Inorganic phosphate(Pi)is one of the main nutrients necessary for plant growth.Phosphate transporters mediate the acquisition,transport and recycling of phosphate,which is essential for plant growth and development.Al...Inorganic phosphate(Pi)is one of the main nutrients necessary for plant growth.Phosphate transporters mediate the acquisition,transport and recycling of phosphate,which is essential for plant growth and development.Although PHT1 has been reported in many plants at home and abroad,it is rarely studied in potato.Therefore,it is of great significance to study the PHT1 family members in order to understand the molecular response mechanism of potato in low phosphate state.In this study,a total of 6 potato PHT1 genes were identified and isolated.It was found that after the expression of different members of potato PHT1 gene,there were certain differences in amino acids and proteins,and the transmembrane domains ranged from 6 to 12.The difference in the secondary and tertiary protein structure of potato PHT1 also led to a difference in protein morphology.In addition,the expression of the PHT1 gene in potato increased obviously during 3~9 h of Pi deficiency stress.Overall,the expression levels of different genes in roots,stems and leaves are distinctly different,but the expression levels of the StPHT1;6 and StPHT1;10 genes are very high in roots,stems and leaves,indicating that these two genes may participate in the absorption of Pi in potato and play a role in Pi translocation.These two genes play a major role in the regulation of expression under short-term Pi deficiency stress.Our results provide an important reference for further understanding the evolution and function of potato phosphate transporters,and have important significance for improving the ability of potato to tolerate low Pi.展开更多
Objective:This study used comprehensive bioinformatics analysis and network pharmacology analysis to investigate the potentially relevant mechanisms of Sophora flavescens against cervical squamous cell carcinoma.Metho...Objective:This study used comprehensive bioinformatics analysis and network pharmacology analysis to investigate the potentially relevant mechanisms of Sophora flavescens against cervical squamous cell carcinoma.Methods:Consistently altered genes involved in cervical squamous cell cancerization were analyzed in the GEO database.The chemical ingredients and target genes of Sophora flavescens were explored using the TCMSP database.We obtained the potential therapeutic targets of Sophora flavescens by intersecting the above genesets and validated them in the GEPIA database.The interaction between Sophora flavescens and target genes was predicted by molecular docking.RT-qPCR was used to verify the changes of target genes in HeLa cells treated with Sophora flavescens.Single-gene GSEA functional analysis were performed to determine the molecular mechanisms.Results:Fifteen genes related to the transformation of cervical squamous cell carcinoma were identified,among which AR and ESR1 were confirmed as targets for kaempferol,wighteone,formononetin,and phaseolinon.These compounds are the active ingredients in Sophora flavescens.Low expressions of AR and ESR1 correlate with a poor prognosis,while Sophora flavescens treatment increases the expression of AR and ESR1 in HeLa.GSEA analysis showed that AR and ESR1 mainly participate in the epithelial-mesenchymal transition in cervical squamous cell carcinoma.Conclusion:Sophora flavescens exert anti-tumor effects by targeting AR and ESR1,which may regulate cancer metastasis.展开更多
Woodpeckers can withstand a fierce impact during pecking.Previous studies have focused on the biomechanical analysis of the pecking process,the properties of the beak and hyoid bone of woodpecker;however,the biologica...Woodpeckers can withstand a fierce impact during pecking.Previous studies have focused on the biomechanical analysis of the pecking process,the properties of the beak and hyoid bone of woodpecker;however,the biological characteristics of the woodpecker brain are also important in resisting impact injuries.We employed impact experiments and biological analysis in normal and injured brains to reveal the impact-resistant biological characteristics of woodpecker brains,as well as the impact energy’s biological effects on the woodpecker brain.The hoopoe,which has a similar size but only a slight pecking behavior,was selected as the control group to compare brain morphology and neuronal cells differences in normal brains between woodpecker and hoopoe by sectioning and staining.A loading device was designed to conduct a quantifiable impact energy to the woodpeckers’head.Four groups of woodpeckers were impacted with the same energy on the forehead,beak,tempus and occiput,respectively.Biological changes in the injured brains were evaluated by Nissl staining and enzyme-linked immunosorbent assay.The results showed that:(1)woodpeckers had a larger cerebellum and a higher density of Nissl bodies than hoopoe;(2)Nissl apoptosis appeared in the brain samples after the forehead and the occiput impact experiments,but no obvious Nissl body apoptosis was observed after impact on the tempus and the beak;(3)β-amyloid protein accumulated in the normal status woodpecker brain.This study reveals that:woodpecker brain morphology is well-adapted to impact,woodpecker heads display location-dependent protective performance,with beak and tempus regions having a better protective performance than the forehead and occiput,Nissl apoptosis appears in injured woodpecker brains,and that the accumulation ofβ-amyloid protein does not show a direct relationship with the injury state of woodpecker’s brain tissue in our study.展开更多
BACKGROUND The impact of racial and regional disparity on younger patients with gastric cancer(GC) remains unclear.AIM To investigate the clinicopathological characteristics, prognostic nomogram, and biological analys...BACKGROUND The impact of racial and regional disparity on younger patients with gastric cancer(GC) remains unclear.AIM To investigate the clinicopathological characteristics, prognostic nomogram, and biological analysis of younger GC patients in China and the United States.METHODS From 2000 to 2018, GC patients aged less than 40 years were enrolled from the China National Cancer Center and the Surveillance Epidemiology and End Results database. Biological analysis was performed based on the Gene Expression Omnibus database. Survival analysis was conducted via Kaplan-Meier estimates and Cox proportional hazards models.RESULTS A total of 6098 younger GC patients were selected from 2000 to 2018, of which 1159 were enrolled in the China National Cancer Center, and 4939 were collected from the Surveillance Epidemiology and End Results database. Compared with the United States group, younger patients in China revealed better survival outcomes(P < 0.01). For race/ethnicity, younger Chinese cases also enjoyed a better prognosis than that in White and Black datasets(P < 0.01). After stratification by pathological Tumor-Node-Metastasis(pTNM) stage, a survival advantage was observed in China with pathological stage Ⅰ, Ⅲ, and Ⅳ(all P < 0.01), whereas younger GC patients with stage Ⅱ showed no difference(P = 0.16). In multivariate analysis, predictors in China involved period of diagnosis, linitis plastica, and pTNM stage, while race, diagnostic period, sex, location, differentiation, linitis plastica, signet ring cell, pTNM stage, surgery, and chemotherapy were confirmed in the United States group. Prognostic nomograms for younger patients were established, with the area under the curve of 0.786 in the China group and of 0.842 in the United States group. Moreover, three gene expression profiles(GSE27342, GSE51105, and GSE38749) were enrolled in further biological analysis, and distinctive molecular characteristics were identified in younger GC patients among different regions.CONCLUSION Except for younger cases with pTNM stage Ⅱ, a survival advantage was observed in the China group with pathological stage Ⅰ, Ⅲ, and Ⅳ compared to the United States group, which might be partly due to differences in surgical approaches and the improvement of the cancer screening in China. The nomogram model provided an insightful and applicable tool to evaluate the prognosis of younger patients in China and the United States. Furthermore, biological analysis of younger patients was performed among different regions, which might partly explain the histopathological behavior and survival disparity in the subpopulations.展开更多
Thanks to the synergistic effect,the bimetallic catalysts show better catalytic activity than the single metal cat-alysts and become a focus of research in heterogeneous catalysis.In this study,we successfully prepare...Thanks to the synergistic effect,the bimetallic catalysts show better catalytic activity than the single metal cat-alysts and become a focus of research in heterogeneous catalysis.In this study,we successfully prepared Pd-Pt icosahedra which show high peroxidase-like activity under the synergistic effects of Pd and Pt.V max of the Pd-Pt icosahedra was significantly enhanced by 1.66 times for 3,3’,5,5’-tetramethylbenzidine(TMB)as the substrate and 1.23 times for H_(2)O_(2) as the substrate,compared to that of the Pd icosahedra alone.By harnessing the supe-rior peroxidase-like activity of Pd-Pt icosahedra,we successfully utilized Pd-Pt icosahedral nanozymes in various biological analyses based on colorimetry.In most cases,using a Pd-Pt icosahedra/H_(2)O_(2)/TMB system,glucose,glutathione(GSH),acid phosphatase(ACP),and alkaline phosphatase(ALP)were detected over a wide range of 0.05∼0.20 mM,0∼20 mM,0∼10 U/L and 0∼12 U/L.In this study,we prepared a novel bimetallic nanozyme that exhibited excellent peroxidase-like activity owing to the bimetallic synergistic effect,thus demonstrating the promising potential of Pd-Pt icosahedra in the field of bioanalysis.展开更多
Two-dimensional(2D)graphitic carbon nitride(g-C_(3)N_(4))possesses a unique geometric configuration featuring a superimposed heterocyclic sp2 carbon and nitrogen framework.Its fluorescence may be attributed to π-π^(...Two-dimensional(2D)graphitic carbon nitride(g-C_(3)N_(4))possesses a unique geometric configuration featuring a superimposed heterocyclic sp2 carbon and nitrogen framework.Its fluorescence may be attributed to π-π^(*),lone pair(LP)-π^(*),or LP-δ^(*)transitions.So far,the manipulation of its fluorescence emissions is largely unexploited and remains challenging.Herein,for the first time,rare-earth doping into the backbone structure of a g-C_(3)N_(4) framework under microwave agitation endows unprecedented fluorescence nature,with the emergence of two exceptional new fluorescence emissions in the 450-700 nm range.With terbium-doped g-C_(3)N_(4):Tb as a representative,these emissions exhibit distinctive features,that is,very sharp fluorescence peaks with narrow full width at half maximum(FWHM)(peak width at half-height)of<12 nm,quantumyields of 2.3±0.0% and 7.6±0.1% for the new emissions at λ_(ex)/λ_(em)=290/490 nm,and 290/545 nm,respectively;and a large Stokes shift of>200 nm.These features of g-C_(3)N_(4):Tb are most advantageous for applications in various fields,as demonstrated by(1)tracking biodistribution of g-C_(3)N_(4) in vivo with mass spectrometric imaging where the doped terbium serves as a tag,(2)a biometrics study facilitating the identification of an individual through fingerprint,and(3)anti-counterfeiting with g-C_(3)N_(4)∶Tb as a dual-functional marker to facilitate fluorescence and mass spectrometric imaging.展开更多
The kernel method,especially the kernel-fusion method,is widely used in social networks,computer vision,bioinformatics,and other applications.It deals effectively with nonlinear classification problems,which can map l...The kernel method,especially the kernel-fusion method,is widely used in social networks,computer vision,bioinformatics,and other applications.It deals effectively with nonlinear classification problems,which can map linearly inseparable biological sequence data from low to high-dimensional space for more accurate differentiation,enabling the use of kernel methods to predict the structure and function of sequences.Therefore,the kernel method is significant in the solution of bioinformatics problems.Various kernels applied in bioinformatics are explained clearly,which can help readers to select proper kernels to distinguish tasks.Mass biological sequence data occur in practical applications.Research of the use of machine learning methods to obtain knowledge,and how to explore the structure and function of biological methods for theoretical prediction,have always been emphasized in bioinformatics.The kernel method has gradually become an important learning algorithm that is widely used in gene expression and biological sequence prediction.This review focuses on the requirements of classification tasks of biological sequence data.It studies kernel methods and optimization algorithms,including methods of constructing kernel matrices based on the characteristics of biological sequences and kernel fusion methods existing in a multiple kernel learning framework.展开更多
基金supported by the National Natural Science Foundation of China(31460367).
文摘Inorganic phosphate(Pi)is one of the main nutrients necessary for plant growth.Phosphate transporters mediate the acquisition,transport and recycling of phosphate,which is essential for plant growth and development.Although PHT1 has been reported in many plants at home and abroad,it is rarely studied in potato.Therefore,it is of great significance to study the PHT1 family members in order to understand the molecular response mechanism of potato in low phosphate state.In this study,a total of 6 potato PHT1 genes were identified and isolated.It was found that after the expression of different members of potato PHT1 gene,there were certain differences in amino acids and proteins,and the transmembrane domains ranged from 6 to 12.The difference in the secondary and tertiary protein structure of potato PHT1 also led to a difference in protein morphology.In addition,the expression of the PHT1 gene in potato increased obviously during 3~9 h of Pi deficiency stress.Overall,the expression levels of different genes in roots,stems and leaves are distinctly different,but the expression levels of the StPHT1;6 and StPHT1;10 genes are very high in roots,stems and leaves,indicating that these two genes may participate in the absorption of Pi in potato and play a role in Pi translocation.These two genes play a major role in the regulation of expression under short-term Pi deficiency stress.Our results provide an important reference for further understanding the evolution and function of potato phosphate transporters,and have important significance for improving the ability of potato to tolerate low Pi.
基金In 2021,Wuxi Medical Innovation Team CXTD2021023,Jiangsu Province maternal and Child Health research key funding project F201915.
文摘Objective:This study used comprehensive bioinformatics analysis and network pharmacology analysis to investigate the potentially relevant mechanisms of Sophora flavescens against cervical squamous cell carcinoma.Methods:Consistently altered genes involved in cervical squamous cell cancerization were analyzed in the GEO database.The chemical ingredients and target genes of Sophora flavescens were explored using the TCMSP database.We obtained the potential therapeutic targets of Sophora flavescens by intersecting the above genesets and validated them in the GEPIA database.The interaction between Sophora flavescens and target genes was predicted by molecular docking.RT-qPCR was used to verify the changes of target genes in HeLa cells treated with Sophora flavescens.Single-gene GSEA functional analysis were performed to determine the molecular mechanisms.Results:Fifteen genes related to the transformation of cervical squamous cell carcinoma were identified,among which AR and ESR1 were confirmed as targets for kaempferol,wighteone,formononetin,and phaseolinon.These compounds are the active ingredients in Sophora flavescens.Low expressions of AR and ESR1 correlate with a poor prognosis,while Sophora flavescens treatment increases the expression of AR and ESR1 in HeLa.GSEA analysis showed that AR and ESR1 mainly participate in the epithelial-mesenchymal transition in cervical squamous cell carcinoma.Conclusion:Sophora flavescens exert anti-tumor effects by targeting AR and ESR1,which may regulate cancer metastasis.
基金supported by the National Natural Science Foundation of China(Grant Nos.11822201,11421202)。
文摘Woodpeckers can withstand a fierce impact during pecking.Previous studies have focused on the biomechanical analysis of the pecking process,the properties of the beak and hyoid bone of woodpecker;however,the biological characteristics of the woodpecker brain are also important in resisting impact injuries.We employed impact experiments and biological analysis in normal and injured brains to reveal the impact-resistant biological characteristics of woodpecker brains,as well as the impact energy’s biological effects on the woodpecker brain.The hoopoe,which has a similar size but only a slight pecking behavior,was selected as the control group to compare brain morphology and neuronal cells differences in normal brains between woodpecker and hoopoe by sectioning and staining.A loading device was designed to conduct a quantifiable impact energy to the woodpeckers’head.Four groups of woodpeckers were impacted with the same energy on the forehead,beak,tempus and occiput,respectively.Biological changes in the injured brains were evaluated by Nissl staining and enzyme-linked immunosorbent assay.The results showed that:(1)woodpeckers had a larger cerebellum and a higher density of Nissl bodies than hoopoe;(2)Nissl apoptosis appeared in the brain samples after the forehead and the occiput impact experiments,but no obvious Nissl body apoptosis was observed after impact on the tempus and the beak;(3)β-amyloid protein accumulated in the normal status woodpecker brain.This study reveals that:woodpecker brain morphology is well-adapted to impact,woodpecker heads display location-dependent protective performance,with beak and tempus regions having a better protective performance than the forehead and occiput,Nissl apoptosis appears in injured woodpecker brains,and that the accumulation ofβ-amyloid protein does not show a direct relationship with the injury state of woodpecker’s brain tissue in our study.
基金National Key R&D Program of China,No.2017YFC0908300.
文摘BACKGROUND The impact of racial and regional disparity on younger patients with gastric cancer(GC) remains unclear.AIM To investigate the clinicopathological characteristics, prognostic nomogram, and biological analysis of younger GC patients in China and the United States.METHODS From 2000 to 2018, GC patients aged less than 40 years were enrolled from the China National Cancer Center and the Surveillance Epidemiology and End Results database. Biological analysis was performed based on the Gene Expression Omnibus database. Survival analysis was conducted via Kaplan-Meier estimates and Cox proportional hazards models.RESULTS A total of 6098 younger GC patients were selected from 2000 to 2018, of which 1159 were enrolled in the China National Cancer Center, and 4939 were collected from the Surveillance Epidemiology and End Results database. Compared with the United States group, younger patients in China revealed better survival outcomes(P < 0.01). For race/ethnicity, younger Chinese cases also enjoyed a better prognosis than that in White and Black datasets(P < 0.01). After stratification by pathological Tumor-Node-Metastasis(pTNM) stage, a survival advantage was observed in China with pathological stage Ⅰ, Ⅲ, and Ⅳ(all P < 0.01), whereas younger GC patients with stage Ⅱ showed no difference(P = 0.16). In multivariate analysis, predictors in China involved period of diagnosis, linitis plastica, and pTNM stage, while race, diagnostic period, sex, location, differentiation, linitis plastica, signet ring cell, pTNM stage, surgery, and chemotherapy were confirmed in the United States group. Prognostic nomograms for younger patients were established, with the area under the curve of 0.786 in the China group and of 0.842 in the United States group. Moreover, three gene expression profiles(GSE27342, GSE51105, and GSE38749) were enrolled in further biological analysis, and distinctive molecular characteristics were identified in younger GC patients among different regions.CONCLUSION Except for younger cases with pTNM stage Ⅱ, a survival advantage was observed in the China group with pathological stage Ⅰ, Ⅲ, and Ⅳ compared to the United States group, which might be partly due to differences in surgical approaches and the improvement of the cancer screening in China. The nomogram model provided an insightful and applicable tool to evaluate the prognosis of younger patients in China and the United States. Furthermore, biological analysis of younger patients was performed among different regions, which might partly explain the histopathological behavior and survival disparity in the subpopulations.
基金This work was supported by the National Natural Science Foun-dation of China(22172063)the Young Taishan Scholar Pro-gram(tsqn201812080)+1 种基金the Natural Science Foundation of Shandong Province(ZR2019YQ10)the Independent Cultivation Program of Innovation Team of Jinan City(2021GXRC052).
文摘Thanks to the synergistic effect,the bimetallic catalysts show better catalytic activity than the single metal cat-alysts and become a focus of research in heterogeneous catalysis.In this study,we successfully prepared Pd-Pt icosahedra which show high peroxidase-like activity under the synergistic effects of Pd and Pt.V max of the Pd-Pt icosahedra was significantly enhanced by 1.66 times for 3,3’,5,5’-tetramethylbenzidine(TMB)as the substrate and 1.23 times for H_(2)O_(2) as the substrate,compared to that of the Pd icosahedra alone.By harnessing the supe-rior peroxidase-like activity of Pd-Pt icosahedra,we successfully utilized Pd-Pt icosahedral nanozymes in various biological analyses based on colorimetry.In most cases,using a Pd-Pt icosahedra/H_(2)O_(2)/TMB system,glucose,glutathione(GSH),acid phosphatase(ACP),and alkaline phosphatase(ALP)were detected over a wide range of 0.05∼0.20 mM,0∼20 mM,0∼10 U/L and 0∼12 U/L.In this study,we prepared a novel bimetallic nanozyme that exhibited excellent peroxidase-like activity owing to the bimetallic synergistic effect,thus demonstrating the promising potential of Pd-Pt icosahedra in the field of bioanalysis.
基金the financial support of the National Natural Science Foundation of China(nos.22074011,21922402,and 21727811)the Fundamental Research Funds for the Central Universities(nos.N2005003 and N2005017)+1 种基金the Liaoning Revitalization Talents Program(no.XLYC1802016)the Liaoning Innovative Talents Program in Colleges and Universities(no.ZX20200088).
文摘Two-dimensional(2D)graphitic carbon nitride(g-C_(3)N_(4))possesses a unique geometric configuration featuring a superimposed heterocyclic sp2 carbon and nitrogen framework.Its fluorescence may be attributed to π-π^(*),lone pair(LP)-π^(*),or LP-δ^(*)transitions.So far,the manipulation of its fluorescence emissions is largely unexploited and remains challenging.Herein,for the first time,rare-earth doping into the backbone structure of a g-C_(3)N_(4) framework under microwave agitation endows unprecedented fluorescence nature,with the emergence of two exceptional new fluorescence emissions in the 450-700 nm range.With terbium-doped g-C_(3)N_(4):Tb as a representative,these emissions exhibit distinctive features,that is,very sharp fluorescence peaks with narrow full width at half maximum(FWHM)(peak width at half-height)of<12 nm,quantumyields of 2.3±0.0% and 7.6±0.1% for the new emissions at λ_(ex)/λ_(em)=290/490 nm,and 290/545 nm,respectively;and a large Stokes shift of>200 nm.These features of g-C_(3)N_(4):Tb are most advantageous for applications in various fields,as demonstrated by(1)tracking biodistribution of g-C_(3)N_(4) in vivo with mass spectrometric imaging where the doped terbium serves as a tag,(2)a biometrics study facilitating the identification of an individual through fingerprint,and(3)anti-counterfeiting with g-C_(3)N_(4)∶Tb as a dual-functional marker to facilitate fluorescence and mass spectrometric imaging.
基金supported by the National Natural Science Foundation of China (Grant Nos.61922020,61771331,61902259).
文摘The kernel method,especially the kernel-fusion method,is widely used in social networks,computer vision,bioinformatics,and other applications.It deals effectively with nonlinear classification problems,which can map linearly inseparable biological sequence data from low to high-dimensional space for more accurate differentiation,enabling the use of kernel methods to predict the structure and function of sequences.Therefore,the kernel method is significant in the solution of bioinformatics problems.Various kernels applied in bioinformatics are explained clearly,which can help readers to select proper kernels to distinguish tasks.Mass biological sequence data occur in practical applications.Research of the use of machine learning methods to obtain knowledge,and how to explore the structure and function of biological methods for theoretical prediction,have always been emphasized in bioinformatics.The kernel method has gradually become an important learning algorithm that is widely used in gene expression and biological sequence prediction.This review focuses on the requirements of classification tasks of biological sequence data.It studies kernel methods and optimization algorithms,including methods of constructing kernel matrices based on the characteristics of biological sequences and kernel fusion methods existing in a multiple kernel learning framework.
