A pure culture using benzene as sole carbon and energy sources was isolated by screening procedure from gasoline contaminated soil.The analysis of the 16S rDNA gene sequence,morphological and physiological characteris...A pure culture using benzene as sole carbon and energy sources was isolated by screening procedure from gasoline contaminated soil.The analysis of the 16S rDNA gene sequence,morphological and physiological characteristics showed that the isolated strain was a member of genus Bacillus cereus.The biodegradation performance of benzene by B.cereus was evaluated,and the results showed that benzene could be efficiently biodegraded when the initial benzene concentration was below 150 mg/L.The metabolites of anaerobic nitrate-dependent benzene oxidation by strain B.cereus were identified as phenol and benzoate.The results of substrate interaction between binary combinations for benzene,phenol and benzoate showed that the simultaneous presence of benzene stimulated the degradation of benzoate,whereas the addition of benzene inhibited the degradation of phenol.Benzene degradation by B.cereus was enhanced by the addition of phenol and benzoate,the enhanced effects were more pronounced at higher concentration.To our knowledge,this is the first report that the isolated bacterial culture of B.cereus can efficiently degraded benzene under nitrate reducing conditions.展开更多
Developing platinum-group-metal(PGM)catalysts possessing strong metal-support interaction and controllable PGM size is urgent for the sluggish oxygen reduction reaction(ORR)in proton-exchange membrane fuel cells.Herei...Developing platinum-group-metal(PGM)catalysts possessing strong metal-support interaction and controllable PGM size is urgent for the sluggish oxygen reduction reaction(ORR)in proton-exchange membrane fuel cells.Herein,we propose an in-situ self-assembled reduction strategy to successfully induce highly-dispersed sub-3nm platinum nanoparticles(Pt NPs)to attach on resin-derived atomic Co coordinated by N-doped carbon substrate(Pt/Co_(SA)-N-C)for ORR.To be specific,the interfacial electron interaction effect,along with a highly robust Co_(SA)-N-C support endow the as-fabricated Pt/Co_(SA)-N-C catalyst with significantly enhanced catalytic properties,i.e.,a mass activity(MA)of 0.719 A/mgPt at 0.9 ViR-free and a reduction of 24.2%in MA after a 20,000-cycles test.Density functional theory(DFT)calculations demonstrate that the enhanced electron interaction between Pt and Co_(SA)-N-C support decreases the dband center of Pt,which is in favor of lowering the desorption energy of ^(*)OH on Pt/Co_(SA)-N-C surface and accelerating the formation of H_(2)O,thus enhance the instinct activity of ORR.Furthermore,the higher binding energy between Pt and Co_(SA)-N-C compared to Pt and C indicates that the migration of Pt has been suppressed,which theoretically explains the improved durability of Pt/Co_(SA)-N-C.Our work offers an enlightenment on constructing composite Pt-based catalysts with multiple active sites.展开更多
Descriptors play a pivotal role in enzyme design for the greener synthesis of biochemicals,as they could characterize enzymes and chemicals from the physicochemical and evolutionary perspective.This study examined the...Descriptors play a pivotal role in enzyme design for the greener synthesis of biochemicals,as they could characterize enzymes and chemicals from the physicochemical and evolutionary perspective.This study examined the effects of various descriptors on the performance of Random Forest model used for enzyme-chemical relationships prediction.We curated activity data of seven specific enzyme families from the literature and developed the pipeline for evaluation the machine learning model performance using 10-fold cross-validation.The influence of protein and chemical descriptors was assessed in three scenarios,which were predicting the activity of unknown relations between known enzymes and known chemicals(new relationship evaluation),predicting the activity of novel enzymes on known chemicals(new enzyme evaluation),and predicting the activity of new chemicals on known enzymes(new chemical evaluation).The results showed that protein descriptors significantly enhanced the classification performance of model on new enzyme evaluation in three out of the seven datasets with the greatest number of enzymes,whereas chemical descriptors appear no effect.A variety of sequence-based and structure-based protein descriptors were constructed,among which the esm-2 descriptor achieved the best results.Using enzyme families as labels showed that descriptors could cluster proteins well,which could explain the contributions of descriptors to the machine learning model.As a counterpart,in the new chemical evaluation,chemical descriptors made significant improvement in four out of the seven datasets,while protein descriptors appear no effect.We attempted to evaluate the generalization ability of the model by correlating the statistics of the datasets with the performance of the models.The results showed that datasets with higher sequence similarity were more likely to get better results in the new enzyme evaluation and datasets with more enzymes were more likely beneficial from the protein descriptor strategy.This work provides guidance展开更多
Cell-matrix interactions play a critical role in tissue repair and regeneration.With gradual uncovering of substrate mechanical characteristics that can affect cell-matrix interactions,much progress has been made to u...Cell-matrix interactions play a critical role in tissue repair and regeneration.With gradual uncovering of substrate mechanical characteristics that can affect cell-matrix interactions,much progress has been made to unravel substrate stiffness-mediated cellular response as well as its underlying mechanisms.Yet,as a part of cell-matrix interaction biology,this field remains in its infancy,and the detailed molecular mechanisms are still elusive regarding scaffold-modulated tissue regeneration.This review provides an overview of recent progress in the area of the substrate stiffness-mediated cellular responses,including 1)the physical determination of substrate stiffness on cell fate and tissue development;2)the current exploited approaches to manipulate the stiffness of scaffolds;3)the progress of recent researches to reveal the role of substrate stiffness in cellular responses in some representative tissue-engineered regeneration varying from stiff tissue to soft tissue.This article aims to provide an up-to-date overview of cell mechanobiology research in substrate stiffness mediated cellular response and tissue regeneration with insightful information to facilitate interdisciplinary knowledge transfer and enable the establishment of prognostic markers for the design of suitable biomaterials.展开更多
With the advent of tissue engineering and biomedicine,the creation of extracellular matrix(ECM)biomaterials for in vitro applications has become a prominent and promising strategy.These ECM materials provide physical,...With the advent of tissue engineering and biomedicine,the creation of extracellular matrix(ECM)biomaterials for in vitro applications has become a prominent and promising strategy.These ECM materials provide physical,biochemical,and mechanical properties that guide cellular behaviors,such as proliferation,differentiation,migration,and apoptosis.Because micro-and nano-patterned materials have a unique surface topology and low energy replication process that directly affect cellular biological behaviors at the interface,the fabrication of micro-nano pattern biomaterials and the regulation of surface physical and chemical properties are of great significance in the fields of cell regulation,tissue engineering,and regenerative medicine.Herein,we provide a comprehensive review of the progress in the fabrication and application of patterned materials based on the coupling of mechanical action at the micro-and nano-meter scale,including photolithography,micro-contact printing,electron beam lithography,electrospinning,and 3D printing technology.Furthermore,a summary of the fabrication process,underlying principles,as well as the advantages and disadvantages of various technologies are reviewed.We also discuss the influence of material properties on the fabrication of micro-and nano-patterns.展开更多
Histone deacetylase 6 （HDAC6）, a predominantly cyto- plasmic protein deacetylase, participates in a wide range of cellular processes through its deacetylase activity. However, the diverse functions of HDAC6 can- not...Histone deacetylase 6 （HDAC6）, a predominantly cyto- plasmic protein deacetylase, participates in a wide range of cellular processes through its deacetylase activity. However, the diverse functions of HDAC6 can- not be fully elucidated with its known substrates. In an attempt to explore the substrate diversity of HDAC6, we performed quantitative proteomic analyses to monitor changes in the abundance of protein lysine acetylation in response to HDAC6 deficiency. We identified 107 proteins with elevated acetylation in the liver of HDAC6 knockout mice. Three cytoplasmic proteins, including myosin heavy chain 9 （MYH9）, heat shock cognate pro- tein 70 （HscT0）, and dnaJ homolog subfamily A member 1 （DNAJA1）, were verified to interact with HDAC6. The acetylation levels of these proteins were negatively regulated by HDAC6 both in the mouse liver and in cultured cells. Functional studies reveal that HDAC6- mediated deacetylation modulates the actin-binding ability of MYH9 and the interaction between Hsc70 and DNAJA1. These findings consolidate the notion that HDAC6 serves as a critical regulator of proteinacetylation with the capability of coordinating various cellular functions.展开更多
Substrates provide the necessary support for scientific explorations of numerous promising features and exciting potential applications in two-dimensional (2D) transition metal dichalcogenides (TMDs). To utilize subst...Substrates provide the necessary support for scientific explorations of numerous promising features and exciting potential applications in two-dimensional (2D) transition metal dichalcogenides (TMDs). To utilize substrate engineering to alter the properties of 2D TMDs and avoid introducing unwanted adverse effects, various experimental techniques, such as high-frequency Raman spectroscopy, have been used to understand the interactions between 2D TMDs and substrates. However, sample-substrate interaction in 2D TMDs is not yet fully understood due to the lack of systematic studies by techniques that are sensitive to 2D TMD-substrate interaction. This work systematically investigates the interaction between tungsten disulfide (WS_(2)) monolayers and substrates by low-frequency Raman spectroscopy, which is very sensitive to WS_(2)-substrate interaction. Strong coupling with substrates is clearly revealed in chemical vapor deposition (CVD)-grown monolayer WS_(2) by its low-wavenumber interface mode. It is demonstrated that the enhanced sample-substrate interaction leads to tensile strain on monolayer WS_(2), which is induced during the cooling process of CVD growth and could be released for monolayer WS_(2) sample after transfer or fabricated by an annealing-free method such as mechanical exfoliation. These results not only suggest the effectiveness of low-frequency Raman spectroscopy for probing sample-substrate interactions in 2D TMDs, but also provide guidance for the design of high-performance devices with the desired sample-substrate coupling strength based on 2D TMDs.展开更多
The collective cell migration behavior on a substrate was studied using RKPM meshfree method.The cells were modeled as nematic liquid crystal with hyperelastic cell nucleus.The cell-substrate and cell-cell interaction...The collective cell migration behavior on a substrate was studied using RKPM meshfree method.The cells were modeled as nematic liquid crystal with hyperelastic cell nucleus.The cell-substrate and cell-cell interactions were modeled by coarse-grained potential forces.Through this study,the pulling and pushing phenomenon during collective cell migration process was observed and it was found that the individual cell mobility significantly influenced the collective cell migratory behavior.More self-propelled cells are in the system along the same direction,the faster the collective group migrates toward coordinated direction.The parametric study on cell-cell adhesion strength indicated that as the adhesion strength increases,the collective cell migration speed increases.It also showed that the mechanical stress in leader cell is higher than stress in follower cells.展开更多
The effects of the substrate-water interaction on the wetting behavior in water-oil and surfactant-water-oil systems confined by one substrate which has the preferential interaction to one species of particles have be...The effects of the substrate-water interaction on the wetting behavior in water-oil and surfactant-water-oil systems confined by one substrate which has the preferential interaction to one species of particles have been investigated by using the free energy analysis and discontinuous molecular dynamic simulations. As the preferential interaction between the substrate and water particles varies from small repulsion to large attraction, the partial drying, partial wetting and complete wetting state are observed in sequence. In addition, the wetting behavior of surfactant aqueous solution on the substrate is not only dependent on the interaction, but also limited by the maximum equilibrium concentration of surfactants at the interface.展开更多
The B3LYP/LanL1MB and B3LYP/LanL2DZ methods for Ag atom in conjunction with the 6-31G（d） basis set for S, C and H atoms were used to optimize the geometries and calculate the energies for （SCH3）mAg20 （re=1-4）, r...The B3LYP/LanL1MB and B3LYP/LanL2DZ methods for Ag atom in conjunction with the 6-31G（d） basis set for S, C and H atoms were used to optimize the geometries and calculate the energies for （SCH3）mAg20 （re=1-4）, respectively. A single molecular adsorption energy of （SCH3）m （rn=1-4） on Ag20 and the intermolecular substrate-mediated interaction energy were evaluated. The results revealed that there is a proportional relation between the single molecular adsorption energy and the substrate-mediated intermolecular interaction energy. The results qualitatively demonstrated the semi-empirical expression for the substratemediated interaction energy proposed previously by us is consistent with the results of the density functional theory.展开更多
基金supported by the National Natural Science Foundation of China (No. 40873076,40773055)the Scientific Research Foundation for the Returned Overseas Chinese Scholars,State Education Ministry (No.2008890)
文摘A pure culture using benzene as sole carbon and energy sources was isolated by screening procedure from gasoline contaminated soil.The analysis of the 16S rDNA gene sequence,morphological and physiological characteristics showed that the isolated strain was a member of genus Bacillus cereus.The biodegradation performance of benzene by B.cereus was evaluated,and the results showed that benzene could be efficiently biodegraded when the initial benzene concentration was below 150 mg/L.The metabolites of anaerobic nitrate-dependent benzene oxidation by strain B.cereus were identified as phenol and benzoate.The results of substrate interaction between binary combinations for benzene,phenol and benzoate showed that the simultaneous presence of benzene stimulated the degradation of benzoate,whereas the addition of benzene inhibited the degradation of phenol.Benzene degradation by B.cereus was enhanced by the addition of phenol and benzoate,the enhanced effects were more pronounced at higher concentration.To our knowledge,this is the first report that the isolated bacterial culture of B.cereus can efficiently degraded benzene under nitrate reducing conditions.
基金financially supported by the Natural Science Foundation of China(Nos.22169005,22209186,22068009 and 22262006)the Science and Technology Support Project of Guizhou Provincial Science and Technology Department(Nos.ZK[2023]050 and[2023]403)+2 种基金the Open Project of Institute of Dualcarbon and New Energy Technology Innovation and Development of Guizhou Province(No.DCRE-2023-06)Youth Innovation Promotion Association,CAS(No.2023343)Self-deployed Projects of Ganjiang Innovation Academy,CAS(No.E355F006).
文摘Developing platinum-group-metal(PGM)catalysts possessing strong metal-support interaction and controllable PGM size is urgent for the sluggish oxygen reduction reaction(ORR)in proton-exchange membrane fuel cells.Herein,we propose an in-situ self-assembled reduction strategy to successfully induce highly-dispersed sub-3nm platinum nanoparticles(Pt NPs)to attach on resin-derived atomic Co coordinated by N-doped carbon substrate(Pt/Co_(SA)-N-C)for ORR.To be specific,the interfacial electron interaction effect,along with a highly robust Co_(SA)-N-C support endow the as-fabricated Pt/Co_(SA)-N-C catalyst with significantly enhanced catalytic properties,i.e.,a mass activity(MA)of 0.719 A/mgPt at 0.9 ViR-free and a reduction of 24.2%in MA after a 20,000-cycles test.Density functional theory(DFT)calculations demonstrate that the enhanced electron interaction between Pt and Co_(SA)-N-C support decreases the dband center of Pt,which is in favor of lowering the desorption energy of ^(*)OH on Pt/Co_(SA)-N-C surface and accelerating the formation of H_(2)O,thus enhance the instinct activity of ORR.Furthermore,the higher binding energy between Pt and Co_(SA)-N-C compared to Pt and C indicates that the migration of Pt has been suppressed,which theoretically explains the improved durability of Pt/Co_(SA)-N-C.Our work offers an enlightenment on constructing composite Pt-based catalysts with multiple active sites.
基金This work is supported by National Key Research and Development Program of China(no.2022YFC2105900).
文摘Descriptors play a pivotal role in enzyme design for the greener synthesis of biochemicals,as they could characterize enzymes and chemicals from the physicochemical and evolutionary perspective.This study examined the effects of various descriptors on the performance of Random Forest model used for enzyme-chemical relationships prediction.We curated activity data of seven specific enzyme families from the literature and developed the pipeline for evaluation the machine learning model performance using 10-fold cross-validation.The influence of protein and chemical descriptors was assessed in three scenarios,which were predicting the activity of unknown relations between known enzymes and known chemicals(new relationship evaluation),predicting the activity of novel enzymes on known chemicals(new enzyme evaluation),and predicting the activity of new chemicals on known enzymes(new chemical evaluation).The results showed that protein descriptors significantly enhanced the classification performance of model on new enzyme evaluation in three out of the seven datasets with the greatest number of enzymes,whereas chemical descriptors appear no effect.A variety of sequence-based and structure-based protein descriptors were constructed,among which the esm-2 descriptor achieved the best results.Using enzyme families as labels showed that descriptors could cluster proteins well,which could explain the contributions of descriptors to the machine learning model.As a counterpart,in the new chemical evaluation,chemical descriptors made significant improvement in four out of the seven datasets,while protein descriptors appear no effect.We attempted to evaluate the generalization ability of the model by correlating the statistics of the datasets with the performance of the models.The results showed that datasets with higher sequence similarity were more likely to get better results in the new enzyme evaluation and datasets with more enzymes were more likely beneficial from the protein descriptor strategy.This work provides guidance
基金supported by Fundamental Research Funds for National Key Research and Development Program of China(2018YFC1105800)China Postdoctoral Science Foundation(2020M681322)National Natural Science Foundation of China(31870967 and 81671921).
文摘Cell-matrix interactions play a critical role in tissue repair and regeneration.With gradual uncovering of substrate mechanical characteristics that can affect cell-matrix interactions,much progress has been made to unravel substrate stiffness-mediated cellular response as well as its underlying mechanisms.Yet,as a part of cell-matrix interaction biology,this field remains in its infancy,and the detailed molecular mechanisms are still elusive regarding scaffold-modulated tissue regeneration.This review provides an overview of recent progress in the area of the substrate stiffness-mediated cellular responses,including 1)the physical determination of substrate stiffness on cell fate and tissue development;2)the current exploited approaches to manipulate the stiffness of scaffolds;3)the progress of recent researches to reveal the role of substrate stiffness in cellular responses in some representative tissue-engineered regeneration varying from stiff tissue to soft tissue.This article aims to provide an up-to-date overview of cell mechanobiology research in substrate stiffness mediated cellular response and tissue regeneration with insightful information to facilitate interdisciplinary knowledge transfer and enable the establishment of prognostic markers for the design of suitable biomaterials.
基金supported by Key Research Program of Frontier Sciences of CAS(No.QYKJZD-SSW-SLH02).
文摘With the advent of tissue engineering and biomedicine,the creation of extracellular matrix(ECM)biomaterials for in vitro applications has become a prominent and promising strategy.These ECM materials provide physical,biochemical,and mechanical properties that guide cellular behaviors,such as proliferation,differentiation,migration,and apoptosis.Because micro-and nano-patterned materials have a unique surface topology and low energy replication process that directly affect cellular biological behaviors at the interface,the fabrication of micro-nano pattern biomaterials and the regulation of surface physical and chemical properties are of great significance in the fields of cell regulation,tissue engineering,and regenerative medicine.Herein,we provide a comprehensive review of the progress in the fabrication and application of patterned materials based on the coupling of mechanical action at the micro-and nano-meter scale,including photolithography,micro-contact printing,electron beam lithography,electrospinning,and 3D printing technology.Furthermore,a summary of the fabrication process,underlying principles,as well as the advantages and disadvantages of various technologies are reviewed.We also discuss the influence of material properties on the fabrication of micro-and nano-patterns.
基金This work was supported by grants from the National Natural Sci- ence Foundation of China （Grant Nos. 91313302, 31171334, and 31170782） and the Tianjin Natural Science Foundation （11JCYBJC25500）. L.Z. performed most of the experiments. S.L. and Y.Z. carried out proteomics experiments and bioinformatics analysis. L.Z., S.L., N.L., M.L., D.L., and W.S. analyzed data. E.S. gave important suggestions about the research strategy. T.-P.Y. provided HDAC6 knockout mice. L.Z., S.L., W.S., and J.Z. wrote the manuscript. W.S. and J.Z. con- ceived and designed experiments.
文摘Histone deacetylase 6 （HDAC6）, a predominantly cyto- plasmic protein deacetylase, participates in a wide range of cellular processes through its deacetylase activity. However, the diverse functions of HDAC6 can- not be fully elucidated with its known substrates. In an attempt to explore the substrate diversity of HDAC6, we performed quantitative proteomic analyses to monitor changes in the abundance of protein lysine acetylation in response to HDAC6 deficiency. We identified 107 proteins with elevated acetylation in the liver of HDAC6 knockout mice. Three cytoplasmic proteins, including myosin heavy chain 9 （MYH9）, heat shock cognate pro- tein 70 （HscT0）, and dnaJ homolog subfamily A member 1 （DNAJA1）, were verified to interact with HDAC6. The acetylation levels of these proteins were negatively regulated by HDAC6 both in the mouse liver and in cultured cells. Functional studies reveal that HDAC6- mediated deacetylation modulates the actin-binding ability of MYH9 and the interaction between Hsc70 and DNAJA1. These findings consolidate the notion that HDAC6 serves as a critical regulator of proteinacetylation with the capability of coordinating various cellular functions.
基金This work is supported by the National Natural Science Foundation of China(Nos.62004197 and 61774040)the Ministry of Education of Singapore(No.MOE2019-T2-1-004)+5 种基金the Singapore National Research Foundation under the Competitive Research Programs(No.NRF-CRP-21-2018-0007)the National Key R&D Program of China(No.2018YFA0703700)the National Young 1000 Talent Plan of China,the Shanghai Municipal Natural Science Foundation(No.20ZR1403200)the Shanghai Municipal Science and Technology Commission(No.18JC1410300)the Fudan University-CIOMP Joint Fund(No.FC2018-002)the Natural Science Foundation of Liaoning Province,China(Nos.2019-BS-243 and 2019-MS-320).
文摘Substrates provide the necessary support for scientific explorations of numerous promising features and exciting potential applications in two-dimensional (2D) transition metal dichalcogenides (TMDs). To utilize substrate engineering to alter the properties of 2D TMDs and avoid introducing unwanted adverse effects, various experimental techniques, such as high-frequency Raman spectroscopy, have been used to understand the interactions between 2D TMDs and substrates. However, sample-substrate interaction in 2D TMDs is not yet fully understood due to the lack of systematic studies by techniques that are sensitive to 2D TMD-substrate interaction. This work systematically investigates the interaction between tungsten disulfide (WS_(2)) monolayers and substrates by low-frequency Raman spectroscopy, which is very sensitive to WS_(2)-substrate interaction. Strong coupling with substrates is clearly revealed in chemical vapor deposition (CVD)-grown monolayer WS_(2) by its low-wavenumber interface mode. It is demonstrated that the enhanced sample-substrate interaction leads to tensile strain on monolayer WS_(2), which is induced during the cooling process of CVD growth and could be released for monolayer WS_(2) sample after transfer or fabricated by an annealing-free method such as mechanical exfoliation. These results not only suggest the effectiveness of low-frequency Raman spectroscopy for probing sample-substrate interactions in 2D TMDs, but also provide guidance for the design of high-performance devices with the desired sample-substrate coupling strength based on 2D TMDs.
基金This work is supported by a grant from National Institutes of Health(Grant No.SC2GM112575)a grant from the John L.Santikos Charitable Foundation of the San Antonio Area Foundation.
文摘The collective cell migration behavior on a substrate was studied using RKPM meshfree method.The cells were modeled as nematic liquid crystal with hyperelastic cell nucleus.The cell-substrate and cell-cell interactions were modeled by coarse-grained potential forces.Through this study,the pulling and pushing phenomenon during collective cell migration process was observed and it was found that the individual cell mobility significantly influenced the collective cell migratory behavior.More self-propelled cells are in the system along the same direction,the faster the collective group migrates toward coordinated direction.The parametric study on cell-cell adhesion strength indicated that as the adhesion strength increases,the collective cell migration speed increases.It also showed that the mechanical stress in leader cell is higher than stress in follower cells.
文摘The effects of the substrate-water interaction on the wetting behavior in water-oil and surfactant-water-oil systems confined by one substrate which has the preferential interaction to one species of particles have been investigated by using the free energy analysis and discontinuous molecular dynamic simulations. As the preferential interaction between the substrate and water particles varies from small repulsion to large attraction, the partial drying, partial wetting and complete wetting state are observed in sequence. In addition, the wetting behavior of surfactant aqueous solution on the substrate is not only dependent on the interaction, but also limited by the maximum equilibrium concentration of surfactants at the interface.
基金Ⅴ. ACKN0WLEDGMENTSThis work was supported by the National Natural Science Foundation of China （No.20473078） and The Ph.D. Programs Foundation of Ministry of Education of China （No.20020358061）.
文摘The B3LYP/LanL1MB and B3LYP/LanL2DZ methods for Ag atom in conjunction with the 6-31G（d） basis set for S, C and H atoms were used to optimize the geometries and calculate the energies for （SCH3）mAg20 （re=1-4）, respectively. A single molecular adsorption energy of （SCH3）m （rn=1-4） on Ag20 and the intermolecular substrate-mediated interaction energy were evaluated. The results revealed that there is a proportional relation between the single molecular adsorption energy and the substrate-mediated intermolecular interaction energy. The results qualitatively demonstrated the semi-empirical expression for the substratemediated interaction energy proposed previously by us is consistent with the results of the density functional theory.
