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Establishing Modular Cell-Free Expression System for the Biosynthesis of Bicyclomycin from a Chemically Synthesized Cyclodipeptide

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Chinese Journal of Chemistry 2024年第4期42卷 384-390页

作者： Yi-Pei Liu yu-heng zhao Wen-Qi Zhang Lian Wu Linjuan Huang Gong-Li Tang Jun-Bin He Shaanxi Natural Carbohydrate Resource Engineering Research Center College of Food Science and TechnologyNorthwest UniversityXi'anShaanxi710069 China State Key Laboratory of Chemical Biology Shanghai Institute of Organic ChemistryUniversity of Chinese Academy of Sciences(CAS)CASShanghai200032 China School of Chemistry and Materials Science Hangzhou Institute for Advanced StudyUniversity of CAS1 Sub-lane XiangshanHangzhouZhejiang310024 China

Cell-free expression systems have emerged as a versatile and powerful platform for metabolic engineering,biosynthesis and synthetic biology studies.Nevertheless,successful examples of the synthesis of complex natural products using this system are still limited.Bicyclomycin,a structurally unique and complex diketopiperazine alkaloid,is a clinically promising antibiotic that selectively inhibits the transcription termination factor Rho.Here,we established a modular cell-free expression system with cascade catalysis for the biosynthesis of bicyclomycin from a chemically synthesized cyclodipeptide.The six cell-free expressed biosynthetic enzymes,including five iron-andα-ketoglutarate-dependent dioxygenases and one cytochrome P450 monooxygenase,were active in converting their substrates to the corresponding products.The co-expressed enzymes in the cell-free module were able to complete the related partial pathway.In vitro biosynthesis of bicyclomycin was also achieved by reconstituting the entire biosynthetic pathways(i.e.,six enzymes)using the modular cell-free expression system.This study demonstrates that the modular cell-free expression system can be used as a robust and promising platformforthe biosynthesis of complex antibiotics.

关键词： Natural products Bicyclomycin Biosynthesis Iron-andα-ketoglutarate-dependent dioxygenases Cytochrome P450 monooxygenase Cell-freeprotein synthesis Enzyme catalysis

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Identification and validation of novel prognostic fatty acid metabolic gene signatures in colon adenocarcinoma through systematic approaches

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Oncology Research 2024年第2期32卷 297-308页

作者： heng ZHANG WENJING Cheng HAIBO zhao WEIDONG CHEN QIUJIE ZHANG QING-QING yu Department of Laboratory Shandong Daizhuang HospitalJining272051China Jining No.1 People’s Hospital Shandong First Medical UniversityJining272000China

Colorectal cancer(CRC)belongs to the class of significantly malignant tumors found in humans.Recently,dysregulated fatty acid metabolism(FAM)has been a topic of attention due to its modulation in cancer,specifically CRC.However,the regulatory FAM pathways in CRC require comprehensive elucidation.Methods:The clinical and gene expression data of 175 fatty acid metabolic genes(FAMGs)linked with colon adenocarcinoma(COAD)and normal cornerstone genes were gathered through The Cancer Genome Atlas(TCGA)-COAD corroborating with the Molecular Signature Database v7.2(MSigDB).Initially,crucial prognostic genes were selected by uni-and multi-variate Cox proportional regression analyses;then,depending upon these identified signature genes and clinical variables,a nomogram was generated.Lastly,to assess tumor immune characteristics,concomitant evaluation of tumor immune evasion/risk scoring were elucidated.Results:A 8-gene signature,including ACBD4,ACOX1,CD36,CPT2,ELOVL3,ELOVL6,ENO3,and SUCLG2,was generated,and depending upon this,CRC patients were categorized within high-risk(H-R)and low-risk(L-R)cohorts.Furthermore,risk and age-based nomograms indicated moderate discrimination and good calibration.The data confirmed that the 8-gene model efficiently predicted CRC patients’prognosis.Moreover,according to the conjoint analysis of tumor immune evasion and the risk scorings,the H-R cohort had an immunosuppressive tumor microenvironment,which caused a substandard prognosis.Conclusion:This investigation established a FAMGs-based prognostic model with substantially high predictive value,providing the possibility for improved individualized treatment for CRC individuals.

关键词： Fatty acid metabolism Colorectal cancer Gene signatures Machine learning

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Study on Catalytic Behavior of Iron-based Catalyst with IITP as Electron Donor in the Polymerization of Butadiene

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Chinese Journal of Polymer Science 2024年第5期42卷 612-619,I0007页

作者： Shi-Liang Xu Ying-Nan zhao Yao yu Qi Yang Li-Hua Na heng Liu Chun-yu Zhang Xue-Quan Zhang Key Laboratory of Advanced Rubber Material Ministry of EducationSchool of Polymer Science and EngineeringQingdao University of Science&TechnologyQingdao266042China Shandong Provincial College Laboratory of Rubber Material and Engineering School of Polymer Science and EngineeringQingdao University of Science&TechnologyQingdao266042China Key Lab of Rubber-Plastics Ministry of Education/Shandong Provincial Key Lab of Rubber-plasticsSchool of Polymer Science and EngineeringQingdao University of Science&TechnologyQingdao266042China

In this study,a novel iron-based catalyst system,Fe(acac)3/(isocyanoimino)triptenylphosphorane(IITP)/AlR3,was employed for the synthesis of syndiotactic 1,2-polybutadiene in hexane.This catalyst system exhibits remarkably high catalytic activity,achieving a polymerization activity of 762 kgpolymer·molcatalyst^(-1)·h^(-1)at 50℃with a[BD]/[Fe]molar ratio of 20000.Furthermore,living polymerization characteristic were observed during the investigation of the polymerization kinetics of 1,3-butadiene polymerization.These characteristics were well demonstrated by a narrow molecular weight distribution(PDI≈2.0)of the resulting polybutadiene and a linear relationship between-ln(1-c)and polymerization time as well as number average molecular weight and polymer yield.The resultant polymer showed a 1,2-selectivity of approximately 76%and stereoregularity ranging from 62%to 73%(rrrr).Additionally,through kinetic studies on polymerization reaction,an apparent activation energy Ea value of this catalytic system was calculated to be 84.98 kJ·mol^(-1),which suggests that high polymerization temperature favors efficient polymerization.

关键词： Iron catalyst Syndiotactic 1,2-polybutadiene Elastomers Donor Selectivity

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Strategies for improving extraction capacity through preorganization structure:A novel 5,6-bicyclicmalonamide extractant(THPPD)

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Journal of Rare Earths 2024年第4期42卷 768-774页

作者： Miaomiao Zhang Zhen Yang yuhua Cui Jianhui Su heng zhao Chengjin Xu Xiaolei Liu Guoxin Sun Xiujing Peng yu Cui School of Chemistry and Chemical Engineering University of JinanJinan250022China Institute for Smart Materials&Engineering University of JinanJinan250022China Shandong Institute for Food and Drug Control Jinan250101China

Rational design of extractant structure to improve the extraction and separation capacity of rare earth elements(REEs)is a long-standing challenge.Herein,a new strategy was proposed to improve the stability of the chelating structure formed by malonamide and REEs.The stability of the chelating structure is greatly improved by using a double-ring framework structure which makes the two carbonyl groups of malonamide unable to rotate freely and both of them point to the metal ion position.Three benzyl groups were used to construct the hydrophobicity of the extractant and the organic shell of the extracted species.Tribenzylhexahydro-pyrrolo-pyridine-dione(THPPD)was designed and synthesized.The structure reduces the energy consumed by rotating carbonyl group in the coordination with metal ions and then improves the extraction ability of extractant.The crystal structure was preorganized as expected,with the two carbonyls pointing in a favorable coordination direction to the structural complement of the metal ion.The extraction behaviors of REEs with THPPD in a nitric acid medium were studied.Compared with N,N’-dibenzyl-N,N’-dimethylmalonamide(DBDM-MA)with a chain structure,the extraction capacity of THPPD is 360 times higher than that of DBDM-MA at 5.0 mol/L sodium nitrate.Furthermore,the binding energy and Gibbs free energy were investigated by density functional theory(DFT)in conjunction with the B3LYP.The theoretical results show that THPPD has more effective interaction with Pr(NO_(3))3 than DBDM-MA.The construction of chelating groups conformation is a worthy direction to improve the coordination ability and even selectivity of extractant.

关键词： Rare earth elements Extraction separation 5,6-bicyclicdiamide extractant

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One-step hydrothermal synthesis of Cit-NaYbF_(4):Er^(3+)nanocrystals with enhanced red upconversion emission for in vivo fluorescence molecular tomography

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Journal of Rare Earths 2024年第1期42卷 36-45,I0002页

作者： Xiaoli Luo Qichen Chen Hongbo Guo heng Zhang Xiaowei He Wu zhao School of Mathematics and Computer Science Ningxia Normal UniversityGuyuan756099China School of Information Science and Technology Northwest UniversityXi'an710127China

Fluorescence imaging techniques represent essential tools in in vitro,preclinical,and clinical studies.In this study,an improved one-step hydrothermal method to synthesize citric acid(CA)modifiedα-NaYbF_(4):2%Er^(3+)nanocrystals was proposed.The introduction of various doping ions into NaYbF_(4):2%Er^(3+)and the different valence states of the same ions affect both the crystal size and upconversion luminesce nce.There fore,we investigated the upconversion luminesce nce enha ncement of NaYbF_(4):2%Er^(3+)by ion doping and find that the upconversion luminescence intensity of the upconversion nanoparticles(UCNPs)co-doped with 5 mol%Fe^(2+)ions shows the greatest enhancement,especially for red emission at654 nm.Furthermore,HeLa cells incubated with UCNPs allow for imaging with strong red upconversion emission detectio n.Confocal laser scanning microscope(CLSM)fluorescent images of HeLa cells indicate that NaYbF_(4):2%Er/5%Fe^(2+)leads to a clear outline and improves visualization of the cell morphology.In addition,the CA coated NaYbF_(4):2%Er^(3+)/5%Fe^(2+)nanoparticles and NaYbF_(4):2%Er^(3+)/5%Fe^(2+)show low cytotoxicity in HeLa cells.Organ imaging reveals the efficiency of these UCNPs to analyze the lungs,liver,and spleen.Together,these results indicate that the Cit-NaYbF_(4):2%Er^(3+)/5%Fe^(2+)UCNPs are efficient nanoprobes for fluorescence molecular to mography.

关键词： Hydrothermal method Fe^(2+)ion doping Tuning size Nanoprobes Fluorescence imaging Rare earths

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CFD simulation of pumping ventilation in a three-story isolated building with internal partitioning:Effects of partition widths,heights and locations

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Building Simulation 2024年第2期17卷 267-284页

作者： Huai-yu Zhong Jie Sun Chao Lin Song-heng Wu Jin Shang Hideki Kikumoto Fu-Ping Qian Carlos Jimenez-Bescos Fu-yun zhao School of Energy and Environment Anhui University of TechnologyMa-An-ShanAnhui Province243002China State Key Laboratory of Green Building in Western China Xi’an University of Architecture&TechnologyXi’anShaanxi ProvinceChina School of Power and Mechanical Engineering Wuhan UniversityWuhanHubei Province430072China Institute of Industrial Science The University of Tokyo4-6-1 KomabaMeguro-kuTokyo153-8505Japan School of Built and Natural Environment University of DerbyDerbyUK

Pumping ventilation(PV),a special single-sided ventilation(SSV),has been certified as an effective strategy to improve the air exchange rate of SSV.However,most studies targeted on the single space,and few studies have been focused on the effect of internal partitioning on PV.This paper aims to evaluate the ventilation performance of PV influenced by different configurations of internal partitioning.Computational fluid dynamics(CFD)simulation was used to predict the flow fields and ventilation rates.The width(w/H),height(h/H)and location(d/H)are the three main internal partition parameters considered in this study.The simulation results showed that the total,mean and fluctuating ventilation rates all decrease with wider internal partitions.The normalized total ventilation rate decreases by 7.6%when w/H is increased from 50%to 75%.However,the reduction rate is only 0.23%between w/H=0 and 25%,and only 0.61%between w/H=25%and 50%.The ventilation rate is hardly reduced by increasing the partition width when w/H50%.Increasing the partition height will reduce the mean ventilation rate but promote the fluctuating and total ventilation rate in some cases.An increase of total ventilation rate by 1.4%is observed from h/H=50%to 75%.The ventilation rate is larger when the internal partition is attached to the leeward or windward wall.The total,mean and fluctuating ventilation rates for d/H=50%are relatively higher than d/H=0 by 1.5%,3.1%and 0.8%,respectively.Hence the internal partition should be mounted attached to the windward wall so as to obtain the greatest pumping ventilation rate.The periodicity of pumping flow oscillation and pumping frequency are independent of the partition configurations.The peak power of pumping flow is the lowest for the widest internal partition and is negatively affected by the partition height,but it generally has a positive correlation with the distance between the partition and leeward wall.Present research will help to understand pump

关键词： pumping ventilation single-sided ventilation internal partitioning periodic oscillation ventilation rate

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Visible Light-Induced[3+2]Annulation Reaction of Alkenes with Vinyl Azides:Direct Synthesis of Functionalized Pyrroles

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Chinese Journal of Chemistry 2024年第2期42卷 151-156页

作者： Ming Yang Xin-yu Wang Jie Wang yu-Long zhao Jilin Province Key Laboratory of Organic Functional Molecular Design&Synthesis Faculty of ChemistryNortheast Normal UniversityChangchunJilin 130024China

A photocatalytic[3+2]annulation of alkenes with vinyl azides was developed under irradiation by visible light in the presence of organic dye photocatalysts.Broad substrate scope and high functional group tolerance were demonstrated by more than 50 examples.The reaction provides a novel and efficient method for the synthesis of polyfunctionalized pyrroles under very mild metal-free conditions without other additives.

关键词： Photocatalysis Vinyl azides Alkenes Pyrroles Annulation Radical reactions

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How plants sense and respond to osmotic stress

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Journal of Integrative Plant Biology 2024年第3期66卷 394-423页

作者： Bo yu Dai-Yin Chao Yang zhao Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesThe Chinese Academy of SciencesShanghai 200032China Key Laboratory of Plant Carbon Capture The Chinese Academy of SciencesShanghai 200032China National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyThe Chinese Academy of SciencesShanghai 200032China University of Chinese Academy of Sciences Beijing 100049China

Drought is one of the most serious abiotic stresses to land plants.Plants sense and respond to drought stress to survive under water deficiency.Scientists have studied how plants sense drought stress,or osmotic stress caused by drought,ever since Charles Darwin,and gradually obtained clues about osmotic stress sensing and signaling in plants.Osmotic stress is a physical stimulus that triggers many physiological changes at the cellular level,including changes in turgor,cell wall stiffness and integrity,membrane tension,and cell fluid volume,and plants may sense some of these stimuli and trigger downstream responses.In this review,we emphasized water potential and movements in organisms,compared putative signal inputs in cell wall-containing and cell wall-free organisms,prospected how plants sense changes in turgor,membrane tension,and cell fluid volume under osmotic stress according to advances in plants,animals,yeasts,and bacteria,summarized multilevel biochemical and physiological signal outputs,such as plasma membrane nanodomain formation,membrane water permeability,root hydrotropism,root halotropism,Casparian strip and suberin lamellae,and finally proposed a hypothesis that osmotic stress responses are likely to be a cocktail of signaling mediated by multiple osmosensors.We also discussed the core scientific questions,provided perspective about the future directions in this field,and highlighted the importance of robust and smart root systems and efficient source-sink allocations for generating future high-yield stress-resistant crops and plants.

关键词： cell volume drought membrane tension osmotic stress turgor

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Unbalanced private set intersection with linear communication complexity

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Science China(Information Sciences) 2024年第3期67卷 79-93页

作者： Quanyu zhao Bingbing JIANG yuan ZHANG heng WANG yunlong MAO Sheng ZHONG Department of Computer Science and Technology Nanjing University Purple Mountain Lab

The private set intersection(PSI) protocol allows two parties holding a set of integers to compute the intersection of their sets without revealing any additional information to each other. The unbalanced PSI schemes consider a specific setting where a client holds a small set of the size n and a server holds a much larger set of the size m(n ■ m). The communication overhead of state-of-the-art balanced PSI schemes is O(m + n) and the unbalanced PSI schemes are O(nlogm). In this paper, we propose a novel secure unbalanced PSI protocol based on a hash proof system. The communication complexity of our protocol grows only linearly with the size of the small set. In other words, our protocol achieves communication overhead of O(n). We test the performance on a personal computer(PC) machine with a local area network(LAN)setting for the network. The experimental results demonstrate that the client only takes 2.01 s of online computation, 4.27 MB of round trip communication to intersect 1600 pieces of 32-bit integers with 220pieces of 32-bit integers with the security parameter λ = 512. Our protocol is efficient and can be applied to resource-constrained devices, such as cell phones.

关键词： unbalanced private set intersection Hash proof system linear communication complexity small set resource-constrained devices

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Efficient degradation of aqueous dichloromethane by an enhanced microbial electrolysis cell:Degradation kinetics,microbial community and metabolic mechanisms

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Journal of Environmental Sciences 2024年第5期139卷 150-159页

作者： Meng Wu Di zhao Bing Gu ZiruWang Jun Hu Zhiliang yu Jianming yu College of Environment College of Biotechnology and BioengineeringCollaborative Innovation Center of Yangtze River Delta Region Green PharmaceuticalsZhejiang University of TechnologyHangzhou 310014China Shentuo Environment(Hangzhou)Co.Ltd. Hangzhou 311121China Zhejiang Tianyi Environmental Co.Ltd. Hangzhou 310000China

Dichloromethane(DCM)has been listed as a toxic and harmful water pollutant,and its re moval needs attention.Microbial electrolysis cells(MECs)are viewed as a promising alterna tive for pollutant removal,which can be strengthened from two aspects:microbial inocula tion and acclimation.In this study,the MEC for DCM degradation was inoculated with the ac tive sludge enhanced by Methylobacterium rhodesianum H13(strain H13)and then acclimated in the form of a microbial fuel cell(MFC).Both the introduction of strain H13 and the initi ation in MFC form significantly promoted DCM degradation.The degradation kinetics were fitted by the Haldane model,with V_(max),K_(h),K_(i)and v_(max)values of 103.2 mg/L/hr,97.8 mg/L268.3 mg/L and 44.7 mg/L/hr/cm^(2),respectively.The cyclic voltammogram implies that DCM redox reactions became easier with the setup of MEC,and the electrochemical impedance spectrogram shows that the acclimated and enriched microbes reduced the charge transfe resistance from the electrode to the electrolyte.In the biofilm,the dominant genera shifted from Geobacter to Hyphomicrobium in acclimation stages.Moreover,Methylobacterium played an increasingly important role.DCM metabolism mainly occurred through the hydrolytic glutathione S-transferase pathway,given that the gene dcmA was identified rather than the dhlA and P450/MO.The exogenous electrons facilitated the reduction of GSSG,directly o indirectly accelerating the GSH-catalyzed dehalogenation.This study provides support fo the construction of an efficient and stable MEC for DCM removal in water environment.

关键词： Dichloromethane Microbial electrolysis cells Metabolic pathways Electron transfer Degradation kinetics

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