High temperature stress is one of the major environmental factors that affect the growth and development of plants. Although WRKY transcription factors play a critical role in stress responses, there are few studies o...High temperature stress is one of the major environmental factors that affect the growth and development of plants. Although WRKY transcription factors play a critical role in stress responses, there are few studies on the regulation of heat stress by WRKY transcription factors,especially in tomato. Here, we identified a group I WRKY transcription factor, SlWRKY3, involved in thermotolerance in tomato. First, SlWRKY3 was induced and upregulated under heat stress. Accordingly, overexpression of SlWRKY3 led to an increase, whereas knock-out of SlWRKY3 resulted in decreased tolerance to heat stress. Overexpression of SlWRKY3 accumulated less reactive oxygen species(ROS), whereas knock-out of SlWRKY3 accumulated more ROS under heat stress. This indicated that SlWRKY3 positively regulates heat stress in tomato. In addition,SlWRKY3 activated the expression of a range of abiotic stress-responsive genes involved in ROS scavenging, such as a SlGRXS1 gene cluster.Further analysis showed that SlWRKY3 can bind to the promoters of the SlGRXS1 gene cluster and activate their expression. Collectively, these results imply that SlWRKY3 is a positive regulator of thermotolerance through direct binding to the promoters of the SlGRXS1 gene cluster and activating their expression and ROS scavenging.展开更多
An extensively drug-resistant(XDR)Escherichia coli strain 258E was isolated from an anal swab sample of a chicken farm of Anhui province in China.Genomic analyses indicated that the strain 258E harbors an incompatibil...An extensively drug-resistant(XDR)Escherichia coli strain 258E was isolated from an anal swab sample of a chicken farm of Anhui province in China.Genomic analyses indicated that the strain 258E harbors an incompatibility group N(IncN)plasmid pEC258-3,which co-produces bla_(CTX-M-3),bla_(KPC-2),bla_(TEM-1B),qnrS1,aac(6')-Ib-cr,dfrA14,arr-3,and aac(6')-Ib3.Multiple genome arrangement analyses indicated that pEC258-3 is highly homologous with pCRKP-1-KPC discovered in Klebsiella pneumoniae from a patient.Furthermore,conjugation experiments proved that plasmid pEC258-3 can be transferred horizontally and may pose a significant potential threat in animals,community and hospital settings.展开更多
In view of the composition analysis and identification of ancient glass products, L1 regularization, K-Means cluster analysis, elbow rule and other methods were comprehensively used to build logical regression, cluste...In view of the composition analysis and identification of ancient glass products, L1 regularization, K-Means cluster analysis, elbow rule and other methods were comprehensively used to build logical regression, cluster analysis, hyper-parameter test and other models, and SPSS, Python and other tools were used to obtain the classification rules of glass products under different fluxes, sub classification under different chemical compositions, hyper-parameter K value test and rationality analysis. Research can provide theoretical support for the protection and restoration of ancient glass relics.展开更多
Hepatocyte nuclear factor 1 alpha(HNF1A),hepatocyte nuclear factor 4 alpha(HNF4A),and forkhead box protein A2(FOXA2)are key transcription factors that regulate a complex gene network in the liver,cre-ating a regulator...Hepatocyte nuclear factor 1 alpha(HNF1A),hepatocyte nuclear factor 4 alpha(HNF4A),and forkhead box protein A2(FOXA2)are key transcription factors that regulate a complex gene network in the liver,cre-ating a regulatory transcriptional loop.The Encode and ChIP-Atlas databases identify the recognition sites of these transcription factors in many glycosyltransferase genes.Our in silico analysis of HNF1A,HNF4A.and FOXA2 binding to the ten candidate glyco-genes studied in this work confirms a significant enrich-ment of these transcription factors specifically in the liver.Our previous studies identified HNF1A as a master regulator of fucosylation,glycan branching,and galactosylation of plasma glycoproteins.Here,we aimed to functionally validate the role of the three transcription factors on downstream glyco-gene transcriptional expression and the possible effect on glycan phenotype.We used the state-of-the-art clus-tered regularly interspaced short palindromic repeats/dead Cas9(CRISPR/dCas9)molecular tool for the downregulation of the HNF1A,HNF4A,and FOXA2 genes in HepG2 cells-a human liver cancer cell line.The results show that the downregulation of all three genes individually and in pairs affects the transcrip-tional activity of many glyco-genes,although downregulation of glyco-genes was not always followed by an unambiguous change in the corresponding glycan structures.The effect is better seen as an overall change in the total HepG2 N-glycome,primarily due to the extension of biantennary glycans.We propose an alternative way to evaluate the N-glycome composition via estimating the overall complexity of the glycome by quantifying the number of monomers in each glycan structure.We also propose a model showing feedback loops with the mutual activation of HNF1A-FOXA2 and HNF4A-FOXA2 affecting glyco-genes and protein glycosylation in HepG2 cells.展开更多
We study the geometries, stabilities, electronic and magnetic properties of （MgO）n （n=2-10） clusters doped with a single Mn atom using the density functional theory with the gener- alized gradient approximation. T...We study the geometries, stabilities, electronic and magnetic properties of （MgO）n （n=2-10） clusters doped with a single Mn atom using the density functional theory with the gener- alized gradient approximation. The optimized geometries show that the impurity Mn atom prefers to replace the Mg atom which has low coordination number in all the lowest-energy MnMgn-1On （n=2-10） structures. The stability analysis clearly represents that the average binding energies of the doped clusters are larger than those of the corresponding pure （MgO）n clusters. Maximum peaks of the second order energy differences are observed for MnMg~_1On clusters at n=6, 9, implying that these clusters exhibit higher stability than their neighboring clusters. In addition, all the Mn-doped Mg clusters exhibit high total magnetic moments with the exception of MnMgO2 which has 3.00μB. Their magnetic behavior is attributed to the impurity Mn atom, the charge transfer modes, and the size of MnMgn- 1On clusters.展开更多
CO adsorption on small Aun （n = 1 - 7） clusters which are supported by a partially reduced rutile TiO2（110） surface has been investigated by the first-principles method. The low coordinated sites of Au clusters ar...CO adsorption on small Aun （n = 1 - 7） clusters which are supported by a partially reduced rutile TiO2（110） surface has been investigated by the first-principles method. The low coordinated sites of Au clusters are favorable for CO adsorption. CO-Aun-TiO2 system displays surface magnetism. There is a strong interaction between the adsorbed CO molecule and the supported Au clusters.展开更多
WnC0＇± （n= 1-6） clusters are investigated by using the density functional theory （DFT） at the B3LYP/LANL2DZ level. We find that the neutral, anionic and cationic ground state structures are similar within th...WnC0＇± （n= 1-6） clusters are investigated by using the density functional theory （DFT） at the B3LYP/LANL2DZ level. We find that the neutral, anionic and cationic ground state structures are similar within the same size, and constituted by substituting a C atom for one W atom in the structures of Wn＋1 clusters. The natural bond orbital （NBO） charge analyses indicate that the direction of electron transfer is from the W atom to the 2p orbital of the C atom. In addition, the calculated infrared spectra of the WnC0＇± （n= 2-6） clusters manifest that the vibrational frequencies of neutral, anionic and cationic clusters are similar in a range of 80 cm-1-864 cm-1. The high frequency, strong peak modes are found to be an almost stretched deformation of the carbide atom. Finally, the polarizabilities of WnC0＇± （n= 1-6） clusters are also discussed.展开更多
Density functional theory（DFT） with the B3 LYP method and the SDD basis set is selected to investigate In_nNi,In_nNi^-, and In_nNi~＋ （n = 1–14） clusters. For neutral and charged systems, several isomers and diff...Density functional theory（DFT） with the B3 LYP method and the SDD basis set is selected to investigate In_nNi,In_nNi^-, and In_nNi~＋ （n = 1–14） clusters. For neutral and charged systems, several isomers and different multiplicities are studied with the aim to confirm the most stable structures. The structural evolution of neutral, cationic, and anionic In_nNi clusters, which favors the three-dimensional structures for n = 3–14. The main configurations of the In_nNi isomers are not affected by adding or removing an electron, the order of their stabilities is also nearly not affected. The obtained binding energy exhibits that the Ni-doped In_（13） cluster is the most stable species of all different sized clusters. The calculated fragmentation energy and the second-order energy difference as a function of the cluster size exhibit a pronounced even–odd alternation phenomenon. The electronic properties including energy gap（E_g）, adiabatic electron affinity（AEA）, vertical electron detachment energy（VDE）, adiabatic ionization potential energy（AIP）, and vertical ionization potential energy（VIP） are studied. The total magnetic moments show that the different magnetic moments depend on the number of the In atoms for charged In_nNi. Additionally, the natural population analysis of In_nNi^（（0,±1）clusters is also discussed.展开更多
This paper studies supersonic jet-cooled 1-fluoronaphthalene （1FN） clusters by ultraviolet （UV） laser ionization at 281 nm in a time-of-flight mass spectrometer. The （1FN）＋ （n=1-3） series cluster ions are obs...This paper studies supersonic jet-cooled 1-fluoronaphthalene （1FN） clusters by ultraviolet （UV） laser ionization at 281 nm in a time-of-flight mass spectrometer. The （1FN）＋ （n=1-3） series cluster ions are observed where the signal intensity decreases with increasing cluster size. The effects of sample inlet pressures and ionization laser fluxes to mass spectral distribution are measured. Using density functional theory calculations, it obtains a planar geometric structure of 1FN dimer which is combined through two hydrogen bonds. The mass spectra indicate that the intensity of 1FN trimer is much weaker than that of 1FN dimer and this feature is attributed to the fact that the dimer may form the first ＂shell＂ in geometric structure while the larger clusters are generated based on this fundamental unit.展开更多
基金supported by grants from the National Key Research&Development Plan,China (Grant Nos.2021YFD1200201,2022YFD1200502)National Natural Science Foundation of China(31972426,31991182)+3 种基金Key Project of Hubei Hongshan Laboratory(Grant No.2021hszd007)Wuhan Major Project of Key Technologies in Biological Breeding (Grant No.2022021302024852)Fundamental Research Funds for the Central Universities,China (Grant No.2662022YLPY001)International Cooperation Promotion Plan of Shihezi University (Grant No.GJHZ202104)。
文摘High temperature stress is one of the major environmental factors that affect the growth and development of plants. Although WRKY transcription factors play a critical role in stress responses, there are few studies on the regulation of heat stress by WRKY transcription factors,especially in tomato. Here, we identified a group I WRKY transcription factor, SlWRKY3, involved in thermotolerance in tomato. First, SlWRKY3 was induced and upregulated under heat stress. Accordingly, overexpression of SlWRKY3 led to an increase, whereas knock-out of SlWRKY3 resulted in decreased tolerance to heat stress. Overexpression of SlWRKY3 accumulated less reactive oxygen species(ROS), whereas knock-out of SlWRKY3 accumulated more ROS under heat stress. This indicated that SlWRKY3 positively regulates heat stress in tomato. In addition,SlWRKY3 activated the expression of a range of abiotic stress-responsive genes involved in ROS scavenging, such as a SlGRXS1 gene cluster.Further analysis showed that SlWRKY3 can bind to the promoters of the SlGRXS1 gene cluster and activate their expression. Collectively, these results imply that SlWRKY3 is a positive regulator of thermotolerance through direct binding to the promoters of the SlGRXS1 gene cluster and activating their expression and ROS scavenging.
基金the National Key Research and Development Program of China(2018YFE0192600)the Shanghai Agriculture Applied Technology Development Program,China(T20200104)+1 种基金the Fundamental Research Funds for the Central Universities,China(2020JB05)the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences(CAAS-ZDRW202203).
文摘An extensively drug-resistant(XDR)Escherichia coli strain 258E was isolated from an anal swab sample of a chicken farm of Anhui province in China.Genomic analyses indicated that the strain 258E harbors an incompatibility group N(IncN)plasmid pEC258-3,which co-produces bla_(CTX-M-3),bla_(KPC-2),bla_(TEM-1B),qnrS1,aac(6')-Ib-cr,dfrA14,arr-3,and aac(6')-Ib3.Multiple genome arrangement analyses indicated that pEC258-3 is highly homologous with pCRKP-1-KPC discovered in Klebsiella pneumoniae from a patient.Furthermore,conjugation experiments proved that plasmid pEC258-3 can be transferred horizontally and may pose a significant potential threat in animals,community and hospital settings.
文摘In view of the composition analysis and identification of ancient glass products, L1 regularization, K-Means cluster analysis, elbow rule and other methods were comprehensively used to build logical regression, cluster analysis, hyper-parameter test and other models, and SPSS, Python and other tools were used to obtain the classification rules of glass products under different fluxes, sub classification under different chemical compositions, hyper-parameter K value test and rationality analysis. Research can provide theoretical support for the protection and restoration of ancient glass relics.
基金the European Structural and Investment Funded Grant"Cardio Metabolic"(#KK.01.2.1.02.0321)the Croatian National Centre of Research Excellence in Personalized Healthcare Grant(#KK.01.1.1.01.0010)+2 种基金the European Regional Development Fund Grant,project"CRISPR/Cas9-CasMouse"(#KK.01.1.1.04.0085)the European Structural and Investment Funded Project of Centre of Competence in Molecular Diagnostics(#KK.01.2.2.03.0006)the Croatian National Centre of Research Excellence in Personalized Healthcare Grant(#KK.01.1.1.01.0010).
文摘Hepatocyte nuclear factor 1 alpha(HNF1A),hepatocyte nuclear factor 4 alpha(HNF4A),and forkhead box protein A2(FOXA2)are key transcription factors that regulate a complex gene network in the liver,cre-ating a regulatory transcriptional loop.The Encode and ChIP-Atlas databases identify the recognition sites of these transcription factors in many glycosyltransferase genes.Our in silico analysis of HNF1A,HNF4A.and FOXA2 binding to the ten candidate glyco-genes studied in this work confirms a significant enrich-ment of these transcription factors specifically in the liver.Our previous studies identified HNF1A as a master regulator of fucosylation,glycan branching,and galactosylation of plasma glycoproteins.Here,we aimed to functionally validate the role of the three transcription factors on downstream glyco-gene transcriptional expression and the possible effect on glycan phenotype.We used the state-of-the-art clus-tered regularly interspaced short palindromic repeats/dead Cas9(CRISPR/dCas9)molecular tool for the downregulation of the HNF1A,HNF4A,and FOXA2 genes in HepG2 cells-a human liver cancer cell line.The results show that the downregulation of all three genes individually and in pairs affects the transcrip-tional activity of many glyco-genes,although downregulation of glyco-genes was not always followed by an unambiguous change in the corresponding glycan structures.The effect is better seen as an overall change in the total HepG2 N-glycome,primarily due to the extension of biantennary glycans.We propose an alternative way to evaluate the N-glycome composition via estimating the overall complexity of the glycome by quantifying the number of monomers in each glycan structure.We also propose a model showing feedback loops with the mutual activation of HNF1A-FOXA2 and HNF4A-FOXA2 affecting glyco-genes and protein glycosylation in HepG2 cells.
文摘We study the geometries, stabilities, electronic and magnetic properties of （MgO）n （n=2-10） clusters doped with a single Mn atom using the density functional theory with the gener- alized gradient approximation. The optimized geometries show that the impurity Mn atom prefers to replace the Mg atom which has low coordination number in all the lowest-energy MnMgn-1On （n=2-10） structures. The stability analysis clearly represents that the average binding energies of the doped clusters are larger than those of the corresponding pure （MgO）n clusters. Maximum peaks of the second order energy differences are observed for MnMg~_1On clusters at n=6, 9, implying that these clusters exhibit higher stability than their neighboring clusters. In addition, all the Mn-doped Mg clusters exhibit high total magnetic moments with the exception of MnMgO2 which has 3.00μB. Their magnetic behavior is attributed to the impurity Mn atom, the charge transfer modes, and the size of MnMgn- 1On clusters.
基金supported by the National Natural Science Foundation of China (Grant No. 10604035)the National Basic Research Program of China (Grant No. 2006CB605102)
文摘CO adsorption on small Aun （n = 1 - 7） clusters which are supported by a partially reduced rutile TiO2（110） surface has been investigated by the first-principles method. The low coordinated sites of Au clusters are favorable for CO adsorption. CO-Aun-TiO2 system displays surface magnetism. There is a strong interaction between the adsorbed CO molecule and the supported Au clusters.
基金supported by the National Natural Science Foundation of China (Grant No. 51072072)
文摘WnC0＇± （n= 1-6） clusters are investigated by using the density functional theory （DFT） at the B3LYP/LANL2DZ level. We find that the neutral, anionic and cationic ground state structures are similar within the same size, and constituted by substituting a C atom for one W atom in the structures of Wn＋1 clusters. The natural bond orbital （NBO） charge analyses indicate that the direction of electron transfer is from the W atom to the 2p orbital of the C atom. In addition, the calculated infrared spectra of the WnC0＇± （n= 2-6） clusters manifest that the vibrational frequencies of neutral, anionic and cationic clusters are similar in a range of 80 cm-1-864 cm-1. The high frequency, strong peak modes are found to be an almost stretched deformation of the carbide atom. Finally, the polarizabilities of WnC0＇± （n= 1-6） clusters are also discussed.
基金supported by the Cultivating Program of Excellent Innovation Team of Chengdu University of Technology(Grant No.KYTD201704)the Cultivating Program of Middle-aged Backbone Teachers of Chengdu University of Technology(Grant No.10912-KYGG201512)+2 种基金the National Natural Science Foundation of China(Grant No.11404042)the Science Fund from the Science & Technology Department of Sichuan Province,China(Grant No.2016RZ0069)the Research Foundation of Chengdu University of Technology,China(Grant No.2017YG04)
文摘Density functional theory（DFT） with the B3 LYP method and the SDD basis set is selected to investigate In_nNi,In_nNi^-, and In_nNi~＋ （n = 1–14） clusters. For neutral and charged systems, several isomers and different multiplicities are studied with the aim to confirm the most stable structures. The structural evolution of neutral, cationic, and anionic In_nNi clusters, which favors the three-dimensional structures for n = 3–14. The main configurations of the In_nNi isomers are not affected by adding or removing an electron, the order of their stabilities is also nearly not affected. The obtained binding energy exhibits that the Ni-doped In_（13） cluster is the most stable species of all different sized clusters. The calculated fragmentation energy and the second-order energy difference as a function of the cluster size exhibit a pronounced even–odd alternation phenomenon. The electronic properties including energy gap（E_g）, adiabatic electron affinity（AEA）, vertical electron detachment energy（VDE）, adiabatic ionization potential energy（AIP）, and vertical ionization potential energy（VIP） are studied. The total magnetic moments show that the different magnetic moments depend on the number of the In atoms for charged In_nNi. Additionally, the natural population analysis of In_nNi^（（0,±1）clusters is also discussed.
文摘This paper studies supersonic jet-cooled 1-fluoronaphthalene （1FN） clusters by ultraviolet （UV） laser ionization at 281 nm in a time-of-flight mass spectrometer. The （1FN）＋ （n=1-3） series cluster ions are observed where the signal intensity decreases with increasing cluster size. The effects of sample inlet pressures and ionization laser fluxes to mass spectral distribution are measured. Using density functional theory calculations, it obtains a planar geometric structure of 1FN dimer which is combined through two hydrogen bonds. The mass spectra indicate that the intensity of 1FN trimer is much weaker than that of 1FN dimer and this feature is attributed to the fact that the dimer may form the first ＂shell＂ in geometric structure while the larger clusters are generated based on this fundamental unit.
