samples were chosen by systematic sampling from the range-finders between 1987 and 2003 to test the range-finders’ representativeness of the scoring criteria of CET-4 compositions. The samples were analyzed from...Four samples were chosen by systematic sampling from the range-finders between 1987 and 2003 to test the range-finders’ representativeness of the scoring criteria of CET-4 compositions. The samples were analyzed from the perspectives of transitivity, modality, thematic structure and cohesion. Fisher's Exact Test from the SAS system was used to compare two-sidedly the correct rate and the constituent ratio of these functional usages between two neighboring levels. Statistical results indicate that it is the quality, not the quantity of these functional usages that distinguishes two neighboring levels. The range-finders can basically represent the abstract scoring criteria as far as the four functional systems are concerned. However, the validity of CET-4 writing needs to be improved.展开更多
Background:Systemic lupus erythematosus(SLE)is an autoimmune disease that can affect multiple systems.Sjogren's syndrome(SS)is an autoimmune disease that may be primary SS(pSS)or occur together with other autoimmu...Background:Systemic lupus erythematosus(SLE)is an autoimmune disease that can affect multiple systems.Sjogren's syndrome(SS)is an autoimmune disease that may be primary SS(pSS)or occur together with other autoimmune diseases,including SLE.This study aimed to explore the shared gene signatures in SLE and pSS.Methods:Gene expression data sets of SLE(GSE50772 and GSE81622)and pSS(GSE84844 and GSE48378)were obtained and analyzed for differentially expressed genes(DEGs)in peripheral blood mononuclear cells(PBMCs).A protein–protein interaction(PPI)network was constructed.Gene ontology(GO)and KEGG pathway enrichment analysis were carried out for the DEGs.Results:We screened 232 and 110 DEGs from the SLE and pSS data sets,respectively.We found 32 shared DEGs,which were all upregulated in patients compared with controls.Among these 32 DEGs,11 genes showed a more than twofold change in all data sets(IFI27,IFI44L,RSAD2,IFIT1,IFI44,USP18,IFI6,HERC5,EPSTI1,OAS1,and OAS3).PPI analysis showed that 29 genes interacted with each other.GO analysis showed that these 32 shared DEGs were mainly enriched in biological processes associated with the type Ⅰ interferon signaling pathway,defense response to viruses,response to viruses,negative regulation of viral genome replication,and the immune response.Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that these 32 DEGs were related to virus infection.Conclusion:This study showed that alterations to biological processes associated with the response to virus infection play critical roles in both SLE and pSS.展开更多
Phenylalanine ammonia lyase(PAL)is the rate-limiting and pivotal enzyme of the general phenylpropanoid path-way,but few reports have been found on PAL genes in Pinus yunnanensis.In the present study,three PAL genes we...Phenylalanine ammonia lyase(PAL)is the rate-limiting and pivotal enzyme of the general phenylpropanoid path-way,but few reports have been found on PAL genes in Pinus yunnanensis.In the present study,three PAL genes were cloned and identified from P.yunnanensis seedlings for thefirst time,namely,PyPAL-1,PyPAL-2,and PyPAL-3.Our results indicated that the open-reading frames of PyPAL genes were 2184,2157,and 2385 bp.Phylogenetic tree analysis revealed that PyPALs have high homology with other known PAL genes in other plants.In vitro enzymatic analysis showed that all three PyPAL recombinant proteins could catalyze the deamination of L-phenylalanine to form trans-cinnamic acid,but only PAL1 and PAL2 can catalyze the conversion of L-tyrosine toρ-coumaric acid.Three PyPAL genes were expressed in different tissues in 1-year-old P.yunnanensis,and such genes had different expression patterns.This study lays a foundation for further understanding of the biosynthesis of secondary metabolites in P.yunnanensis.展开更多
Introduction:Osteoarthritis(OA)is still an important health problem,and understanding its pathological mechanisms is essential for its diagnosis and treatment.There is evidence that autophagy may play a role in OA pro...Introduction:Osteoarthritis(OA)is still an important health problem,and understanding its pathological mechanisms is essential for its diagnosis and treatment.There is evidence that autophagy may play a role in OA progression,but the exact mechanism remains unclear.Methods:In this study,we adopted a multi-prong approach to systematically identify the key autophagy-related genes(ARGs)associated with OA.Through weighted gene coexpression network analysis,we initially identified significant gene modules associated with OA.Subsequent differential gene analysis performed on normal and OA specimens.Further analysis later using the MCC algorithm highlighted hub ARGs.These genes were then incorporated into the prediction model of OA.In addition,the expression patterns of these DEGs were verified by in vitro experiments.Results:A total of 104 differentially expressed genes(DEGs)were identified by differential gene analysis,of which 102 were up-regulated and 2 were down-regulated.These differentially expressed genes were closely related to key signaling pathways,such as PI3K-Akt signaling pathway,IL-17 signaling pathway and osteoclast differentiation.Further MCC analysis highlighted 10 hub ARGs,among which ATF3,CYCS,FOXO3,KLF6,NFKBIA and SOCS3 were particularly significant,which were then included in the prediction model of OA,which showed robust prediction ability with an area under the curve of 0.783.In vitro experiments confirmed that the expression pattern of these DEGs was consistent with our prediction.Conclusion:In summary,our comprehensive analysis not only provides new insights into the molecular basis of OA,but also suggests potential biomarkers for its diagnosis.展开更多
A MADS-box gene,CiMADS9,was cloned from the male flowers of Carya illinoinensis by rapid amplification of cDNA ends. The gene was 1 077 bp with a 768 bp open reading frame encoding 255 amino acids. Multiple sequence c...A MADS-box gene,CiMADS9,was cloned from the male flowers of Carya illinoinensis by rapid amplification of cDNA ends. The gene was 1 077 bp with a 768 bp open reading frame encoding 255 amino acids. Multiple sequence comparisons revealed that Ci MADS9 is a typical MIKC-type MADS-box gene with a MADS-box domain and a K semi-conserved region. Phylogenetic analysis indicated that CiMADS9 belongs to the AGL15 group of the MADS-box gene family. Quantitative reverse transcription polymerase chain reaction analysis indicated that the expression levels in reproductive organs(i.e.,flowers and young fruits) were considerably higher than in vegetative tissues(i.e.,leaves and branches). The highest expression levels were observed in male flowers. An overexpression vector for CiMADS9 was constructed and the gene was inserted into the Arabidopsis thaliana genome. CiMADS9 expression was confirmed in all transgenic lines. Compared with wild-type plants,transgenic A. thaliana plants overexpressing CiMADS9 exhibited delayed flowering and an increased number of leaves.展开更多
Since entering the era of Industry 4.0,the concept of Healthcare 4.0 has also been put forward and explored by researchers.How to use Information Technology(IT)to better serve people’s healthcare is one of the most f...Since entering the era of Industry 4.0,the concept of Healthcare 4.0 has also been put forward and explored by researchers.How to use Information Technology(IT)to better serve people’s healthcare is one of the most featured emerging directions in the academic circle.An important field of Healthcare 4.0 research is the reliability engineering of healthcare service.Because healthcare systems often affect the health and even life of their users,developers must be very cautious in the design,development,and operation of these healthcare systems and services.The problems to be solved include the reliability of business process,system functions,and personal healthcare data.The Functional Resonance Analysis Method(FRAM)has been applied in reliability engineering for safety-critical systems in available studies,using both qualitative and quantitative approaches.However,the method has not been applied in the field of digital healthcare services development.Therefore,to narrow the gap,we present in this paper a semi-quantitative functional resonance analysis method to develop reliable healthcare services for diabetics.Moreover,this paper has tried to improve the reliability design of the service-oriented architecture(SOA)of traditional insulin pump therapy by system thinking.展开更多
Within a framework of Halliday＇s SFL （Systemic Functional Linguistics）, this paper takes a functional approach to the analysis of the fairy tale--＂The Little Match-Seller＂ （Andersen, 1846）. The analysis is carr...Within a framework of Halliday＇s SFL （Systemic Functional Linguistics）, this paper takes a functional approach to the analysis of the fairy tale--＂The Little Match-Seller＂ （Andersen, 1846）. The analysis is carried out in three respects： genre, register and language. Genre analysis indicates that the schematic structure of the fairy tale is very much in line with the one mentioned by Hasan. Register analysis shows that the material process is the most dominant one; the Finite in the clauses is predominantly in past tenses, and most of the Themes in the text are unmarked ones. Language analysis reveals that the lexical density in the fairy tale is relatively low. The findings in this paper can help deepen people＇s understanding of the textual features of English fairy tales.展开更多
As two main approaches to analyzing literary discourses,literary criticism and stylistic analysis have been employed for a long period of time.With the application of the theories of Functional Grammar,this paper is w...As two main approaches to analyzing literary discourses,literary criticism and stylistic analysis have been employed for a long period of time.With the application of the theories of Functional Grammar,this paper is written for the purpose of being helpful for the readers of Dylan Thomas’poem“Do not Go Gentle into That Good Night”to understand the poem’s theme better as well as appreciate the artistic adaptation of language.Furthermore,because the poem is analyzed with the application of Functional Grammar,it helps the readers to appreciate“Do not Go Gentle into That Good Night”from a new perspective.展开更多
基金Supported by the National Natural Science Foundation of China, No. 30370403the Key Project of Chinese Ministry of Education, No. 705046the Doctoral Foundation of Xi’an Jiaotong University, grants No. DFXJTU2005-05
文摘AIM： TO investigate the protein profile of human hepatocarcinoma cell line SMMC-7721, to analyze the specific functions of abundant expressed proteins in the processes of hepatocarcinoma genesis, growth and metastasis, to identify the hepatocarcinoma-specific biomarkers for the early prediction in diagnosis, and to explore the new drug targets for liver cancer therapy. METHODS： Total proteins from human hepatocarcinoma cell line SMMC-7721 were separated by two-dimensional electrophoresis （2DE）. The silver-stained gel was analyzed by 2DE software Image Master 2D Elite. Interesting protein spots were identified by peptide mass fingerprinting based on matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry （MALDI-TOF-MS） and database searching. RESULTS： We obtained protein profile of human hepatocarcinoma cell line SMMC-7721. Among the twenty-one successfully identified proteins, mitofilin, endoplasmic reticulum protein ERp29, ubiquinol-cytochrome C reductase complex core protein I, peroxisomal enoyl CoA hydratase, peroxiredoxin-4 and probable 3-oxoacid CoA transferase 1 precursor were the six novel proteins identified in human hepatocarcinoma cells or tissues. Specific functions of the identified heat-shock proteins were analyzed in detail, and the results suggested that these proteins might promote tumorigenesis via inhibiting cell death induced by several cancer-related stresses or via inhibiting apoptosis at multiple points in the apoptotic signal pathway. Other identified chaperones and cancer-related proteins were also analyzed.CONCLUSION： Based on the protein profile of SMMC-7721 cells, functional analysis suggests that the identified chaperones and cancer-related proteins have their own pathways to contribute to the tumorigenesis, tumor growth and metastasis of liver cancer. Furthermore, proteomic analysis is indicated to be feasible in the cancer study.
基金supported by the China Agriculture Research System (Sweetpotato)the National High-Tech Research and Development Project of China(2011AA100607 and 2012AA101204)
文摘This paper reported firstly successful cloning of lycopene ε-cyclase （lbLCYe） gene from sweetpotato, lpomoea batatas （L.） Lam. Using rapid amplification of cDNA ends （RACE）, lbLCYe gene was cloned from sweetpotato cv. Nongdafu 14 with high carotenoid content. The 1 805 bp cDNA sequence oflbLCYe gene contained a 1236 bp open reading frame （ORF） encoding a 411 amino acids polypeptide with a molecular weight of 47 kDa and an isoelectric point （pI） of 6.95. IbLCYe protein contained one potential lycopene ε-cyclase domain and one potential FAD （flavinadenine dinucleotide）/NAD（P） （nicotinamide adenine dinucleotide phosphate）-binding domain, indicating that this protein shares the typical characteristics of LCYe proteins. The gDNA oflbLCYe gene was 4 029 bp and deduced to contain 5 introns and 6 exons. Real-time quantitative PCR analysis revealed that the expression level of IbLCYe gene was significantly higher in the storage roots of Nongdafu 14 than those in the leaves and stems. Transgenic tobacco （cv. Wisconsin 38） expressing [bLCYe gene accumulated significantly more ^-carotene compared to the untransformed control plants. These results showed that lbLCYe gene has an important function for the accumulation of carotenoids of sweetpotato.
基金supported by the National Natural Science Foundation of China(Grant No.32072049)Open Foundation of State Key Laboratory of Rice Biology,China(Grant No.20210208).
文摘An EMS(ethy methanesulfonate)-induced lethal etiolated(le)mutant obtained from the rice variety Zhongjian 100 was characterized by lethal etiolated phenotypes,with significantly reduced levels of chlorophyll a,chlorophyll b,total chlorophyll,and carotenoids.Additionally,the mutant displayed a significantly decreased number of chloroplast grana,along with irregular and less-stacked grana lamellae.The le mutant showed markedly diminished root length,root surface area,and root volume compared with the wild type.It also exhibited significantly lower catalase activity and total protein content,while peroxidase activity was significantly higher.Using the map-based cloning method,we successfully mapped the LE gene to a 48-kb interval between markers RM16107 and RM16110 on rice chromosome 3.A mutation(from T to C)was identified at nucleotide position 692 bp of LOC_Os03g59640(ChlD),resulting in a change from leucine to proline.By crossing HM133(a pale green mutant with a single-base substitution of A for G in exon 10 of ChlD subunit)with a heterozygous line of le(LEle),we obtained two plant lines heterozygous at both the LE and HM133 loci.Among 15 transgenic plants,3 complementation lines displayed normal leaf color with significantly higher total chlorophyll,chlorophyll a,and chlorophyll b contents.The mutation in le led to a lethal etiolated phenotype,which has not been observed in other ChlD mutants.The mutation in the AAA+domain of ChlD disrupted the interaction of ChlDle with ChlI as demonstrated by a yeast two-hybrid assay,leading to the loss of ChlD function and hindering chlorophyll synthesis and chloroplast development.Consequently,this disruption is responsible for the lethal etiolated phenotype in the mutant.
文摘Fiber cell initiation is a complex process involving many pathways,including phytohormones and components for transcriptional and posttranscriptional regulation.Here we report expression
基金supported by the Zhejiang Provincial Natural Science Foundation,China(Grant No.LD24C130001)the National Natural Science Foundation of China(Grant Nos.W2412006 and 32372125)+3 种基金the Hainan Provincial Natural Science Foundation,China(Grant Nos.GHYF2025029 and YBXM2422)the Innovation Platform for Academicians of Hainan Province,China(Grant No.YSPTZX202502)the National Modern Agricultural Industry Technology System Project,China(Grant No.CARS-01-18)the Special Support Program of Chinese Academy of Agricultural Sciences(Grant Nos.NKYCLJ-C-2021-015 and CAAS-ZDRW202401)。
文摘The width of rice leaves determines the size of the photosynthetic area.Optimizing rice leaf width can improve the photosynthetic rate,thereby increasing rice yield.In this study,a genome-wide association study(GWAS)was conducted by 225 rice germplasm resources to explore the genetic basis of rice flag leaf width(FLW).We identified nine QTLs associated with FLW(qFLWs),with phenotypic contribution rates ranging from 3.17%to 14.37%.Near-isogenic lines(NILs)were developed for fine-mapping of qFLW11,and the function of FLW11 was further verified.We narrowed down q FLW11 to an 87-kb interval,which contains five genes.
基金supported by grants from the National Natural Science Foundation of China(Grant No.31960585)Science and Technology Major Project of Guangxi(Grant No.Guike AA22068092)+1 种基金Guangxi Science and Technology Vanguard Special Action Project(Grant No.202204)State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources(Grant Nos.SKLCUSA-a201906,SKLCU-SA-c201901)。
文摘The SKP1 gene is an important component of the SCF(SKP1-Cullin1-F-box)complex and serves as a bridge connecting the F-box and Cullin1genes(F-box-SKP1-Cullin1).The pattern of S-RNase being ubiquitously labelled by the SCF complex and degraded by the 26S protease accounts for the bulk of the available self-incompatibility studies.In this study,15 ClSKP1s from the‘Xiangshui'lemon genome and ubiquitome exist in the same SKP1 conserved domain(CD)as SKP1s in other species.The q PCR results showed that SKP1-6 and SKP1-14 have tissue expression patterns specific for expression in pollen.In addition,SKP1-6 and SKP1-14 in the stigma,style and ovary were significantly upregulated after self-pollination compared to those after cross-pollination.A subcellular location showed that SKP1-6 and SKP1-14 were located in the nucleus.In addition,yeast two-hybrid(Y2H)assays,bimolecular fluorescence complementation(BiFC)and luciferase complementation imaging(LCI)assays showed that SKP1-6 interacted with F-box1,F-box33,F-box34,F-box17,F-box19,Cullin1-2 and 26S proteasome subunit 4 homolog A(26S PS4HA).SKP1-14 interacted with F-box17,F-box19,F-box35,Cullin1-2 and 26S PS4HA.The interaction of Cullin1-2 and the F-box with SKP1 as a bridge was verified by a yeast three-hybrid experiment.The ability of S3-RNase to inhibit pollen and pollen tube growth and development was assessed using in vitro pollen co-culture experiments with recombinant S3-RNase proteins.Overall,this study provides important experimental evidence and theoretical basis for understanding the mechanism of self-incompatibility in plants by revealing the key role of the SCF complex in‘Xiangshui'lemon,which is bridged by ClSKP1-6,in self-incompatibility.The results of this study are of great significance for the future indepth exploration of the molecular mechanism of the SCF complex and its wide application in the self-incompatibility of plants.
基金Supported by the National Natural Science Foundation of China,No.81970454.
文摘BACKGROUND ATP-binding cassette subfamily B member 4(ABCB4)deficiency is associated with cholestatic liver disease primarily because of missense mutations,and many variants remain unidentified.Here,we validate the pathogenicity and mechanism of ABCB4 variants in clinical and in vitro trials,hypothesizing that these variants are responsible for impaired biliary function and contribute to the development of cholestatic liver diseases.AIM To clarify the functional features and pathogenicity of ABCB4 variants.METHODS Clinical data were collected from five patients with cholestatic liver disease that was initially not detected by routine examinations.Later,whole-exome sequencing confirmed ABCB4 variants and the patients were treated from January 2017 to December 2023.Pathogenic mechanisms were analyzed using bioinformatics tools,and a cell model in vitro was established to investigate ABCB4 mRNA expression,multidrug resistance protein 3(MDR3)expression,cellular localization,and phosphatidylcholine secretion.Results were compared using Student's t-tests.RESULTS Five missense variants(c.1757T>A,c.1865G>A,c.2362C>T,c.2777C>T and c.3250C>T),one intron variant(c.537-32G>T),and one synonymous(c.C504T)variant were identified.Three of the five patients had various degrees of cholestasis,two presented with liver cirrhosis,and all had elevated gamma-glutamyl transferase.Three of the four patients who underwent a liver biopsy had bile duct dilation,and one had gallstones.Two of the four patients had normal and reduced MDR3 immunohistochemical levels.Bioinformatic analysis indicated that these variants were likely pathogenic except c.C504T variant.None of the missense variants influenced subcellular MDR3 Localization in vitro.However,the c.1865G>A variant significantly decreased ABCB4 mRNA values,and all missense variants down-regulated phosphatidylcholine secretion.CONCLUSION This study uncovered new ABCB4 variants and emphasized the pathogenic potential of specific variants.The findings from five patients provided insight into the pathogenic mechanisms underlying ABCB4-related diseases.
基金Supported by Agricultural Science and Technology Innovation Fund of Hunan Province(XCNZ[2021]No.15)Loudi Science and Technology Innovation Program(LKF[2022]29)+1 种基金Applied Characteristic Discipline Construction Project of Hunan Province:Plant ProtectionPostgraduate Research and Innovation Project of Hunan University of Humanities,Science and Technology(ZSCX2022Y12).
文摘[Objectives]This study was conducted to comprehensively understand the changes in gene expression of plants under environmental stress during different growth and development stages.[Methods]The effects of continuous cropping on the roots and leaves of Polygonatum sibiricum were investigated using transcriptome sequencing.Normally-grown first crop P.sibiricum was used as the control group,while continuous cropping plants served as the treatment group.Transcriptomic differences in roots and leaves under different conditions were compared.[Results]The leaf materials of first crop and continuous cropping P.sibiricum(CCLZ vs FCLZ)showed 21916 differentially expressed genes(DEGs),while the root materials of first crop and continuous cropping P.sibiricum(CCRZ vs FCRZ)exhibited 12726 DEGs(the lowest DEG count)(12726).Among them,1896 DEGs were common.GO enrichment analysis revealed that DEGs were mainly enriched in metabolism,cell wall degradation,and pathogen defense.KEGG enrichment analysis indicated that DEGs in CCLZ vs FCLZ and CCRZ vs FCRZ primarily affected hormone signal transduction and pathogen interaction pathways.[Conclusions]This study preliminarily elucidate the regulatory mechanisms in the roots and leaves of continuous cropping P.sibiricum at the molecular level,providing reference for research on its adaptation to continuous cropping.
基金supported by the National Natural Science Foundation of China(No.52270138)。
文摘Temperature plays a crucial role in shaping microbial ecosystems during anaerobic digestion.However,the specific microbial communities and their functions across a wide temperature range still remain elusive.This study employed a genome-centric metagenomic approach to explore microbial metabolic pathways and synergistic networks at temperatures of 35,44,53,55,and 65℃.A total of 84 metagenome assembled genomes(MAGs)were assembled,with over 65%of these MAGs corresponding to novel bacterial and archaeal species(including Firmicutes,Chloroflexota,Bacteroidia and Methanobacteriota),greatly enhancing our current comprehension anaerobic digestion process.Notably,functional annotation identified that 44_bin.2(Methanothrix_A sp.001602645)harbors enzymes associated with hydrogenotrophic metabolism.Additionally,this microorganism exhibited diverse metabolic capabilities at 44℃,a temperature commonly employed in industrial practice yet less explored in bench studies.Consequently,it implies a promising potential for conducting anaerobic digestion at a moderate thermophilic temperature,as opposed to the conventional mesophilic range.The microorganism exhibited a variety of metabolic capabilities at 44℃,a temperature frequently employed in industrial applications but underexplored in laboratory investigations.The findings suggest that anaerobic digestion carried out at moderate thermophilic temperatures may have a higher potential for methane production.
基金supported in part by the Young Scientists Fund of the National Natural Science Foundation of China(Grant Nos.82304253)(and 82273709)the Foundation for Young Talents in Higher Education of Guangdong Province(Grant No.2022KQNCX021)the PhD Starting Project of Guangdong Medical University(Grant No.GDMUB2022054).
文摘Objective Humans are exposed to complex mixtures of environmental chemicals and other factors that can affect their health.Analysis of these mixture exposures presents several key challenges for environmental epidemiology and risk assessment,including high dimensionality,correlated exposure,and subtle individual effects.Methods We proposed a novel statistical approach,the generalized functional linear model(GFLM),to analyze the health effects of exposure mixtures.GFLM treats the effect of mixture exposures as a smooth function by reordering exposures based on specific mechanisms and capturing internal correlations to provide a meaningful estimation and interpretation.The robustness and efficiency was evaluated under various scenarios through extensive simulation studies.Results We applied the GFLM to two datasets from the National Health and Nutrition Examination Survey(NHANES).In the first application,we examined the effects of 37 nutrients on BMI(2011–2016 cycles).The GFLM identified a significant mixture effect,with fiber and fat emerging as the nutrients with the greatest negative and positive effects on BMI,respectively.For the second application,we investigated the association between four pre-and perfluoroalkyl substances(PFAS)and gout risk(2007–2018 cycles).Unlike traditional methods,the GFLM indicated no significant association,demonstrating its robustness to multicollinearity.Conclusion GFLM framework is a powerful tool for mixture exposure analysis,offering improved handling of correlated exposures and interpretable results.It demonstrates robust performance across various scenarios and real-world applications,advancing our understanding of complex environmental exposures and their health impacts on environmental epidemiology and toxicology.
基金funded by the 2023 Inner Mongolia Public Institution High-Level Talent Introduction Scientific Research Support Project,and the Ordos Municipal Science and Technology Major Special Project(Grant No.2022EEDSKJZDZX021).
文摘In this paper,a standardized analysis method is established for identifying meat quality-related genes in Ordos finewool sheep using transcriptome sequencing data.A meticulously standardized approach is utilized to investigate the genetic determinants of meat quality in Ordos fine-wool sheep through transcriptome sequencing analysis.Muscle samples from the longissimus dorsi of one-year-old sheep are collected under controlled conditions,and key texture properties—hardness,elasticity,and chewiness—are measured to categorize samples into high-and low-textural-value groups.Genes significantly associated with meat quality traits are identified through standardized RNA extraction,high-throughput sequencing,and differential gene expression analysis.Functional enrichment analysis reveals their involvement in biological processes such as extracellular matrix organization and metabolic pathways.The findings underscore the pivotal role of standardization in meat quality research,laying a solid scientific foundation for future research on meat quality improvement and molecular breeding.
基金This paper is one of the outcomes of the university project ( XB200349)
文摘Four samples were chosen by systematic sampling from the range-finders between 1987 and 2003 to test the range-finders’ representativeness of the scoring criteria of CET-4 compositions. The samples were analyzed from the perspectives of transitivity, modality, thematic structure and cohesion. Fisher's Exact Test from the SAS system was used to compare two-sidedly the correct rate and the constituent ratio of these functional usages between two neighboring levels. Statistical results indicate that it is the quality, not the quantity of these functional usages that distinguishes two neighboring levels. The range-finders can basically represent the abstract scoring criteria as far as the four functional systems are concerned. However, the validity of CET-4 writing needs to be improved.
基金Scientist Fund of Tangdu Hospital,Grant/Award Number:2021SHRC004Natural Science Foundation of Shaanxi Province,Grant/Award Number:2020JM‐315。
文摘Background:Systemic lupus erythematosus(SLE)is an autoimmune disease that can affect multiple systems.Sjogren's syndrome(SS)is an autoimmune disease that may be primary SS(pSS)or occur together with other autoimmune diseases,including SLE.This study aimed to explore the shared gene signatures in SLE and pSS.Methods:Gene expression data sets of SLE(GSE50772 and GSE81622)and pSS(GSE84844 and GSE48378)were obtained and analyzed for differentially expressed genes(DEGs)in peripheral blood mononuclear cells(PBMCs).A protein–protein interaction(PPI)network was constructed.Gene ontology(GO)and KEGG pathway enrichment analysis were carried out for the DEGs.Results:We screened 232 and 110 DEGs from the SLE and pSS data sets,respectively.We found 32 shared DEGs,which were all upregulated in patients compared with controls.Among these 32 DEGs,11 genes showed a more than twofold change in all data sets(IFI27,IFI44L,RSAD2,IFIT1,IFI44,USP18,IFI6,HERC5,EPSTI1,OAS1,and OAS3).PPI analysis showed that 29 genes interacted with each other.GO analysis showed that these 32 shared DEGs were mainly enriched in biological processes associated with the type Ⅰ interferon signaling pathway,defense response to viruses,response to viruses,negative regulation of viral genome replication,and the immune response.Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that these 32 DEGs were related to virus infection.Conclusion:This study showed that alterations to biological processes associated with the response to virus infection play critical roles in both SLE and pSS.
基金This study received financial support from the Youth Talents Special Project of Yunnan Province,“Xingdian Talents Support Program”(XDYC-QNRC-2022-0203)Southwest Forestry University Scientific Research Start-Up Funds(112116).
文摘Phenylalanine ammonia lyase(PAL)is the rate-limiting and pivotal enzyme of the general phenylpropanoid path-way,but few reports have been found on PAL genes in Pinus yunnanensis.In the present study,three PAL genes were cloned and identified from P.yunnanensis seedlings for thefirst time,namely,PyPAL-1,PyPAL-2,and PyPAL-3.Our results indicated that the open-reading frames of PyPAL genes were 2184,2157,and 2385 bp.Phylogenetic tree analysis revealed that PyPALs have high homology with other known PAL genes in other plants.In vitro enzymatic analysis showed that all three PyPAL recombinant proteins could catalyze the deamination of L-phenylalanine to form trans-cinnamic acid,but only PAL1 and PAL2 can catalyze the conversion of L-tyrosine toρ-coumaric acid.Three PyPAL genes were expressed in different tissues in 1-year-old P.yunnanensis,and such genes had different expression patterns.This study lays a foundation for further understanding of the biosynthesis of secondary metabolites in P.yunnanensis.
文摘Introduction:Osteoarthritis(OA)is still an important health problem,and understanding its pathological mechanisms is essential for its diagnosis and treatment.There is evidence that autophagy may play a role in OA progression,but the exact mechanism remains unclear.Methods:In this study,we adopted a multi-prong approach to systematically identify the key autophagy-related genes(ARGs)associated with OA.Through weighted gene coexpression network analysis,we initially identified significant gene modules associated with OA.Subsequent differential gene analysis performed on normal and OA specimens.Further analysis later using the MCC algorithm highlighted hub ARGs.These genes were then incorporated into the prediction model of OA.In addition,the expression patterns of these DEGs were verified by in vitro experiments.Results:A total of 104 differentially expressed genes(DEGs)were identified by differential gene analysis,of which 102 were up-regulated and 2 were down-regulated.These differentially expressed genes were closely related to key signaling pathways,such as PI3K-Akt signaling pathway,IL-17 signaling pathway and osteoclast differentiation.Further MCC analysis highlighted 10 hub ARGs,among which ATF3,CYCS,FOXO3,KLF6,NFKBIA and SOCS3 were particularly significant,which were then included in the prediction model of OA,which showed robust prediction ability with an area under the curve of 0.783.In vitro experiments confirmed that the expression pattern of these DEGs was consistent with our prediction.Conclusion:In summary,our comprehensive analysis not only provides new insights into the molecular basis of OA,but also suggests potential biomarkers for its diagnosis.
基金supported by grants from the National Natural Science Foundation of China(31200502,31401854)the Natural Science Foundation of Jiangsu Province(Grant No.BK20140760,BK20150552)
文摘A MADS-box gene,CiMADS9,was cloned from the male flowers of Carya illinoinensis by rapid amplification of cDNA ends. The gene was 1 077 bp with a 768 bp open reading frame encoding 255 amino acids. Multiple sequence comparisons revealed that Ci MADS9 is a typical MIKC-type MADS-box gene with a MADS-box domain and a K semi-conserved region. Phylogenetic analysis indicated that CiMADS9 belongs to the AGL15 group of the MADS-box gene family. Quantitative reverse transcription polymerase chain reaction analysis indicated that the expression levels in reproductive organs(i.e.,flowers and young fruits) were considerably higher than in vegetative tissues(i.e.,leaves and branches). The highest expression levels were observed in male flowers. An overexpression vector for CiMADS9 was constructed and the gene was inserted into the Arabidopsis thaliana genome. CiMADS9 expression was confirmed in all transgenic lines. Compared with wild-type plants,transgenic A. thaliana plants overexpressing CiMADS9 exhibited delayed flowering and an increased number of leaves.
文摘Since entering the era of Industry 4.0,the concept of Healthcare 4.0 has also been put forward and explored by researchers.How to use Information Technology(IT)to better serve people’s healthcare is one of the most featured emerging directions in the academic circle.An important field of Healthcare 4.0 research is the reliability engineering of healthcare service.Because healthcare systems often affect the health and even life of their users,developers must be very cautious in the design,development,and operation of these healthcare systems and services.The problems to be solved include the reliability of business process,system functions,and personal healthcare data.The Functional Resonance Analysis Method(FRAM)has been applied in reliability engineering for safety-critical systems in available studies,using both qualitative and quantitative approaches.However,the method has not been applied in the field of digital healthcare services development.Therefore,to narrow the gap,we present in this paper a semi-quantitative functional resonance analysis method to develop reliable healthcare services for diabetics.Moreover,this paper has tried to improve the reliability design of the service-oriented architecture(SOA)of traditional insulin pump therapy by system thinking.
文摘Within a framework of Halliday＇s SFL （Systemic Functional Linguistics）, this paper takes a functional approach to the analysis of the fairy tale--＂The Little Match-Seller＂ （Andersen, 1846）. The analysis is carried out in three respects： genre, register and language. Genre analysis indicates that the schematic structure of the fairy tale is very much in line with the one mentioned by Hasan. Register analysis shows that the material process is the most dominant one; the Finite in the clauses is predominantly in past tenses, and most of the Themes in the text are unmarked ones. Language analysis reveals that the lexical density in the fairy tale is relatively low. The findings in this paper can help deepen people＇s understanding of the textual features of English fairy tales.
文摘As two main approaches to analyzing literary discourses,literary criticism and stylistic analysis have been employed for a long period of time.With the application of the theories of Functional Grammar,this paper is written for the purpose of being helpful for the readers of Dylan Thomas’poem“Do not Go Gentle into That Good Night”to understand the poem’s theme better as well as appreciate the artistic adaptation of language.Furthermore,because the poem is analyzed with the application of Functional Grammar,it helps the readers to appreciate“Do not Go Gentle into That Good Night”from a new perspective.
