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| 1 | Sedimentary Characteristics and Paleoenvironmental Records of Zabuye Salt Lake,Tibetan Plateau,since 128 ka BP显示文摘This paper for the first time reveals high-resolution core records of Zabuye Salt Lake in the interior of the Qinghai-Tibet Plateau.According to 1346 samples taken continuously,relatively accurate ^(14)C,U-series disequilibrium and ESR ages have been obtained,thus revealing that the lake core ages from 0 to 83.63m of hole SZK02 are~800 to over 128 ka.In the paper,the lake core sedimentary characteristics(including the lithologies and mineral assemblages)are analyzed in detail and correlated with ostracod assemblages I to XX and sporopollen zones A to I,and on the basis of an integrated analysis of theδ^(18)0 values of authigenic calcium-magnesium carbonate and environmental proxies of minerals,sporopollen and microfossils in the lake core,a correlation has been made of oxygen isotope change between this lake core and the Greenland GISP2 and GRIP and Guliya ice cores,and the climate of Zabuye Salt Lake since 128 ka BP is divided into the last interglacial stage (including substages e,d,c,b and a)of oxygen isotope stage(OIS)5,early glacial stadial of the last glacial stage of OIS 4,interglacial stadial of the last glacial stage of OIS 3,late glacial stadial of the last glacial stage or Last Glacial Maximum of OIS 2 and postglacial state of OIS 1;in addition,6 Heinrich (H_6-H_1)events,Younger Dryas event and 8.2 ka BP cold event have been recognized. | ZHENG Mianping YUAN Heran LIU Junying LI Yanhe MA Zhibang SUN Qing | 2007 | Acta Geologica Sinica(English Edition)2007，81，5： | 10 |
| 2 | Chromosome-level genome of Himalayan yew provides insights into the origin and evolution of the paclitaxel biosynthetic pathway显示文摘Taxus,commonly known as yew,is a well-known gymnosperm with great ornamental and medicinal value.In this study,by assembling a chromosome-level genome of the Himalayan yew(Taxus wallichiana)with 10.9 Gb in 12 chromosomes,we revealed that tandem duplication acts as the driving force of gene family evolution in the yew genome,resulting in the main genes for paclitaxel biosynthesis,i.e.those encoding the taxadiene synthase,P450s,and transferases,being clustered on the same chromosome.The tandem duplication may also provide genetic resources for the nature to sculpt the core structure of taxoids at different positions and subsequently establish the complex pathway of paclitaxel by neofunctionalization.Furthermore,we confirmed that there are two genes in the cluster encoding isoenzymes of a known enzyme in the paclitaxel biosynthetic pathway.The reference genome of the Himalayan yew will serve as a platform for decoding the complete biosynthetic pathway of paclitaxel and understanding the chemodi-versity of taxoids in gymnosperms. | Jian Cheng Xiao Wang Xiaonan Liu Xiaoxi Zhu Zihe Li Huanyu Chu Qian Wang QianQian Lou Bijun Cai Yiqun Yang Xiaoyun Lu Kai Peng Dingyu Liu Yuwan Liu Lina Lu Huan Liu Ting Yang Qijin Ge Chengcheng Shi Guichun Liu Zhiwei Dong Xun Xu Wen Wang Huifeng Jiang Yanhe Ma | 2021 | Molecular Plant2021，14，7： | 6 |
| 3 | Crystal structures of D-psicose 3-epimerase from Clostridium cellulolyticum H10 and its complex with ketohexose sugars显示文摘D-Psicose 3-epimerase(DPEase)is demonstrated to be useful in the bioproduction of D-psicose,a rare hexose sugar,from D-fructose,found plenty in nature.Clostridium cellulolyticum H10 has recently been identified as a DPEase that can epimerize D-fructose to yield D-psicose with a much higher conversion rate when compared with the conventionally used DTEase.In this study,the crystal structure of the C.cellulolyticum DPEase was determined.The enzyme assembles into a tetramer and each subunit shows a(β/α)8 TIM barrel fold with a Mn2+metal ion in the active site.Additional crystal structures of the enzyme in complex with substrates/products(D-psicose,D-fructose,D-tagatose and D-sorbose)were also determined.From the complex structures of C.cellulolyticum DPEase with D-psicose and D-fructose,the enzyme has much more interactions with D-psicose than D-fructose by forming more hydrogen bonds between the substrate and the active site residues.Accordingly,based on these ketohexosebound complex structures,a C3-O3 proton-exchange mechanism for the conversion between D-psicose and D-fructose is proposed here.These results provide a clear idea for the deprotonation/protonation roles of E150 and E244 in catalysis. | Hsiu-Chien Chan Yueming Zhu Yumei Hu Tzu-Ping Ko Chun-Hsiang Huang Feifei Ren Chun-Chi Chen Yanhe Ma Rey-Ting Guo Yuanxia Sun | 2012 | Protein & Cell2012，3，2： | 6 |
| 4 | Occurrence of the Iron–rich Melt in the Heijianshan Iron Deposit, Eastern Tianshan, NW China: Insights into the Origin of Volcanic Rock–hosted Iron Deposits显示文摘Long-standing controversy persists over the presence and role of iron–rich melts in the formation of volcanic rock-hosted iron deposits. Conjugate iron–rich and silica–rich melt inclusions observed in thin-sections are considered as direct evidence for the presence of iron-rich melt, yet unequivocal outcrop-scale evidence of iron-rich melts are still lacking in volcanic rock-hosted iron deposits. Submarine volcanic rock-hosted iron deposits, which are mainly distributed in the western and eastern Tianshan Mountains in Xinjiang, are important resources of iron ores in China, but it remains unclear whether iron-rich melts have played a role in the mineralization of such iron ores. In this study, we observed abundant iron-rich agglomerates in the brecciated andesite lava of the Heijianshan submarine volcanic rock–hosted iron deposit, Eastern Tianshan, China. The iron-rich agglomerates occur as irregular and angular masses filling fractures of the host brecciated andesite lava. They show concentric potassic alteration with silicification or epidotization rims, indicative of their formation after the wall rocks. The iron-rich agglomerates have porphyritic and hyalopilitic textures, and locally display chilled margins in the contact zone with the host rocks. These features cannot be explained by hydrothermal replacement of wall rocks(brecciated andesite lava) which is free of vesicle and amygdale, rather they indicate direct crystallization of the iron-rich agglomerates from iron-rich melts. We propose that the iron-rich agglomerates were formed by open-space filling of volatile-rich iron-rich melt in fractures of the brecciated andesite lava. The iron-rich agglomerates are compositionally similar to the wall-rock brecciated andesite lava, but have much larger variation. Based on mineral assemblages, the iron-rich agglomerates are subdivided into five types, i.e., albite-magnetite type, albite-K-feldsparmagnetite type, K-feldspar–magnetite type, epidote-magnetite type and quartz-magnetite type, representing that products formed at different stages during the evolution of a magmatic-hydrothermal system. The albite-magnetite type represents the earliest crystallization product from a residual ironrich melt; the albite-K-feldspar-magnetite and K-feldspar-magnetite types show features of magmatichydrothermal transition, whereas the epidote-magnetite and quartz-magnetite types represent products of hydrothermal alteration. The occurrence of iron-rich agglomerates provides macroscopic evidence for the presence of iron-rich melts in the mineralization of the Heijianshan iron deposit. It also indicates that iron mineralization of submarine volcanic rock-hosted iron deposits is genetically related to hydrothermal fluids derived from iron-rich melts. | LI Houmin LI Lixing DING Jianhua LI Yanhe SONG Zhe MENG Jie MA Yubo | 2018 | Acta Geologica Sinica(English Edition)2018，92，2： | 5 |
| 5 | The origin and evolution of the diosgenin biosynthetic pathway in yam显示文摘Diosgenin,mainly produced by Dioscorea species,is a traditional precursor of most hormonal drugs in the pharmaceutical industry.The mechanisms that underlie the origin and evolution of diosgenin biosynthesis in plants remain unclear.After sequencing the whole genome of Dioscorea zingiberensis,we revealed the evolutionary trajectory of the diosgenin biosynthetic pathway in Dioscorea and demonstrated the de novo biosynthesis of diosgenin in a yeast cell factory.First,we found that P450 gene duplication and neofunctionalization,driven by positive selection,played important roles in the origin of the diosgenin biosynthetic pathway.Subsequently,we found that the enrichment of diosgenin in the yam lineage was regulated by CpG islands,which evolved to regulate gene expression in the diosgenin pathway and balance the carbon flux between the biosynthesis of diosgenin and starch.Finally,by integrating genes fromplants,animals,and yeast,weheterologously synthesized diosgenin to 10mg/l in genetically-engineered yeast.Our study not only reveals the origin and evolutionary mechanisms of the diosgenin biosynthetic pathway in Dioscorea,but also introduces an alternative approach for the production of diosgenin through synthetic biology. | Jian Cheng Jing Chen Xiaonan Liu Xiangchen Li Weixiong Zhang Zhubo Dai Lina Lu Xiang Zhou Jing Cai Xueli Zhang Huifeng Jiang Yanhe Ma | 2021 | Plant Communications2021，2，1： | 2 |
| 6 | Comparative proteome analysis of alkaliphilic Bacillus sp.N16-5 grown on different carbon sources显示文摘To determine the impact of carbohydrates on the metabolic pathway in alkaliphiles, proteomes were obtained from cultures containing different carbohydrates and were resolved on two-dimensional gel electrophoresis (2-DE). The proteomes were compared to determine differentially expressed proteins. A novel alkaliphilic bacterium (alkaliphilic Bacillus sp. N16-5 isolated from Wudunur Soda Lake, China) was isolated in media with five different carbon sources (glucose, mannose, galactose, arabinose, and xylose). Comparative proteome analysis identified 61 differentially expressed proteins, which were mainly involved in carbohydrate metabolism, amino acid transport, and metabolism, as well as energy production and conversion. The comparison was based on the draft genome sequence of strain N16-5. The abundance of enzymes involved in central metabolism was significantly changed when exposed to various carbohydrates. Notably, catabolite control protein A (CcpA) was up-regulated under all carbon sources compared with glucose. In addition, pentose exhibited a stronger effect than hexose in CcpA-mediated carbon catabolite repression. These results provided a fundamental understanding of carbohydrate metabolism in alkaliphiles. | LI Gang SONG YaJian XUE YanFen RAO Lang ZHOU Chen WANG QuanHui MA YanHe | 2011 | Science China(Life Sciences)2011，54，1： | 2 |
| 7 | Crystal structure of histidine-containing phosphocarrier protein from Thermoanaerobacter tengcongensis MB4 and the implications for thermostability显示文摘Protein thermostability is an inherent characteristic of proteins from thermophilic microorganisms,and therefore enables these organisms to survive at extreme temperatures.Although it is well-known that thermostable proteins are critical for the growth of thermophilic organisms,the structural basis of protein thermostability is not yet fully understood.The histidine-containing phosphocarrier (HPr) protein,a phosphate shuttle protein in the phosphoenolpyruvate-dependent sugar transport system (PTS) of bacterial species,is an ideal model for investigating protein thermostability with respect to its small size and deficiency in disulphide bonds or cofactors.In this study,the HPr protein from Thermoanaerobacter tengcongensis (TtHPr) is cloned and purified.Crystal structure with good quality has been determined at 2.3 resolution,which provides a firm foundation for exploring the thermostable mechanism.However,it shows that the crystal structure is conserved and no clue can be obtained from this single structure.Furthermore,detailed comparison of sequence and structure with the homologs from mesoor thermophilic bacteria shows no obvious rule for thermostability,but the extra salt-bridge existing only in thermophilic bacteria might be a better explanation for thermostability of HPr.Thus,mutations are performed to interrupt the salt-bridge in HPrs in thermophilic bacteria.Using site-directed mutations and the circular dichroism method,thermostability is evaluated,and the mutational variations are shown to have a faster denaturing rate than for wild-type viruses,indicating that mutations cause instability in the HPrs.Understanding the higher-temperature resistance of thermophilic and hyperthermophilic proteins is essential to studies on protein folding and stability,and is critical in engineering efficient enzymes that can work at a high temperature. | FENG ChunYan GAO Feng LIU YiWei WANG GuiHua PENG Hao MA YanHe YAN JingHua GAO George Fu | 2011 | Science China(Life Sciences)2011，54，6： | 2 |
| 8 | Bacterial diversity of the Inner Mongolian Baer Soda Lakes revealed by 16SrRNA gene sequence analyses 显示文摘 | Ma Yanhe | 2004 | Extremophiles2004，，8： | 1 |
| 9 | Medium optimization by combination of response surface methodology and desirability function: an application in glutamine production显示文摘 | Jinshan Li Cuiqing Ma Yanhe Ma Yan Li Wei Zhou Ping Xu | 2007 | Applied Microbiology and Biotechnology2007，，3： | 1 |
| 10 | Monitoring the microbial community during solid-state acetic acid fermentation of Zhenjiang aromatic vinegar显示文摘 | Wei Xu Zhiyong Huang Xiaojun Zhang Qi Li Zhenming Lu Jinsong Shi Zhenghong Xu Yanhe Ma | 2011 | Food Microbiology2011，，6： | 1 |
| 11 | Overexpression of d -psicose 3-epimerase from Ruminococcus sp. in Escherichia coli and its potential application in d -psicose production显示文摘 | Yueming Zhu Yan Men Wei Bai Xiaobo Li Lili Zhang Yuanxia Sun Yanhe Ma | 2012 | Biotechnology Letters2012，，10： | 1 |
| 12 | Medium Optimization by Combination of Response Surface Methodology and Desirability Function :an Application in Glutamine Production显示文摘 | Jinshan Li Cuiqing Ma Yanhe Ma | 2007 | Appl Micrabiol Biotechnol2007，74，： | 1 |
| 13 | Biosynthesis, property comparison, and hemocompatibility of bacterial and haloarchaeal poly(3-hydroxybutyrate-co-3-hydroxyvalerate)显示文摘Polyhydroxyalkanoates(PHAs) are a class of natural biopolyesters accumulated intracellularly by many microorganisms. These polymers have attracted particular attention as green plastic in biomedical and industrial applications due to their good biodegradability and biocompatibility. Poly(3-hydroxybutyrate-co-3-hydroxyvalerate)(PHBV) is one of the most common members of PHAs. However, there is no report comparing the properties of PHBV from different groups of producers, e.g.,bacteria and haloarchaea. In this study, two types of PHBV copolymers were synthesized in Halogranum amylolyticum and Ralstonia eutropha, respectively, by feeding different carbon sources. They possessed a similar concentration of3 HV monomers(21 mol%) and were named PHBV-H(produced by H. amylolyticum) and PHBV-B(produced by R. eutropha) based on their source. Interestingly, they exhibited different behaviors especially in thermal stability, melting temperature, crystallinity percentage, and mechanical properties. Furthermore, the films of PHBV-Hand PHBV-B possessed different surface properties, such as surface roughness, wettability, and surface free energy.The value of hemolysis on the PHBV-H film was lower in comparison with the PHBV-B film, although both values were within the limit of 5 % permissible for biomaterials.Notably, few inactivated platelets adhered to the surface of the PHBV-H film, whereas numerous activated platelets were seen on film PHBV-B. These results indicated that PHBV-H was a better potential component of blood-contact biomaterials than PHBV-B. Our study clearly revealed that the properties of PHAs are source dependent and haloarchaeal species provide a new opportunity for the production of desired PHAs. | Youxi Zhao Zhiming Rao Yanfen Xue Ping Gong Yizhi Ji Yanhe Ma | 2015 | Science Bulletin2015，60，22： | 1 |
| 14 | Mesocrystalline TiO2 nanosheet arrays with exposed {001} facets: Synthesis via topotactic transformation and applications in dye-sensitized solar cells显示文摘为垂直地综合的一条灵巧的、没有氟的符号的途径排列了 mesocrystalline 锐钛矿 TiO 2 nanosheets 的数组与高度暴露了 { 001 } 方面通过 topotactic 被开发转变。唯一的 mesocrystalline { 001 } 垂直地在传导性的做氟的符号的锡氧化物玻璃上排列的 -faceted TiO 2 nanosheet 数组基于格子在先锋和锐钛矿晶体之间匹配从单人赛水晶的先锋 nanosheet 数组通过 topotactic 变换被认识到。形态学和微观结构 { 001 }-faceted TiO 2 nanosheets 能被改变反应物集中并且退火乐意地调制温度。由于提高的染料吸附,减少了费用再结合,并且提高了散布产生从的光暴露{ 001 }方面,除了低维的结构数组的有益的特征(例如,快电子运输和有效费用收集),当他们为敏化染料的太阳能电池( DSSC )被用作阳极时,获得的 TiO 2 nanosheet 数组展出了优异性能。特别地, { 001 }-faceted TiO 2 nanosheet 数组 ~ 15 m 长在 500 敨攠癮 退火了?? | Yanhe Zhang Jinguang Cai Yurong Ma Limin Qi | 2017 | Nano Research2017，10，8： | 1 |
| 15 | Alkalimonas amylolytica gen. nov., sp. nov., and Alkalimonas delamerensis gen. nov., sp. nov., novel alkaliphilic bacteria from soda lakes in China and East Africa显示文摘 | Yanhe Ma Yanfen Xue William D. Grant Nadine C. Collins Andrew W. Duckworth Robert P. Steenbergen Brian E. Jones | 2004 | Extremophiles2004，，3： | 1 |
| 16 | Data-Driven Synthetic Cell Factories Development for Industrial Biomanufacturing显示文摘Revolutionary breakthroughs in artificial intelligence (AI) and machine learning (ML) have had a profound impact on a widerange of scientific disciplines, including the development of artificial cell factories for biomanufacturing. In this paper, wereview the latest studies on the application of data-driven methods for the design of new proteins, pathways, and strains. Wefirst briefly introduce the various types of data and databases relevant to industrial biomanufacturing, which are the basis fordata-driven research. Different types of algorithms, including traditional ML and more recent deep learning methods, are alsopresented. We then demonstrate how these data-based approaches can be applied to address various issues in cell factorydevelopment using examples from recent studies, including the prediction of protein function, improvement of metabolicmodels, and estimation of missing kinetic parameters, design of non-natural biosynthesis pathways, and pathway optimization.In the last section, we discuss the current limitations of these data-driven approaches and propose that data-driven methodsshould be integrated with mechanistic models to complement each other and facilitate the development of synthetic strains forindustrial biomanufacturing. | Zhenkun Shi Pi Liu Xiaoping Liao Zhitao Mao Jianqi Zhang Qinhong Wang Jibin Sun Hongwu Ma Yanhe Ma | 2022 | BioDesign Research2022，，1： | 0 |
| 17 | High level expression of Saccharomyces cerevisiae chitinase(ScCTS1)in Pichia pastoris for degrading chitin显示文摘Chitin is the second most abundant renewable biopolymer in the world.Chitinases play important roles in the degradation of chitin.Chitinases are produced by different organisms for different purposes,which are widely expressed in the three domains of life,ranging from archaea,bacteria,to fungi,yeasts,plants,insects,and even vertebrates.But there are few reports about Saccharomyces cerevisiae chitinase(ScCTS1).The aim of this study was to realize the high level expression of ScCTS1.The ScCTS1 was cloned into the expression vector pPIC9K.The recombinant plasmid was linearized and transformed into competent Pichia pastoris GS115.After screening by G418 plate,the fermentation conditions were optimized.Ultimately,under the optimal fermentation conditions,ScCTS1 enzymatic activity reached up to 94.6 U/mL.This paper presents the first report on the heterologous expression of a full-length ScCTS1 with considerably high activity.The work will not only make a great stride towards its potential applications in biotechnology,but also facilitate elucidating the precise mechanism of yeast cell division. | Zhao Youxi Jiang Huihui Rao Zhiming Ji Yizhi Cheng Yanling Ma Yanhe | 2015 | International Journal of Agricultural and Biological Engineering2015，8，5： | 0 |
| 18 | Mapping soil organic matter in cultivated land based on multi-year composite images on monthly time scales显示文摘Rapid and accurate acquisition of soil organic matter(SOM)information in cultivated land is important for sustainable agricultural development and carbon balance management.This study proposed a novel approach to predict SOM with high accuracy using multiyear synthetic remote sensing variables on a monthly scale.We obtained 12 monthly synthetic Sentinel-2 images covering the study area from 2016 to 2021 through the Google Earth Engine(GEE)platform,and reflectance bands and vegetation indices were extracted from these composite images.Then the random forest(RF),support vector machine(SVM)and gradient boosting regression tree(GBRT)models were tested to investigate the difference in SOM prediction accuracy under different combinations of monthly synthetic variables.Results showed that firstly,all monthly synthetic spectral bands of Sentinel-2 showed a significant correlation with SOM(P<0.05)for the months of January,March,April,October,and November.Secondly,in terms of single-monthly composite variables,the prediction accuracy was relatively poor,with the highest R^(2)value of 0.36 being observed in January.When monthly synthetic environmental variables were grouped in accordance with the four quarters of the year,the first quarter and the fourth quarter showed good performance,and any combination of three quarters was similar in estimation accuracy.The overall best performance was observed when all monthly synthetic variables were incorporated into the models.Thirdly,among the three models compared,the RF model was consistently more accurate than the SVM and GBRT models,achieving an R^(2)value of 0.56.Except for band 12 in December,the importance of the remaining bands did not exhibit significant differences.This research offers a new attempt to map SOM with high accuracy and fine spatial resolution based on monthly synthetic Sentinel-2 images. | Jie Song Dongsheng Yu Siwei Wang Yanhe Zhao Xin Wang Lixia Ma Jiangang Li | 2024 | Journal of Integrative Agriculture2024，23，4： | 0 |
| 19 | Active knee joint exoskeleton for stair ascent augmentation显示文摘Dear editor,Stair climbing is a strenuous daily movement that is challenging for older adults and those with lower limb weakness.In this study,we describe a novel stairclimbing exoskeleton that was designed to help weak-kneed people to climb stairs and help workers to carry heavy loads up stairs(Figure 1(a)). | Zongwei ZHANG Jizhuang FAN Hongzhe JIN Tianjiao ZHENG Sikai ZHAO Shun MA Jie ZHAO Yanhe ZHU | 2021 | Science China(Information Sciences)2021，64，3： | 0 |
| 20 | An internal circulation iron-carbon micro-electrolysis reactor for aniline wastewater treatment:Parameter optimization,degradation pathways and mechanism显示文摘Aniline is a vital industrial raw material.However,highly-toxic aniline wastewater usually deteriorated effluent quality,posed a threat to human health and ecosystem safety.Therefore,this study reported a novel internal circulation iron-carbon micro-electrolysis(ICE)reactor to treat aniline wastewater.The effects of reaction time,pH,aeration rate and iron-carbon(Fe/C)ratio on the removal rate of aniline and the chemical oxygen demand were investigated using single-factor experiments.This process exhibited high aniline degradation performance of approximately 99.86% under optimal operating conditions(reaction time=20 min,pH=3,aeration rate=0.5 m3·h^(-1),and Fe/C=1:2).Based on the experimental results,the response surface method was applied to optimize the aniline removal rate.The Box–Behnken method was used to obtain the interaction effects of three main factors.The result showed that the reaction time had a dominant effect on the removal rate of aniline.The highest aniline removal rate was obtained at pH of 2,aeration rate of 0.5 m^(3)·h^(-1)and reaction time of 30 min.Under optional experimental conditions,the aniline content of effluent was reduced to 3 mg·L^(-1)and the removal rate was as high as 98.24%,within the 95% confidence interval(97.84%-99.32%)of the predicted values.The solution was treated and the reaction intermediates were identified by high-performance liquid chromatography,ultraviolet-visible spectroscopy,Fourier-transform infrared spectroscopy,gas chromatography-mass spectrometry,and ion chromatography.The main intermediates were phenol,benzoquinone,and carboxylic acid.These were used to propose the potential mechanism of aniline degradation in the ICE reactor.The results obtained in this study provide optimized conditions for the treatment of industrial wastewater containing aniline and can strengthen the understanding of the degradation mechanism of iron-carbon micro-electrolysis. | Yanhe Han Han Xu Lei Zhang Xuejiao Ma Yang Man Zhimin Su Jing Wang | 2023 | Chinese Journal of Chemical Engineering2023，63，11： | 0 |
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