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Association analysis of an anti-obesity mechanism and key ripened Pu-erh tea bioactive components by mimicking human general tea drinking

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Food Science and Human Wellness 2024年

作者： Junyu Liu Zhengyang Song Haihong Chen Wen Zeng Guirong Han Wei Li Bing Xu Yuan Lu Canyang Zhang Zhenglian Xue Bin Lü Chong Zhang Song Yang Yi Wang Xinhui Xing MOE Key laboratory for Industrial biocatalysis， Centre for Synthetic and Systems Biology， Department of Chemical Engineering， Tsinghua University Shenzhen International Graduate School， Tsinghua University Institute of Biomedical Health Technology and Engineering Shenzhen Bay Laboratory Anhui University of Technology Yunnan Shujian Tea Co.， Ltd. Shandong Province Key laboratory of applied Mycology， Qingdao International Center on Microbes Utilizing Biogas， School of Life Sciences， Qingdao Agricultural University

Pu-erh tea， a traditional Chinese beverage， performs an anti-obesity function， but the correlation between its components and efficacy remains unknown. Here， we screened two Pu-erh teas with significant anti-obesity efficacies from 11 teas. In vitro experiments revealed that lipid accumulation in L02 cells and lipid synthesis in 3T3-L1 cells were significantly better inhibited by Tea-B than Tea-A. Further in vivo experiments using model mice revealed that the differences in chemical components generated two pathways in the anti-obesity efficacy and mechanism of Pu-erh teas. Tea-A changes the histomorphology of brown adipose tissue (BAT) and increases the abundance of Coriobacteriaceae＿UCG＿002 and cyclic AMP in guts through high chemical contents of cyclopentasiloxane， decamethyl， tridecane and 1，2，3-trimethoxybenzene， eventually increasing BAT activation and fat browning gene expression; the high content of hexadecane and 1，2-dimethoxy-benzene in Tea-B reduces white adipose tissue (WAT) accumulation and the process of fatty liver， increases the abundance of Odoribacter and sphinganine 1-phosphate， inhibits the expression of lipid synthesis and transport genes. These mechanistic findings on the association of the representative bioactive components in Pu-erh teas with the anti-obesity phenotypes， gut microbes， gut metabolite structure and anti-obesity pathways， which were obtained for the first time， provide foundations for developing functional Pu-erh tea.

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Quantitative evaluation of DNA damage caused by atmospheric and room-temperature plasma (ARTP) and other mutagenesis methods using a rapid umu-microplate test protocol for microbial mutation breeding

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Chinese Journal of Chemical Engineering 2021年第11期34卷 205-210页

作者： Yuting Huang Liyang Wang Xue Zhang Nan Su Heping Li Yoshimitsu Oda Xinhui Xing Key laboratory for Industrial biocatalysis Ministry of Education of ChinaDepartment of Chemical EngineeringTsinghua UniversityBeijing 100084China Biobreeding Research Center Wuxi Research Institute of Applied TechnologiesTsinghua UniversityWuxi 214072China Department of Entomology College of Plant ProtectionChina Agricultural UniversityBeijing 100193China Department of Engineering Physics Tsinghua UniversityBeijing 100084China Institute of Life and Environmental Sciences Osaka Shin-Ai CollegeTsurumiTsurumi-kuOsaka 5380052Japan Centre for Synthetic and Systems Biology Tsinghua UniversityBeijing 100084China Institute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate SchoolShenzhen 518055China Institute of Biomedical Health Technology and Engineering Shenzhen Bay LaboratoryShenzhen 518055China

Mutagenesis is an important technique for microbial mutation *** the source of mutations,DNA damage extent is a key indicator for the effectiveness of ***,a rapid and easy DNA damage quantification method is required for the comparison of mutagenesis effects and development of mutagenesis ***,we used the umu-microplate test system to quantitatively compare the DNA damage strength caused by atmospheric and room-temperature plasma(ARTP)and other traditional mutagenesis methods including:ultraviolet radiation(UV),diethyl sulfate(DES)and 4-nitroquinoline-1-oxide(4-NQO).The test strain of Salmonella typhimurium TA1535/pSK1002 was used to monitor the time-course profile of b-galactosidase activity induced by DNA damage caused by different mutagenesis methods using a microplate *** umu-microplate test results showed that ARTP caused higher extent of DNA damage than UV and chemical mutagens,which agrees well with the result obtained by SOS-FACS-based quantification method as reported *** umu-microplate test is accessible for broad researchers who are lack of the expensive FACS instruments and allows the quick quantitative evaluation of DNA damage among living cells for different mutagenesis methods in the study of the microbial mutation breeding.

关键词： ARTP mutagenesis umu-Microplate test Biological engineering Cell engineering Biotechnology

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A Chromosome-level Genome Assembly of Wild Castor Provides New Insights into Its Adaptive Evolution in Tropical Desert

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Genomics, Proteomics & Bioinformatics 2022年第1期20卷 42-59页

作者： Jianjun Lu Cheng Pan Wei Fan Wanfei Liu Huayan Zhao Donghai Li Sen Wang Lianlian Hu Bing He Kun Qian Rui Qin Jue Ruan Qiang Lin Shiyou Lü Peng Cui CAS Key laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical GardenChinese Academy of SciencesWuhan 430074China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China University of Chinese Academy of Sciences Beijing 100049China Sino-Africa Joint Research Center Chinese Academy of SciencesWuhan 430074China State Key laboratory of biocatalysis and Enzyme Engineering School of Life SciencesHubei UniversityWuhan 434200China

Wild castor grows in the high-altitude tropical desert of the African Plateau,a region known for high ultraviolet radiation,strong light,and extremely dry *** investigate the potential genetic basis of adaptation to both highland and tropical deserts,we generated a chromosome-level genome sequence assembly of the wild castor accession WT05,with a genome size of 316 Mb,a scaffold N50 of 31.93 Mb,and a contig N50 of 8.96 Mb,*** with cultivated castor and other Euphorbiaceae species,the wild castor exhibits positive selection and gene family expansion for genes involved in DNA repair,photosynthesis,and abiotic stress *** variations associated with positive selection were identified in several key genes,such as LIG1,DDB2,and RECG1,involved in nucleotide excision ***,a study of genomic diversity among wild and cultivated accessions revealed genomic regions containing selection signatures associated with the adaptation to extreme *** identification of the genes and alleles with selection signatures provides insights into the genetic mechanisms underlying the adaptation of wild castor to the high-altitude tropical desert and would facilitate direct improvement of modern castor varieties.

关键词： Ricinus communis L. Adaptive evolution Selection signature Genetic variation Genome assembly

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Enhanced production of poly-γ-glutamic acid via optimizing the expression cassette of Vitreoscilla hemoglobin in Bacillus licheniformis

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Synthetic and Systems Biotechnology 2022年第1期7卷 567-573页

作者： Qing Zhang Yaozhong Chen Lin Gao Jian’gang Chen Xin Ma Dongbo Cai Dong Wang Shouwen Chen State Key laboratory of biocatalysis and Enzyme Engineering Environmental Microbial Technology Center of Hubei ProvinceCollege of Life SciencesHubei UniversityWuhan430062PR China Wuhan Junan Biotechnology Co.Ltd. WuhanChina Tobacco Research Institute Chinese Academy of Agricultural SciencesQingdaoChina

Poly-γ-glutamic acid(γ-PGA)is a natural polymer with various applications,and its high-viscosity hinders ox-ygen transmission and improvement of synthesis *** hemoglobin(VHB)has been introduced into various hosts as oxygen carrier,however,its expression strength and contact efficiency with oxygen hindered efficient oxygen transfer and metabolite ***,we want to optimize the expression cassette of VHB for γ-PGA ***,our results implied that γ-PGA yields were enhanced when introducing twin-arginine translocation(Tat)signal peptides(SP_(YwbN),SP_(PhoD) and SP_(TorA))into VHB expression cassette,and the best per-formance was attained by SP YwbN from Bacillus subtilis,theγ-PGA yield of which was 18.53% higher than that of control strain,and intracellular ATP content and oxygen transfer coefficient(K_(L)a)were increased by 29.71% and 73.12%,respectively,indicating that VHB mediated by SP YwbN benefited oxygen transfer and ATP generation forγ-PGA ***,four promoters were screened,and P vgb was proven as the more suitable promoter for VHB expression andγ-PGA synthesis,andγ-PGA yield of attaining strain WX/pPvgb-YwbN-Vgb was further increased to 40.59 g/L by 10.18%.Finally,WX/pPvgb-YwbN-Vgb was cultivated in 3 L fermentor for fed-batch fermentation,and 46.39 g/Lγ-PGA was attained by glucose feeding,increased by 49.26%compared with the initial yield(31.01 g/L).Taken together,this study has attained an efficient VHB expression cassette for oxygen transfer andγ-PGA synthesis,which could also be applied in the production of other metabolites.

关键词： Vitreoscilla hemoglobin Expression element Twin-arginine translocation Poly-γ-glutamic acid Bacillus licheniformis

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The Triple Combination of Meropenem,Avibactam,and a Metallo-β-Lactamase Inhibitor Optimizes Antibacterial Coverage Against Different β-Lactamase Producers

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Engineering 2024年第7期38卷 124-132页

作者： Zhuoren Ling Alistair James Macdonald Farley Aditya Lankapalli Yanfang Zhang Shonnette Premchand-Branker Kate Cook Andrei Baran Charlotte Gray-Hammerton Claudia Orbegozo Rubio Edgars Suna Jordan Mathias Jürgen Brem Kirsty Sands Maria Nieto-Rosado Maria Mykolaivna Trush Nadira Naznin Rakhi Willames Martins Yuqing Zhou Christopher Joseph Schofield Timothy Walsh Department of Biology&Ineos Oxford Institute for Antimicrobial Research University of OxfordOxford OX13REUK Chemistry Research laboratory Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordOxford OX13TAUK Latvian Institute of Organic Synthesis Riga LV-1006Latvia Department of Medical Microbiology Division of Infection and ImmunitySchool of MedicineCardiff UniversityCardiff CF144XNUK Enzymology and applied biocatalysis Research Center Faculty of Chemistry and Chemical EngineeringBabes-Bolyai UniversityCluj-Napoca 400028Romania

This work explores the potential of a triple combination of meropenem(MEM),a novel metallo-blactamase(MBL)inhibitor(indole-2-carboxylate 58(InC58)),and a serine-b-lactamase(SBL)inhibitor(avibactam(AVI))for broad-spectrum activity against carbapenemase-producing bacteria.A diverse panel comprising MBL-and SBL-producing strains was used for susceptibility testing of the triple combination using the agar dilution *** frequency of resistance(FoR)to MEM combined with InC58 was *** were sequenced and tested for cross resistance,fitness,and the stability of the resistance *** with the double combinations of MEM plus an SBL or MBL inhibitor,the triple combination extended the spectrum of activity to most of the isolates bearing SBLs(oxacillinase-48(OXA-48)and Klebsiella pneumoniae carbapenemase-2(KPC-2))and MBLs(New Delhi metallo-blactamases(NDMs)),although it was not effective against Verona integron-encoded metallo-blactamase(VIM)-carrying Pseudomonas aeruginosa(***)and OXA-23-carrying Acinetobacter baumannii(***).The FoR to MEM plus InC58 ranged from 2.22×10^(-7)to 1.13×10^(-6).The resistance correlated with mutations to ompC and comR,affecting porin C and copper permeability,*** mutants manifested a fitness cost,a decreased level of resistance during passage without antibiotic pressure,and cross resistance to another carbapenem(imipenem)and a b-lactamase inhibitor(taniborbactam).In conclusion,compared with the dual combinations,the triple combination of MEM with InC58 and AVI showed a much wider spectrum of activity against different carbapenemaseproducing bacteria,revealing a new strategy to combat b-lactamase-mediated antimicrobial resistance.

关键词： Carbapenemase Metallo/serine-b-lactamase inhibitor Avibactam Meropenem Antimicrobial resistance

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Nutritional and medicinal characteristics of Chinese giant salamander (Andrias davidianus) for applications in healthcare industry by artificial cultivation: A review

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Food Science and Human Wellness 2018年第1期7卷 1-10页

作者： Dong He Wenming Zhu Wen Zenga Jun Lin Yang Ji Yi Wang Chong Zhang Yuan Lu Daoquan Zhao Nan Su Xin-Hui Xing Key laboratory for Industrial biocatalysis Ministry of EducationInstitute of Biochemical EngineeringDepartment of Chemical EngineeringRoom 601Yingshi BuildingBeijing100084China Centre for Synthetic and Systems Biology Tsinghua UniversityBeijing100084China Henan Academy of Aquatic Sciences No.38 Jiangshan RoadZhengzhouHenan450001China

Andrias davidianus,*** giant salamander(CGS),is one of the largest and oldest amphibians existing in the world and is also one of the valuable biological resources of *** CGS has been threatened with extinction in the past decades due to over capturing,deterioration of natural environment,the slow breeding and growth of the wild species in ***,in the past twenty years,with the breakthrough and progress of artificial breeding technology by artificial insemination,the number of artificially cultivated CGS has increased *** cultivated CGS can either be released to the CGS living environment to increase the population in nature or legally applied in food and medicinal industry as a feedstock due to the unique nutritional and medicinal values of CGS as recorded *** this review,the nutritional components,bioactive components and medicinal activities of the artificially cultivated CGS will be *** mucus,skin,meat and bone of CGS contain many different bioactive substances thereby having various medicinal activities including anti-aging,anti-fatigue,anti-tumor,therapy of burn and anti-infection and other physiological *** paper will further discuss the potential applications of the artificially cultivated CGS in healthcare industry and prospects of future technological development.

关键词： Andrias davidianus Artificial breeding Chinese giant salamander Functional foods Medicinal activity Natural resource protection Nutrition

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Applications of cold atmospheric plasmas(CAPs)in agriculture:a brief review and the novel development of a radio-frequency CAP jet generator for plant mutation

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Plasma Science and Technology 2022年第9期24卷 1-14页

作者： Heping LI Jing LI Xiting ZHAO Liyan WANG Chuan FANG Nan SU Chong ZHANG Yan XU Meng LV Mingjun LI Xinhui XING Department of Engineering Physics Tsinghua UniversityBeijing 100084People’s Republic of China College of Life Sciences Henan Normal UniversityXinxiang 453007People’s Republic of China Biobreeding Research Center Wuxi Research Institute of Applied TechnologiesTsinghua UniversityWuxi 214072People’s Republic of China MOE Key laboratory of Industrial biocatalysis Department of Chemical EngineeringTsinghua UniversityBeijing 100084People’s Republic of China Center for Systems and Synthetic Biology Tsinghua UniversityBeijing 100084People’s Republic of China Institute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate SchoolShenzhen 518055People’s Republic of China

Cold atmospheric plasmas(CAPs)have shown great applicability in *** kinds of CAP sources have been studied in agricultural applications to promote plant growth and cure plant *** briefly review the state-of-the-art stimulating effects of atmospheric-pressure dielectricbarrier-discharge(AP-DBD)plasmas,after the direct or indirect treatment of plants for growth promotion and disease *** then discuss the special demands on the characteristics of the CAP sources for their applications in plant mutation *** atmospheric and room temperature plasma(ARTP)jet generator with a large plasma irradiation area,a high enough concentration of chemically reactive species and a low gas temperature is designed for direct plant *** measurements of the electrical,thermal and optical features of the ARTP generator are ***,an ARTP-P(ARTP for plant mutagenesis)mutation breeding machine is developed,and a typical case of plant mutation breeding by the ARTP-P mutation machine is presented using Coreopsis tinctoria *** and agricultural experiments show that the newly-developed ARTP-P mutation breeding machine with a large irradiation area can generate uniform CAP jets with high concentrations of chemically reactive species and mild gas temperatures,and have signiflcant mutagenesis effects on the Coreopsis tinctoria *** ARTP-P mutation breeding machine may provide a platform for systematic studies on mutation mechanisms and results for various plant seeds under different operating conditions in future research.

关键词： cold atmospheric plasma radio-frequency glow discharge mutation plant breeding ARTP agricultural application

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Effects of Tobacco Pathogens and Their Antagonistic Bacteria on Tobacco Root Exudates

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Open Journal of applied Sciences 2018年第11期8卷 518-531页

作者： Cheng Li Jun Yu Lu Gan Jingguo Sun Changjun Wang Qin Wang Shouwen Chen Yong Yang State Key laboratory of biocatalysis and Enzyme Engineering School of Life Sciences Hubei University Wuhan China Tobacco Research Institute of Hubei Province Wuhan China

The research on relationship between rhizosphere microbes and root exudates has a great significance on discussion of interaction between rhizosphere microbes and plants, as well as control of soil-borne diseases and insect pest. GC-MS was used to analyze changes of tobacco root exudates under the antagonistic action of tobacco bacterial wilt and black shank. It turned out that when pathogens of tobacco bacterial wilt and black shank in tobacco root microorganisms increase, tobacco root exudates augmented rapidly among of which organic acids have the biggest growth, followed by amines. When the pathogens of tobacco bacterial wilt and black shank are inhibited by the active substance of antagonistic antibacterial, 20 - 23 kinds of root exudates are added;besides, the content of 7 substances was reduced to 0. Another inter-esting finding was that the fluctuations of phthalic acid, isophthalic acid and benzoic acid, which have caused continuous cropping obstacles, were very dis-tinct. The results of this study have provided novel clues for the exploration of continuous tobacco cropping obstacles and soil-borne diseases.

关键词： Root Exudates Rhizosphere Microbes Allelochemical GC-MS

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Genome-scale metabolic models applied for human health and biopharmaceutical engineering

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Quantitative Biology 2023年第4期11卷 363-375页

作者： Feiran Li Yu Chen Johan Gustafsson Hao Wang YiWang Chong Zhang Xinhui Xing nstitute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina Key laboratory of Quantitative Synthetic Biology Shenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina Department of Biology and Biological Engineering Chalmers University of TechnologyGothenburgSweden Key laboratory for Industrial biocatalysis Ministry of EducationInstitute of Biochemical EngineeringDepartment of Chemical EngineeringTsinghua University BeijingChina Center for Synthetic and Systems Biology Tsinghua UniversityBejingChina Institute of Biomedical Health Technology and Engineering Shenzhen Bay LaboratoryShenzhenChina

Over the last 15 years,genome-scale metabolic models(GEMs)have been reconstructed for human and model animals,such as mouse and rat,to systematically understand metabolism,simulate multicellular or multi-tissue interplay,understand human diseases,and guide cell factory design for biopharmaceutical protein ***,we describe how metabolic networks can be represented using stoichiometric matrices and well-defined constraints for flux ***,we review the history of GEM development for quantitative understanding of Homo sapiens and other relevant animals,together with their *** describe how model develops from *** to other animals and from generic purpose to precise context-specific *** progress of GEMs for animals greatly expand our systematic understanding of metabolism in human and related *** discuss the difficulties and present perspectives on the GEM development and the quest to integrate more biological processes and omics data for future research and *** truly hope that this review can inspire new models developed for other mammalian organisms and generate new algorithms for integrating big data to conduct more in-depth analysis to further make progress on human health and biopharmaceutical engineering.

关键词： constraint-based modeling disease genome-scale metabolicmodel metabolism

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The biological principles and advanced applications of DSB repair in CRISPR-mediated yeast genome editing

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Synthetic and Systems Biotechnology 2023年第4期8卷 584-596页

作者： Wenxin Bai Meilan Huang Chun Li Jun Li Institute of Biochemical Engineering School of Chemistry and Chemical EngineeringBeijing Institute of Technology100081BeijingPR China School of Chemistry and Chemical Engineering David Keir BuildingQueen’s University BelfastStranmillis RoadNorthern IrelandBT95AGBelfastUnited Kingdom The BIT-QUB International Joint laboratory in Synthetic Biology Beijing100081PR China Key Lab for Industrial biocatalysis Ministry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084PR China

To improve the performance of yeast cell factories for industrial production,extensive CRISPR-mediated genome editing systems have been applied by artificially creating double-strand breaks(DSBs)to introduce mutations with the assistance of intracellular DSB *** strategies of DSB repair are required to meet various demands,including precise editing or random editing with customized gRNAs or a gRNA *** most yeasts remodeling techniques have shown rewarding performance in laboratory verification,industrial yeast strain manipulation relies only on very limited ***,we comprehensively reviewed the molecular mechanisms underlying recent industrial applications to provide new insights into DSB cleavage and repair pathways in both Saccharomyces cerevisiae and other unconventional yeast *** discussion of DSB repair covers the most frequently used homologous recombination(HR)and nonhomologous end joining(NHEJ)strategies to the less well-studied illegitimate recombination(IR)pathways,such as single-strand annealing(SSA)and microhomology-mediated end joining(MMEJ).Various CRISPR-based genome editing tools and corresponding gene editing efficiencies are ***,we summarize recently developed CRISPR-based strategies that use optimized DSB repair for genome-scale editing,providing a direction for further development of yeast genome editing.

关键词： Yeast genome editing CRISPR Double-strand break(DSB) Homologous recombination(HR) Nonhomologous end joining(NHEJ) Illegitimate recombination(IR)

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