The harm of pathogenic bacteria to humans has promoted extensive research on physiological processes of pathogens,such as the mechanism of bacterial infection,antibiotic mode of action,and bacterial antimicrobial resi...The harm of pathogenic bacteria to humans has promoted extensive research on physiological processes of pathogens,such as the mechanism of bacterial infection,antibiotic mode of action,and bacterial antimicrobial resistance.Most of these processes can be better investigated by timely tracking of fluorophore-derived antibiotics in living cells.In this paper,we will review the recent development of fluorescent antibiotics featuring the conjugation with various fluorophores,and focus on their applications in fluorescent imaging and real-time detection for various physiological processes of bacteria in vivo.展开更多
A metabonomic approach was undertaken in order to detect urinary endogenous and exogenous metabolites and to evaluate the effects of passive exposure to cigarette sidestream smoke on rats. Urinary samples from three g...A metabonomic approach was undertaken in order to detect urinary endogenous and exogenous metabolites and to evaluate the effects of passive exposure to cigarette sidestream smoke on rats. Urinary samples from three groups of rats were determined including control rats, rats treated with blended cigarettes(nonmenthol cigarettes) and rats treated with menthol cigarettes. The total urinary 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol(NNAL), total 1-hydroxypyrene(1-HOP) and 3-hydroxybenzo[a] pyrene(3-HOBaP) were determined for assessing exposure to cigarette sidestream smoke toxins. Urinary endogenous metabolites in the three groups of rats were also analyzed and the data were processed by chemometrics. Eleven endogenous metabolites were found and identified. Their relative levels were compared among the three groups. The results show that cigarette sidestream smoke has complex effect on rats. Blended cigarette group makes difference to menthol cigarette group in the rats' urinary metabolic changes. Menthol adding to cigarettes has positive and negative effects on rats, respectively. The urinary metabolic profiling of menthol cigarette group is closer to that of control group.展开更多
Semi-artificial photosynthesis interfacing catalytic protein machinery with synthetic photocatalysts exhibits great potential in solar-to-chemical energy conversion. However, characterizing and manipulating the molecu...Semi-artificial photosynthesis interfacing catalytic protein machinery with synthetic photocatalysts exhibits great potential in solar-to-chemical energy conversion. However, characterizing and manipulating the molecular integration structure at the biotic-abiotic interface remain a challenging task. Herein,the biointerface molecular integration details of photosystem II(PSII)-semiconductor hybrids, including the PSII orientation, interfacial microdomains, and overall structure modulation, are systematically interrogated by lysine reactivity profiling mass spectrometry. We demonstrate the semiconductor surface biocompatibility is essential to the PSII self-assembly with uniform orientation and electroactive structure.Highly directional localization of PSII onto more hydrophilic Ru/Sr Ti O_(3):Rh surface exhibits less disturbance on PSII structure and electron transfer chain, beneficial to the high water splitting activity.Further, rational modification of hydrophobic Ru_(2)S_(3)/Cd S surface with biocompatible protamine can improve the hybrid O_(2)-evolving activity 83.3%. Our results provide the mechanistic understanding to the structure–activity relationship of PSII-semiconductor hybrids and contribute to their rational design in the future.展开更多
Exhaled ammonia(NH_(3))is an essential noninvasive biomarker for disease diagnosis.In this study,an acetone-modifier positive photoionization ion mobility spectrometry(AM-PIMS)method was developed for accurate qualita...Exhaled ammonia(NH_(3))is an essential noninvasive biomarker for disease diagnosis.In this study,an acetone-modifier positive photoionization ion mobility spectrometry(AM-PIMS)method was developed for accurate qualitative and quantitative analysis of exhaled NH_(3)with high selectivity and sensitivity.Acetone was introduced into the drift tube along with the drift gas as a modifier,and the characteristic NH_(3)product ion peak of(C_(3)H_(6)O)_(4)NH_(4)^(+)(K_(0)=1.45 cm^(2)/V·s)was obtained through the ion-molecule reaction with acetone reactant ions(C_(3)H_(6)O)_(2)H^(+)(K_(0)=1.87 cm^(2)/V·s),which significantly increased the peak-to-peak resolution and improved the accuracy of exhaled NH_(3)qualitative identification.Moreover,the interference of high humidity and the memory effect of NH_(3)molecules were significantly reduced via online dilution and purging sampling,thus realizing breath-by-breath measurement.As a result,a wide quantitative range of 5.87-140.92μmol/L with a response time of 40 ms was achieved,and the exhaled NH_(3)profile could be synchronized with the concentration curve of exhaled CO_(2).Finally,the analytical capacity of AM-PIMS was demonstrated by measuring the exhaled NH_(3)of healthy subjects,demonstrating its great potential for clinical disease diagnosis.展开更多
Breast cancer remains a leading cause of morbidity and mortality among women worldwide,emphasizing the urgent need for enhanced diagnostic and therapeutic approaches.Leucine-rich-alpha-2-glycoprotein 1(LRG1)has emerge...Breast cancer remains a leading cause of morbidity and mortality among women worldwide,emphasizing the urgent need for enhanced diagnostic and therapeutic approaches.Leucine-rich-alpha-2-glycoprotein 1(LRG1)has emerged as a notable target due to its markedly elevated expression in breast tumors,suggesting the viability of LRG1 as a theranostic target.In our study,we employed phage display technology to identify a peptide,termed ET,that binds to LRG1 with a dissociation constant of 48.4μM.After modified with fluorescent cyanine dye,the ET peptide showcased effective tumor-targeting imaging across three different primary breast tumor models and a metastatic breast tumor model.We also undertook a comprehensive safety evaluation,which verified the good biosafety credentials of ET peptide.In summary,the ET peptide identified in this study shows effective LRG1-targeting ability both in vitro and in vivo,thus exhibiting immense potential for clinical translation.展开更多
The demand for enhanced optical properties in advanced fluorescence technologies has driven research into the structure-property relationship of fluorophores.In this paper,we use naphthalene fluorophores Na DC-Aze and...The demand for enhanced optical properties in advanced fluorescence technologies has driven research into the structure-property relationship of fluorophores.In this paper,we use naphthalene fluorophores Na DC-Aze and PhDO-Aze as a case study to emphasize the pivotal role of cross conjugation in tuning the optical structure-property relationship.Na DC-Aze and PhDO-Aze,formed by hybridizing two distinct conjugated systems in a single naphthalene molecule,exhibit spectral characteristics from both conjugated systems.Experimental data and theoretical calculations demonstrate the coexistence of two electron-delocalization systems in a cross-conjugation manner in both Na DC-Aze and PhDO-Aze.The cross-conjugation fluorophores exhibit high brightness,large Stokes shift,and a broad absorption wavelength range by combining distinct spectral properties from its parent fluorophores.These spectral properties will be advantageous for certain applications(i.e.,panchromatic absorption in organic solar cells,and fluorophores compatible with a wide range of excitation wavelengths).展开更多
Targeting the PD-1/PD-L1 axis with small-molecular inhibitors is a promising approach for immunotherapy.Here,we identify a natural pentacyclic triterpenoid,Pygenic Acid A(PA),as a PD-1 signaling inhibitor.PA exerts an...Targeting the PD-1/PD-L1 axis with small-molecular inhibitors is a promising approach for immunotherapy.Here,we identify a natural pentacyclic triterpenoid,Pygenic Acid A(PA),as a PD-1 signaling inhibitor.PA exerts anti-tumor activity in hPD-1 knock-in C57BL/6 mice and enhances effector functions of T cells to promote immune responses by disrupting the PD-1 signaling transduction.Furthermore,we identify SHP-2 as the direct molecular target of PA for inhibiting the PD-1 signaling transduction.Subsequently,mechanistic studies suggest that PA binds to a new druggable site in the phosphorylated PD-1 ITSM recognition site of SHP-2,inhibiting the recruitment of SHP-2 by PD1.Taken together,our findings demonstrate that PA has a potential application in cancer immunotherapy and occupying the phosphorylated ITSM recognition site of SHP-2 may serve as an alternative strategy to develop PD-1 signaling inhibitors.In addition,our success in target recognition provides a paradigm of target identification and confirmation for natural products.展开更多
Methylotrophic yeast Ogataea polymorpha is capable to utilize multiple carbon feedstocks especially methanol as sole carbon source and energy,making it an ideal host for bio-manufacturing.However,the lack of gene inte...Methylotrophic yeast Ogataea polymorpha is capable to utilize multiple carbon feedstocks especially methanol as sole carbon source and energy,making it an ideal host for bio-manufacturing.However,the lack of gene integration sites limits its systems metabolic engineering,in particular construction of genome-integrated pathway.We here screened the genomic neutral sites for gene integration without affecting cellular fitness,by genomic integration of an enhanced green fluorescent protein(eGFP)gene via CRISPR-Cas9 technique.After profiling the growth and fluorescent intensity in various media,17 genome positions were finally identified as potential neutral sites.Finally,integration of fatty alcohol synthetic pathway genes into neutral sites NS2 and NS3,enabled the production of 4.5 mg/L fatty alcohols,indicating that these neutral sites can be used for streamline metabolic engineering in O.polymorpha.We can anticipate that the neutral sites screening method described here can be easily adopted to other eukaryotes.展开更多
Current yeast metabolic engineering in isoprenoids production mainly focuses on rewiring of cytosolic metabolic pathway.However,the precursors,cofactors and the enzymes are distributed in various sub-cellular compartm...Current yeast metabolic engineering in isoprenoids production mainly focuses on rewiring of cytosolic metabolic pathway.However,the precursors,cofactors and the enzymes are distributed in various sub-cellular compartments,which may hamper isoprenoid biosynthesis.On the other side,pathway compartmentalization provides several advantages for improving metabolic flux toward target products.We here summarize the recent advances on harnessing sub-organelle for isoprenoids biosynthesis in yeast,and analyze the knowledge about the localization of enzymes,cofactors and metabolites for guiding the rewiring of the sub-organelle metabolism.This review may provide some insights for constructing efficient yeast cell factories for production of isoprenoids and even other natural products.展开更多
Bio-manufacturing via microbial cell factory requires large promoter library for fine-tuned metabolic engi-neering.Ogataea polymorpha,one of the methylotrophic yeasts,possesses advantages in broad substrate spec-trum,...Bio-manufacturing via microbial cell factory requires large promoter library for fine-tuned metabolic engi-neering.Ogataea polymorpha,one of the methylotrophic yeasts,possesses advantages in broad substrate spec-trum,thermal-tolerance,and capacity to achieve high-density fermentation.However,a limited number of available promoters hinders the engineering of O.polymorpha for bio-productions.Here,we systematically characterized native promoters in O.polymorpha by both GFP fluorescence and fatty alcohol biosynthesis.Ten constitutive promoters(P_(PDH),P_(PYK),P_(FBA),P_(PGM),P_(GLK),P_(TRI),P(GPI),P_(ADH1),P_(TEF1) and P_(GCW14))were obtained with the activity range of 13%–130% of the common promoter P_(GAP)(the promoter of glyceraldehyde-3-phosphate de-hydrogenase),among which P_(PDH) and P_(GCW14) were further verified by biosynthesis of fatty alcohol.Furthermore,the inducible promoters,including ethanol-induced P_(ICL1),rhamnose-induced P_(LRA3) and P_( LRA4),and a bidirectional promoter(P_(Mal)-P_(Per))that is strongly induced by sucrose,further expanded the promoter toolbox in O.polymorpha.Finally,a series of hybrid promoters were constructed via engineering upstream activation sequence(UAS),which increased the activity of native promoter P LRA3 by 4.7–10.4 times without obvious leakage expression.Therefore,this study provided a group of constitutive,inducible,and hybrid promoters for metabolic engineering of O.polymorpha,and also a feasible strategy for rationally regulating the promoter strength.展开更多
The need for temporal resolution and long-term stability in super-resolution fluorescence imaging has motivated research to improve the photostability of fluorescent probes.Due to the inevitable photobleaching of fluo...The need for temporal resolution and long-term stability in super-resolution fluorescence imaging has motivated research to improve the photostability of fluorescent probes.Due to the inevitable photobleaching of fluorophores,it is difficult to obtain long-term super-resolution imaging regardless of the self-healing strategy of introducing peroxide scavengers or the strategy of fluorophore structure modification to suppress TICT formation.The buffered fluorogenic probe uses the intact probes in the buffer pool to continuously replace the photobleached ones in the target,which greatly improves the photostability and enables stable dynamic super-resolution imaging for a long time.But the buffering capacity comes at the expense of reducing the number of fluorescent probes in targets,resulting in low staining fluorescence intensity.In this paper,we selected BODIPY 493,a lipid droplet probe with high fluorescence brightness,to explore the dynamic process of lipid droplet staining of this probe in cells.We found that BODIPY 493 only needs very low laser power for lipid droplet imaging due to the high molecular accumulation in lipid droplets and the high brightness,and the spatiotemporal resolution is greatly improved.More importantly,we found that BODIPY 493 also has a certain buffering capacity,which enables BODIPY 493 to be used for super-resolution imaging of lipid droplet dynamics.This work reminds researchers to coordinate the buffering capacity and brightness of fluorogenic probes.展开更多
Dear Editor,Multisite phosphorylation is observed in many signaling proteins,which confers the proteins new functions.A multisite phosphorylated protein can exhibit switch-like response to cellular stimuli,with ...Dear Editor,Multisite phosphorylation is observed in many signaling proteins,which confers the proteins new functions.A multisite phosphorylated protein can exhibit switch-like response to cellular stimuli,with the often-clustered phosphorylation sites either unphosphorylated or fully phosphorylated by the same kinase(Kapuy et al..2009).Multisite phosphorylation has also been reported to promote the folding of an intrinsically disordered protein,and consequently modulate the binding affinity to other proteins(Bah et al.,2015).Here we show that multisite phosphorylation makes a protein a better pH sensor,promptly switching between alternative conformational states in response to pH change under physiological conditions.展开更多
The methylotrophic yeast Pichia pastoris(also known as Komagataella phaffii)is widely used as a yeast cell factory for producing heterologous proteins.Recently,it has gained attention for its potential in producing ch...The methylotrophic yeast Pichia pastoris(also known as Komagataella phaffii)is widely used as a yeast cell factory for producing heterologous proteins.Recently,it has gained attention for its potential in producing chemicals from inexpensive feedstocks,which requires efficient genetic engineering platforms.This review provides an overview of the current advances in developing genetic tools for metabolic engineering of P.pastoris.The topics cover promoters,terminators,plasmids,genome integration sites,and genetic editing systems,with a special focus on the development of CRISPR/Cas systems and their comparison to other genome editing tools.Additionally,this review highlights the prospects of multiplex genome integration,fine-tuning gene expression,and single-base editing systems.Overall,the aim of this review is to provide valuable insights into current genetic engineering and discuss potential directions for future efforts in developing efficient genetic tools in P.pastoris.展开更多
The complications of hemodialysis accompanied the hemodialysis and threaten the patients’life.Besides the loss of nutrient substance,such as amino acid and vitamin,we found new clues that the adsorbed proteins on com...The complications of hemodialysis accompanied the hemodialysis and threaten the patients’life.Besides the loss of nutrient substance,such as amino acid and vitamin,we found new clues that the adsorbed proteins on common-used polysulfone-based dialysis membrane might be the reason according to the qualitative proteomic study by ionic liquid assisted sample preparation method.Our results indicated that the adsorbed proteins on the membrane were related with complement activation,blood coagulation,and leukocyte-related biological process.The quantitative proteome further demonstrated some significant changes of signal proteins in the post-dialysis plasma after the hemodialysis,such as beta-2-microglobulin and platelet factor-4,which would further verify these new clues.展开更多
The combination of super-resolution microscopy and synthetic fluorescence probes has emerged as a universal tool to monitor dynamic biological events at the nanometer scale.However,the limited site-specificity and flu...The combination of super-resolution microscopy and synthetic fluorescence probes has emerged as a universal tool to monitor dynamic biological events at the nanometer scale.However,the limited site-specificity and fluorogenicity of synthetic fluorescent probes make it still difficult to realize long-term super-resolution imaging.Herein,we introduce a dynamic aggregation mediated SNAP-tag fluorogenic probe,BGAN-Aze,which can specifically bind to various SNAP-tag fusion proteins with 41-fold fluorescence enhancement.The equilibrium between the non-fluorescent aggregate/dimer(A–D)and the fluorescent monomer(M)of BGAN-Aze acts as an effective method to reduce the fluorescence background and endow BGAN-Aze with the capability of conducting washing-free super-resolution imaging of various intracellular and extracellular proteins.Using this probe,we monitored multiple dynamic biological events,such as MMC,mitophagy,the fusion of nucleolus,and the growth and contact of filopodia.We expect that BGAN-Aze will become a widely used SNAP-tag for super-resolution imaging of dynamic biological events and the A-D-M equilibrium can be a general strategy for designing fluorogenic probes.展开更多
Deep proteome profiling from trace biological samples are needed for important biomedical applications[1],but the sample losses from traditional sample preparation procedures are a major limitation[2].Therefore,consid...Deep proteome profiling from trace biological samples are needed for important biomedical applications[1],but the sample losses from traditional sample preparation procedures are a major limitation[2].Therefore,considerable efforts have been made to improve it[3,4].Filter-aided sample preparation(FASP)developed by Mann’s group[5]is recognized one of the most popular methods,by which protein extraction,reduction,alkylation,and digestion are performed on a commercial spin filter.展开更多
The formation of protein coronas on nanomaterial will significantly alter the surface properties of nanomaterial in biological systems and subsequently impact biological responses including signaling, cellular uptake,...The formation of protein coronas on nanomaterial will significantly alter the surface properties of nanomaterial in biological systems and subsequently impact biological responses including signaling, cellular uptake, transport, and toxicity etc. It is of critical importance to understand the formation of protein coronas on the surface of nanomaterial. Analytical techniques, especially mass spectrometry-based proteomics methods, are playing a key role for the qualitative and quantitative analyses of protein coronas on nanomaterial. In this review, the proteomic approaches developed for the characterization of protein coronas on various nanomaterials are introduced with the emphasis on the mass spectrometry-based proteomic strategies.展开更多
Water-insoluble organic compounds(WIOCs)are an important fraction of atmospheric fine particulate matters(PM_(2.5)),which could affect the climate system and threaten human health potentially.In this study,molecular c...Water-insoluble organic compounds(WIOCs)are an important fraction of atmospheric fine particulate matters(PM_(2.5)),which could affect the climate system and threaten human health potentially.In this study,molecular characterization of WIOCs in PM_(2.5) were investigated by 15 T Fourier transform ion cyclotron resonance mass spectrometry(FT-ICR MS)with atmospheric pressure photoionization(APPI)source in positive ion mode.A total of 2573 and1875 molecular formulas were identified in WIOCs extracted by dichloromethane,which were collected in hazy and normal days,respectively.The identified molecular formulas were further classified into four major subgroups,including CH,CHN,CHO and CHNO compounds.CHO compounds predominated in WIOCs,accounting for more than 60%in both samples.CHNO compounds(26.6%)and CH compounds(16.1%)were the second highest subgroups in WIOCs from the hazy days and normal days,respectively.The relative abundance and number of nitro-substituted aromatic compounds were significantly higher in hazy days than in normal days.The molecular composition of WIOCs was more complex in hazy days while more aromatic compounds were identified in normal days.展开更多
Trimethylphenol is an organic toxic byproduct of industrial process,which is difficult to be eliminated through conventional degradation without harsh conditions.In this work,a sulfite-based oxidation process activate...Trimethylphenol is an organic toxic byproduct of industrial process,which is difficult to be eliminated through conventional degradation without harsh conditions.In this work,a sulfite-based oxidation process activated by ZnO-embedded hydrogel was studied for the degradation of 2,4,6-trimethylphenols in the ambient conditions.The ZnO/Na_(2)SO_(3)oxidative system can effectively degrade trimethylphenol via the generation of radicals such as SO_(4)^(-)·,OH·,and SO_(3)^(−)·.The presence of hydrogel matrix facilitates the distribution and recyclability of ZnO catalysts while maintaining high degradation kinetics and little leaching of metal ions.Results suggest the promising potential of ZnO-hydrogel in wastewater treatment with good performance in terms of pH sensitivity,anion interference,recyclability,etc.The combination of ZnO catalysts,hydrogel,and sulfite-based advanced oxidation process may provide essential support for the current treatment of alkylated phenols with strong potential in the commercial scale-ups.展开更多
High-resolution liquid chromatography separation is essential to in-depth proteomic profiling of complex biological samples.Herein,we established an ion-pair reversed-phase×reversed-phase two-dimensional liquid c...High-resolution liquid chromatography separation is essential to in-depth proteomic profiling of complex biological samples.Herein,we established an ion-pair reversed-phase×reversed-phase two-dimensional liquid chromatography(IPRP×RP 2DLC)strategy for comprehensive proteomic analysis.Both RPLC separation dimensions were performed at low pH,with trifluoroacetic acid(TFA)and formic acid(FA)as mobile phase addictive,respectively.As the good separation resolution offered by ion-pairing effect of TFA,the fractionation efficiency was greatly improved with 74.0%peptides identified in just one fraction.Comparing with conventional high pH RP fractionation,the overall separation rate of IPRP was about 1.6 times that of high-pH RP,which increased the number of identified peptides by 21%.Further,2169 proteins and 8540 peptides were confidently identified from crude serum sample by our IPRP×RP 2DLC strategy,exhibiting great potential in clinical proteomics in the future.展开更多
基金We are grateful for the financial support from the National Natural Science Foundation of China(21878286,21908216,21576043)Dalian Institute of Chemical Physics(DICPI201938,DICP I202006).
文摘The harm of pathogenic bacteria to humans has promoted extensive research on physiological processes of pathogens,such as the mechanism of bacterial infection,antibiotic mode of action,and bacterial antimicrobial resistance.Most of these processes can be better investigated by timely tracking of fluorophore-derived antibiotics in living cells.In this paper,we will review the recent development of fluorescent antibiotics featuring the conjugation with various fluorophores,and focus on their applications in fluorescent imaging and real-time detection for various physiological processes of bacteria in vivo.
基金Project(20805045)supported by National Natural Science Foundation of China
文摘A metabonomic approach was undertaken in order to detect urinary endogenous and exogenous metabolites and to evaluate the effects of passive exposure to cigarette sidestream smoke on rats. Urinary samples from three groups of rats were determined including control rats, rats treated with blended cigarettes(nonmenthol cigarettes) and rats treated with menthol cigarettes. The total urinary 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol(NNAL), total 1-hydroxypyrene(1-HOP) and 3-hydroxybenzo[a] pyrene(3-HOBaP) were determined for assessing exposure to cigarette sidestream smoke toxins. Urinary endogenous metabolites in the three groups of rats were also analyzed and the data were processed by chemometrics. Eleven endogenous metabolites were found and identified. Their relative levels were compared among the three groups. The results show that cigarette sidestream smoke has complex effect on rats. Blended cigarette group makes difference to menthol cigarette group in the rats' urinary metabolic changes. Menthol adding to cigarettes has positive and negative effects on rats, respectively. The urinary metabolic profiling of menthol cigarette group is closer to that of control group.
基金the financial supported by National Key R&D Program of China,China(2019YFE0119300)the National Natural Science Foundation of China,China(32088101,91853101,and 22075280)+2 种基金the Original Innovation Project of CAS,China(ZDBSLY-SLH032)the Excellent Young Scientist Grant of Liaoning Province,China(2019-YQ-07)the grant from DICP(DICPI202007)。
文摘Semi-artificial photosynthesis interfacing catalytic protein machinery with synthetic photocatalysts exhibits great potential in solar-to-chemical energy conversion. However, characterizing and manipulating the molecular integration structure at the biotic-abiotic interface remain a challenging task. Herein,the biointerface molecular integration details of photosystem II(PSII)-semiconductor hybrids, including the PSII orientation, interfacial microdomains, and overall structure modulation, are systematically interrogated by lysine reactivity profiling mass spectrometry. We demonstrate the semiconductor surface biocompatibility is essential to the PSII self-assembly with uniform orientation and electroactive structure.Highly directional localization of PSII onto more hydrophilic Ru/Sr Ti O_(3):Rh surface exhibits less disturbance on PSII structure and electron transfer chain, beneficial to the high water splitting activity.Further, rational modification of hydrophobic Ru_(2)S_(3)/Cd S surface with biocompatible protamine can improve the hybrid O_(2)-evolving activity 83.3%. Our results provide the mechanistic understanding to the structure–activity relationship of PSII-semiconductor hybrids and contribute to their rational design in the future.
基金This work was supported by the National Natural Science Foundation of China(Grant Nos.:22027804,21974141,and 21904125)Natural Science Foundation of Liaoning Province(Grant Nos.:2022-MS-019 and 2022-MS-016)+2 种基金Science and Technology Innovation Foundation of Dalian(Grant No.:2022JJ13SN096)Dalian Institute of Chemical Physics(Grant Nos.:DICP I202141 and DICP I202144)1+X Program for Large Cohort Study-Clinical Research Incubation Project,The Second Hospital of Dalian Medical University(Project No.:2022DXDL01).
文摘Exhaled ammonia(NH_(3))is an essential noninvasive biomarker for disease diagnosis.In this study,an acetone-modifier positive photoionization ion mobility spectrometry(AM-PIMS)method was developed for accurate qualitative and quantitative analysis of exhaled NH_(3)with high selectivity and sensitivity.Acetone was introduced into the drift tube along with the drift gas as a modifier,and the characteristic NH_(3)product ion peak of(C_(3)H_(6)O)_(4)NH_(4)^(+)(K_(0)=1.45 cm^(2)/V·s)was obtained through the ion-molecule reaction with acetone reactant ions(C_(3)H_(6)O)_(2)H^(+)(K_(0)=1.87 cm^(2)/V·s),which significantly increased the peak-to-peak resolution and improved the accuracy of exhaled NH_(3)qualitative identification.Moreover,the interference of high humidity and the memory effect of NH_(3)molecules were significantly reduced via online dilution and purging sampling,thus realizing breath-by-breath measurement.As a result,a wide quantitative range of 5.87-140.92μmol/L with a response time of 40 ms was achieved,and the exhaled NH_(3)profile could be synchronized with the concentration curve of exhaled CO_(2).Finally,the analytical capacity of AM-PIMS was demonstrated by measuring the exhaled NH_(3)of healthy subjects,demonstrating its great potential for clinical disease diagnosis.
基金supported by grants from the National Natural Science Foundation of China(Nos.32000998 and 32201240)The Young Elite Scientists Sponsorship Program by Henan Association for Science and Technology(No.2022HYTP046)+2 种基金the China Postdoctoral Science Foundation(No.2021TQ0298)Science and Technology Development Project of Henan Province(Nos.222102310525,232102310351)National College Students’innovation and entrepreneurship training program(No.202310459197).
文摘Breast cancer remains a leading cause of morbidity and mortality among women worldwide,emphasizing the urgent need for enhanced diagnostic and therapeutic approaches.Leucine-rich-alpha-2-glycoprotein 1(LRG1)has emerged as a notable target due to its markedly elevated expression in breast tumors,suggesting the viability of LRG1 as a theranostic target.In our study,we employed phage display technology to identify a peptide,termed ET,that binds to LRG1 with a dissociation constant of 48.4μM.After modified with fluorescent cyanine dye,the ET peptide showcased effective tumor-targeting imaging across three different primary breast tumor models and a metastatic breast tumor model.We also undertook a comprehensive safety evaluation,which verified the good biosafety credentials of ET peptide.In summary,the ET peptide identified in this study shows effective LRG1-targeting ability both in vitro and in vivo,thus exhibiting immense potential for clinical translation.
基金supported by the National Natural Science Foundation of China(Nos.22225806,22078314,21908216,22378385)Dalian Institute of Chemical Physics(Nos.DICPI202142,DICPI202436)+1 种基金Agency for Science,Technology and Research(No.A*STAR,Singapore)under its Advanced Manufacturing and Engineering Program(No.A2083c0051)SUTD Kickstarter Initiative(No.SKI 2021_03_10)。
文摘The demand for enhanced optical properties in advanced fluorescence technologies has driven research into the structure-property relationship of fluorophores.In this paper,we use naphthalene fluorophores Na DC-Aze and PhDO-Aze as a case study to emphasize the pivotal role of cross conjugation in tuning the optical structure-property relationship.Na DC-Aze and PhDO-Aze,formed by hybridizing two distinct conjugated systems in a single naphthalene molecule,exhibit spectral characteristics from both conjugated systems.Experimental data and theoretical calculations demonstrate the coexistence of two electron-delocalization systems in a cross-conjugation manner in both Na DC-Aze and PhDO-Aze.The cross-conjugation fluorophores exhibit high brightness,large Stokes shift,and a broad absorption wavelength range by combining distinct spectral properties from its parent fluorophores.These spectral properties will be advantageous for certain applications(i.e.,panchromatic absorption in organic solar cells,and fluorophores compatible with a wide range of excitation wavelengths).
基金supported in part by the National Natural Science Foundation of China (81825020, 82150208, 82260682)the National Key R&D Program of China (2022YFC3400501, 2022YFC3400504)+3 种基金the Shanghai Science and Technology Commission Biomedical Science and Technology Support Special Project (21S11907900, 20S11901000)Project of Yunnan Characteristic Plant Screening and R&D Service CXO Platform (2022YKZY001)sponsored by the National Program for Special Supports of Eminent ProfessionalsNational Program for Support of Top-notch Young Professionals
文摘Targeting the PD-1/PD-L1 axis with small-molecular inhibitors is a promising approach for immunotherapy.Here,we identify a natural pentacyclic triterpenoid,Pygenic Acid A(PA),as a PD-1 signaling inhibitor.PA exerts anti-tumor activity in hPD-1 knock-in C57BL/6 mice and enhances effector functions of T cells to promote immune responses by disrupting the PD-1 signaling transduction.Furthermore,we identify SHP-2 as the direct molecular target of PA for inhibiting the PD-1 signaling transduction.Subsequently,mechanistic studies suggest that PA binds to a new druggable site in the phosphorylated PD-1 ITSM recognition site of SHP-2,inhibiting the recruitment of SHP-2 by PD1.Taken together,our findings demonstrate that PA has a potential application in cancer immunotherapy and occupying the phosphorylated ITSM recognition site of SHP-2 may serve as an alternative strategy to develop PD-1 signaling inhibitors.In addition,our success in target recognition provides a paradigm of target identification and confirmation for natural products.
基金supported by National Natural Science Foundation of China(21922812 and 21808216)Dalian Science and Technology Innovation Funding(2019J12GX030)+1 种基金DMTO research grant(grant no.DICP DMTO201701)BioChE research grant(grant no.DICP BioChE-X201801)from Dalian Institute of Chemicals Physics,CAS.
文摘Methylotrophic yeast Ogataea polymorpha is capable to utilize multiple carbon feedstocks especially methanol as sole carbon source and energy,making it an ideal host for bio-manufacturing.However,the lack of gene integration sites limits its systems metabolic engineering,in particular construction of genome-integrated pathway.We here screened the genomic neutral sites for gene integration without affecting cellular fitness,by genomic integration of an enhanced green fluorescent protein(eGFP)gene via CRISPR-Cas9 technique.After profiling the growth and fluorescent intensity in various media,17 genome positions were finally identified as potential neutral sites.Finally,integration of fatty alcohol synthetic pathway genes into neutral sites NS2 and NS3,enabled the production of 4.5 mg/L fatty alcohols,indicating that these neutral sites can be used for streamline metabolic engineering in O.polymorpha.We can anticipate that the neutral sites screening method described here can be easily adopted to other eukaryotes.
基金This study was financially supported by National Natural Science Foundation of China(Grant no.21877111 and no.21922812)China Postdoctoral Science Foundation(199936).
文摘Current yeast metabolic engineering in isoprenoids production mainly focuses on rewiring of cytosolic metabolic pathway.However,the precursors,cofactors and the enzymes are distributed in various sub-cellular compartments,which may hamper isoprenoid biosynthesis.On the other side,pathway compartmentalization provides several advantages for improving metabolic flux toward target products.We here summarize the recent advances on harnessing sub-organelle for isoprenoids biosynthesis in yeast,and analyze the knowledge about the localization of enzymes,cofactors and metabolites for guiding the rewiring of the sub-organelle metabolism.This review may provide some insights for constructing efficient yeast cell factories for production of isoprenoids and even other natural products.
基金National Natural Science Foundation of China(21808216,22161142008 and M-0246)Key project at central government level:The ability establishment of sustainable use for valuable Chinese medicine resources(2060302)DICP innovation grant(DICP I202021 and I201920)from Dalian Institute of Chemicals Physics,CAS.
文摘Bio-manufacturing via microbial cell factory requires large promoter library for fine-tuned metabolic engi-neering.Ogataea polymorpha,one of the methylotrophic yeasts,possesses advantages in broad substrate spec-trum,thermal-tolerance,and capacity to achieve high-density fermentation.However,a limited number of available promoters hinders the engineering of O.polymorpha for bio-productions.Here,we systematically characterized native promoters in O.polymorpha by both GFP fluorescence and fatty alcohol biosynthesis.Ten constitutive promoters(P_(PDH),P_(PYK),P_(FBA),P_(PGM),P_(GLK),P_(TRI),P(GPI),P_(ADH1),P_(TEF1) and P_(GCW14))were obtained with the activity range of 13%–130% of the common promoter P_(GAP)(the promoter of glyceraldehyde-3-phosphate de-hydrogenase),among which P_(PDH) and P_(GCW14) were further verified by biosynthesis of fatty alcohol.Furthermore,the inducible promoters,including ethanol-induced P_(ICL1),rhamnose-induced P_(LRA3) and P_( LRA4),and a bidirectional promoter(P_(Mal)-P_(Per))that is strongly induced by sucrose,further expanded the promoter toolbox in O.polymorpha.Finally,a series of hybrid promoters were constructed via engineering upstream activation sequence(UAS),which increased the activity of native promoter P LRA3 by 4.7–10.4 times without obvious leakage expression.Therefore,this study provided a group of constitutive,inducible,and hybrid promoters for metabolic engineering of O.polymorpha,and also a feasible strategy for rationally regulating the promoter strength.
基金supported by the National Natural Science Foundation of China(Nos.22078314,21878286,21908216).
文摘The need for temporal resolution and long-term stability in super-resolution fluorescence imaging has motivated research to improve the photostability of fluorescent probes.Due to the inevitable photobleaching of fluorophores,it is difficult to obtain long-term super-resolution imaging regardless of the self-healing strategy of introducing peroxide scavengers or the strategy of fluorophore structure modification to suppress TICT formation.The buffered fluorogenic probe uses the intact probes in the buffer pool to continuously replace the photobleached ones in the target,which greatly improves the photostability and enables stable dynamic super-resolution imaging for a long time.But the buffering capacity comes at the expense of reducing the number of fluorescent probes in targets,resulting in low staining fluorescence intensity.In this paper,we selected BODIPY 493,a lipid droplet probe with high fluorescence brightness,to explore the dynamic process of lipid droplet staining of this probe in cells.We found that BODIPY 493 only needs very low laser power for lipid droplet imaging due to the high molecular accumulation in lipid droplets and the high brightness,and the spatiotemporal resolution is greatly improved.More importantly,we found that BODIPY 493 also has a certain buffering capacity,which enables BODIPY 493 to be used for super-resolution imaging of lipid droplet dynamics.This work reminds researchers to coordinate the buffering capacity and brightness of fluorogenic probes.
基金The work has been supported by the National Key R&D Program of China(2018YFA0507700 to C.Tang,Z.Liu,Z.Gong and Q.Zhao2017YFA0505400 to X.Dong+1 种基金2016YFA0501200 to C.Tang,Z.Gong and X.Dong)by the National Natural Science Foundation of China(91753132 and 31770799 to C.Tang).
文摘Dear Editor,Multisite phosphorylation is observed in many signaling proteins,which confers the proteins new functions.A multisite phosphorylated protein can exhibit switch-like response to cellular stimuli,with the often-clustered phosphorylation sites either unphosphorylated or fully phosphorylated by the same kinase(Kapuy et al..2009).Multisite phosphorylation has also been reported to promote the folding of an intrinsically disordered protein,and consequently modulate the binding affinity to other proteins(Bah et al.,2015).Here we show that multisite phosphorylation makes a protein a better pH sensor,promptly switching between alternative conformational states in response to pH change under physiological conditions.
基金supported by supported by the National Key R&D Program of China(2021YFC2103500)DICP innovation grant(DICP I202111)from Dalian Institute of Chemical Physics,CAS.
文摘The methylotrophic yeast Pichia pastoris(also known as Komagataella phaffii)is widely used as a yeast cell factory for producing heterologous proteins.Recently,it has gained attention for its potential in producing chemicals from inexpensive feedstocks,which requires efficient genetic engineering platforms.This review provides an overview of the current advances in developing genetic tools for metabolic engineering of P.pastoris.The topics cover promoters,terminators,plasmids,genome integration sites,and genetic editing systems,with a special focus on the development of CRISPR/Cas systems and their comparison to other genome editing tools.Additionally,this review highlights the prospects of multiplex genome integration,fine-tuning gene expression,and single-base editing systems.Overall,the aim of this review is to provide valuable insights into current genetic engineering and discuss potential directions for future efforts in developing efficient genetic tools in P.pastoris.
基金supported by the National Key Research and Development Program of China (2017YFA0505003,2016YFA0501401)the National Natural Science Foundation of China (21375126, 21405154)
文摘The complications of hemodialysis accompanied the hemodialysis and threaten the patients’life.Besides the loss of nutrient substance,such as amino acid and vitamin,we found new clues that the adsorbed proteins on common-used polysulfone-based dialysis membrane might be the reason according to the qualitative proteomic study by ionic liquid assisted sample preparation method.Our results indicated that the adsorbed proteins on the membrane were related with complement activation,blood coagulation,and leukocyte-related biological process.The quantitative proteome further demonstrated some significant changes of signal proteins in the post-dialysis plasma after the hemodialysis,such as beta-2-microglobulin and platelet factor-4,which would further verify these new clues.
基金National Natural Science Foundation of China,Grant/Award Numbers:22078314,21878286,21908216Dalian Institute of Chemical Physics,Grant/Award Numbers:DICPI202142,DICPI201938,DICPZZBS201805+1 种基金Advanced Manufacturing and Engineering Program,Grant/Award Number:A2083c0051Ministry of Education,Singapore,Grant/Award Number:MOE-MOET2EP10120-0007。
文摘The combination of super-resolution microscopy and synthetic fluorescence probes has emerged as a universal tool to monitor dynamic biological events at the nanometer scale.However,the limited site-specificity and fluorogenicity of synthetic fluorescent probes make it still difficult to realize long-term super-resolution imaging.Herein,we introduce a dynamic aggregation mediated SNAP-tag fluorogenic probe,BGAN-Aze,which can specifically bind to various SNAP-tag fusion proteins with 41-fold fluorescence enhancement.The equilibrium between the non-fluorescent aggregate/dimer(A–D)and the fluorescent monomer(M)of BGAN-Aze acts as an effective method to reduce the fluorescence background and endow BGAN-Aze with the capability of conducting washing-free super-resolution imaging of various intracellular and extracellular proteins.Using this probe,we monitored multiple dynamic biological events,such as MMC,mitophagy,the fusion of nucleolus,and the growth and contact of filopodia.We expect that BGAN-Aze will become a widely used SNAP-tag for super-resolution imaging of dynamic biological events and the A-D-M equilibrium can be a general strategy for designing fluorogenic probes.
基金supported by the National Key Research and Development Program of China(2020YFE0202200,2017YFA0505003,and 2018YFC0910202)the National Natural Science Foundation of China(21974136,21725506,and 21775149)+1 种基金Talent Innovation Support Program of Dalian(2019CT07)Innovation Program of Science and Research from Dalian Institute of Chemical Physics,Chinese Academy of Sciences(DICP I202143)。
文摘Deep proteome profiling from trace biological samples are needed for important biomedical applications[1],but the sample losses from traditional sample preparation procedures are a major limitation[2].Therefore,considerable efforts have been made to improve it[3,4].Filter-aided sample preparation(FASP)developed by Mann’s group[5]is recognized one of the most popular methods,by which protein extraction,reduction,alkylation,and digestion are performed on a commercial spin filter.
基金supported by the National Natural Science Foundation of China(21175134,21375125)the Creative Research Group Project of National Natural Science Foundation of China(21321064)
文摘The formation of protein coronas on nanomaterial will significantly alter the surface properties of nanomaterial in biological systems and subsequently impact biological responses including signaling, cellular uptake, transport, and toxicity etc. It is of critical importance to understand the formation of protein coronas on the surface of nanomaterial. Analytical techniques, especially mass spectrometry-based proteomics methods, are playing a key role for the qualitative and quantitative analyses of protein coronas on nanomaterial. In this review, the proteomic approaches developed for the characterization of protein coronas on various nanomaterials are introduced with the emphasis on the mass spectrometry-based proteomic strategies.
基金supported by the National Natural Science Foundation of China(Grant No.91643104)for the financial support。
文摘Water-insoluble organic compounds(WIOCs)are an important fraction of atmospheric fine particulate matters(PM_(2.5)),which could affect the climate system and threaten human health potentially.In this study,molecular characterization of WIOCs in PM_(2.5) were investigated by 15 T Fourier transform ion cyclotron resonance mass spectrometry(FT-ICR MS)with atmospheric pressure photoionization(APPI)source in positive ion mode.A total of 2573 and1875 molecular formulas were identified in WIOCs extracted by dichloromethane,which were collected in hazy and normal days,respectively.The identified molecular formulas were further classified into four major subgroups,including CH,CHN,CHO and CHNO compounds.CHO compounds predominated in WIOCs,accounting for more than 60%in both samples.CHNO compounds(26.6%)and CH compounds(16.1%)were the second highest subgroups in WIOCs from the hazy days and normal days,respectively.The relative abundance and number of nitro-substituted aromatic compounds were significantly higher in hazy days than in normal days.The molecular composition of WIOCs was more complex in hazy days while more aromatic compounds were identified in normal days.
基金the Natural Science Foundation of Shandong Province(No.ZR2017LB028)the Key Research and Development Program of Shandong Province(Nos.2018GSF118032 and 2022CXGC020415)the Fundamental Research Funds for the Central Universities in China(No.18CX02125A).Y.X.L.is grateful for the Research Subsidy Funds of Marine Science Research Institute of Shandong Province.X.W.C.is grateful for Ministry of Science,Innovation and Universities of Spain with project reference number of PID2020-113809RBC33 and by Junta de Andalucía(Spain)with reference number of PY18-2727.
文摘Trimethylphenol is an organic toxic byproduct of industrial process,which is difficult to be eliminated through conventional degradation without harsh conditions.In this work,a sulfite-based oxidation process activated by ZnO-embedded hydrogel was studied for the degradation of 2,4,6-trimethylphenols in the ambient conditions.The ZnO/Na_(2)SO_(3)oxidative system can effectively degrade trimethylphenol via the generation of radicals such as SO_(4)^(-)·,OH·,and SO_(3)^(−)·.The presence of hydrogel matrix facilitates the distribution and recyclability of ZnO catalysts while maintaining high degradation kinetics and little leaching of metal ions.Results suggest the promising potential of ZnO-hydrogel in wastewater treatment with good performance in terms of pH sensitivity,anion interference,recyclability,etc.The combination of ZnO catalysts,hydrogel,and sulfite-based advanced oxidation process may provide essential support for the current treatment of alkylated phenols with strong potential in the commercial scale-ups.
基金National Key R&D Program of China(No.2019YFE0119300)National Natural Science Foundation of China(No.32088101)+1 种基金Original Innovation Project of CAS(No.ZDBS-LY-SLH032)Project of Dalian Institute of Chemical Physics,CAS,China(No.DICPI202007).
文摘High-resolution liquid chromatography separation is essential to in-depth proteomic profiling of complex biological samples.Herein,we established an ion-pair reversed-phase×reversed-phase two-dimensional liquid chromatography(IPRP×RP 2DLC)strategy for comprehensive proteomic analysis.Both RPLC separation dimensions were performed at low pH,with trifluoroacetic acid(TFA)and formic acid(FA)as mobile phase addictive,respectively.As the good separation resolution offered by ion-pairing effect of TFA,the fractionation efficiency was greatly improved with 74.0%peptides identified in just one fraction.Comparing with conventional high pH RP fractionation,the overall separation rate of IPRP was about 1.6 times that of high-pH RP,which increased the number of identified peptides by 21%.Further,2169 proteins and 8540 peptides were confidently identified from crude serum sample by our IPRP×RP 2DLC strategy,exhibiting great potential in clinical proteomics in the future.
