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Numeric modelling and risk assessment of pollutions in the Chinese Bohai Sea

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Science China Earth Sciences 2017年第8期60卷 1546-1557页

作者： liu YongZhi SHEN YouLi LV xianqing liu Qiang Key Laboratory of Physical Oceanography Ocean University of China Beihai Marine Environmental Monitoring Centre Station of State Oceanic Administration College of Engineering Ocean University of China

To simulate the dynamic process of total nitrogen(TN) in seas, numerical modelling combined with the adjoint method is implemented in this study. Because nonpoint source terms(ST) and initial values(IV) of TN are essential but difficult to determine, the adjoint method was applied to a numerical model, and the ST and IV terms of TN were inverted via routine monitoring data in the Bohai Sea. In twin experiments, the adjoint method was capable of inverting the prescribed spatio-temporally distributed ST and the spatial distributed IV. In practical experiments, the results demonstrated that the simulation precision with ST inversion was higher than that with IV inversion and was accurate with joint initial values and source term(IST) inversion. This result indicates that nonpoint source TN is essential for the simulation of TN concentration. Furthermore, the simulated results indicate that the pollution in three bays of the Bohai Sea is rather severe. The model in this study is not specific to the Bohai Sea and can be generalized to other areas, such as the Beibu Gulf. These findings may assist in the development of cost-effective controls for accidental or planned industrial pollutant releases into coastal waters.

关键词：数值模拟渤海海域海域污染风险评估中国伴随方法数据反演数值模型

Comprehensive profiling and natural variation of flavonoids in rice

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Journal of Integrative Plant Biology 2014年第9期56卷 876-886页

作者： Xuekui Dong Wei Chen Wensheng Wang Hongyan Zhang Xianqing Liu Jie Luo National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Huazhong Agricultural University Key Laboratory of Horticultural Plant Biology(Ministry of Education) Huazhong Agricultural University College of Life Science and Technology Huazhong Agricultural University

Flavonoids constitute a major group of plant phenolic compounds.While extensively studied in Arabidopsis,profiling and naturally occurring variation of these compounds in rice（Oryza sativa）,the monocot model plant,are less reported.Using a collection of rice germplasm,comprehensive profiling and natural variation of flavonoids were presented in this report.Application of a widely targeted metabolomics method facilitated the simultaneous identification and quantification of more than 90 flavonoids using liquid chromatography tandem mass spectrometry（LC-MS/MS）.Comparing flavonoid contents in various tissues during different developmental stages revealed tissue-specific accumulation of most flavonoids.Further investigation indicated that flavone mono-C-glycosides,malonylated flavonoid O-hexosides,and some flavonoid O-glycosides accumulated at significantly higher levels in indica than in japonica,while the opposite was observed for aromatic acylated flavone C-hexosyl-O-hexosides.In contrast to the highly differential accumulation between the two subspecies,relatively small variations within subspecies were detected for most flavonoids.Besides,an association analysis between flavonoid accumulation and its biosynthetic gene sequence polymorphisms disclosed that natural variation of flavonoids was probably caused by sequence polymorphisms in the coding region of flavonoid biosynthetic genes.Our work paves the way for future dissection of biosynthesis and regulation of flavonoid pathway in rice.

关键词： Flavonoids metabolic profiling natural variation Oryza sativa single-nucleotide polymorphisms

Does Security of Land Operational Rights Matter for the Improvement of Agricultural Production Efficiency under the Collective Ownership in China?

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China & World Economy 2021年第1期29卷 87-108页

作者： xianqing Ji Shouying liu Jianan Yan Youyi Li School of Public Administraiton Nanjing Audit UniversityChina School of Economics Renmin UniversityChina School of Public Administration Nanjing Agricultural UniversityChina

Under the"separation of three rights"policy,the impact of security of land operationalrights on agricultural production efficiency has attracted much attention in recentyears.Data envelopment analysis and mediation effect analysis were applied to 888family farms run by new-type agricultural operators from Songjiang to identify themechanism of the effect of land operational rights security on agricultural productionefficiency through long-term investment.The results show that greater security of landoperational rights generally increased agricultural production efficiency.Approximately37.94 percent of the impact could be explained by long-term investment.The resultsalso indicate that significant heterogeneity exists in the effect of land operational rightssecurity on agricultural production efficiency at various levels of the family farms'efficiency distributions.lt is suggested that government should legalize land operationalrights and give them a status equal to those of households'contractual rights and landownership rights in China's future land tenure reform.

关键词： agricultural production efficiency new-type agricultural operator security of land operational rights

A UV-B-responsive glycosyltransferase,OsUGT706C2,modulates flavonoid metabolism in rice

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Science China(Life Sciences) 2020年第7期63卷 1037-1052页

作者： Feng Zhang Hao Guo Jiacheng Huang Chenkun Yang Yufei Li Xuyang Wang Lianghuan Qu Xianqing Liu Jie Luo National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Hu az hong Agricultural UniversityWuhan 430070China Institute of Tropical Agriculture and Forestry of Hainan University Haikou 570288China

Although natural variations in rice flavonoids exist, and biochemical characterization of a few flavonoid glycosyltransferases has been reported, few studies focused on natural variations in tricin-lignan-glycosides and their underlying genetic basis. In this study, we carried out metabolic profiling of tricin-lignan-glycosides and identified a major quantitative gene annotated as a UDPdependent glycosyltransferase OsUGT706C2 by metabolite-based genome-wide association analysis. The putative flavonoid glycosyltransferase OsUGT706C2 was characterized as a flavonoid 7-O-glycosyltransferas in vitro and in vivo. Although the in vitro enzyme activity of OsUGT706C2 was similar to that of OsUGT706D1, the expression pattern and induced expression profile of OsUGT706C2 were very different from those of OsUGT706D1. Besides, OsUGT706C2 was specifically induced by UV-B. Constitutive expression of OsUGT706C2 in rice may modulate phenylpropanoid metabolism at both the transcript and metabolite levels. Furthermore, overexpressing OsUGT706C2 can enhance UV-B tolerance by promoting ROS scavenging in rice. Our findings might make it possible to use the glycosyltransferase OsUGT706C2 for crop improvement with respect to UVB adaptation and/or flavonoid accumulation, which may contribute to stable yield.

关键词： flavone glycosyltransferase natural variation Oryza sativa tricin-lignan-glycosides metabolomics UV-B tolerance

Fluorescein-based monitoring of RNA N^(6)-methyladenosine at single-nucleotide resolution

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Journal of Molecular Cell Biology 2021年第4期13卷 325-328页

作者： Xiao-Min liu Shen Wang xianqing Gan Shu-Bing Qian Jun Zhou School of Life Science and Technology China Pharmaceutical UniversityNanjing 210009China State Key Laboratory of Natural Medicines China Pharmaceutical UniversityNanjing 210009China Division of Nutritional Sciences Cornell UniversityIthacaNY 14853USA

Dear Editor,N^(6)-methyladenosine(m^(6)A)emerges as an abundant chemical modification on RNAs,which enriches in distinct internal regions linked to divergent aspects of RNA fate(Zhao et al.,2017).Transcriptome-wide mapping of m^(6)A sites using high-throughput sequencing enables comparative analysis of cellular^(6)A dynamics on particular RNAs under both physiological and stress conditions(Dominissini et al.,2012;Meyer et al.,2015),yet is confined to low resolution of coverage and indistinction of adjacent m6A sites.

关键词： al. 6 resolution

OsRLCK160 contributes to flavonoid accumulation and UV-B tolerance by regulating OsbZIP48 in rice

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Science China(Life Sciences) 2022年第7期65卷 1380-1394页

作者： Feng Zhang Jiacheng Huang Hao Guo Chenkun Yang Yufei Li Shuangqian Shen Chuansong Zhan Lianghuan Qu Xianqing Liu Shouchuang Wang Wei Chen Jie Luo National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China College of Plant Science and Technology Huazhong Agricultural UniversityWuhan 430070China College of Tropical Crops Hainan UniversityHaikouHainan 570288China

Plants produce specialized metabolites to adapt to the ever-changing environments.Flavonoids are antioxidants essential for growth,development,and breeding with increased stress resistance in crops.However,the mechanism of the involvement of flavonoids in ultraviolet-B(UV-B)stress in rice(Oryza sativa)is largely unknown.In this study,we cloned and functionally identified a receptor-like kinase(OsRLCK160)and a bZIP transcription factor(OsbZIP48)positively regulating flavonoid accumulation through metabolite-based genome-wide association study of the flavonoid content in rice.Meanwhile,OsRLCK160 interacted with and phosphorylated OsbZIP48 to regulate the flavonoid accumulation and participate in UV-B tolerance in rice.Our study indicates the importance of applying OsRLCK160 and OsbZIP48 to advance the fundamental understanding of stable rice production and breed UV-B-tolerant rice varieties,which may contribute to breeding high-yield rice varieties.

关键词： flavonoids natural variation Oryza sativa receptor-like kinase transcription factor UV-B tolerance

Development of a widely targeted volatilomics method for profiling volatilomes in plants

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Molecular Plant 2022年第1期15卷 189-202页

作者： Honglun Yuan Guangping Cao Xiaodong Hou Menglan Huang Pengmeng Du Tingting Tan Youjin Zhang Haihong Zhou Xianqing Liu Ling liu Yiding Jiangfang Yufei Li Zhenhuan liu Chuanying Fang Liqing Zhao Alisdair R.Fernie Jie Luo College of Tropical Crops Hainan UniversityHaikou 570288China Sanya Nanfan Research Institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya572025China College of Chemistry and Environmental Engineering Shenzhen UniversityShenzhen 518060China National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China Department of Molecular Physiology Max-Planck-lnstitute of Molecular Plant PhysiologyAm Muhlenberg 114476 Potsdam-GolmGermany

Volatile organic compounds play essential roles in plant environment interactions as well as determining the fragrance of plants.Although gas chromatography-mass spectrometry-based untargeted metabolo-mics is commonly used to assess plant volatiles,it suffers from high spectral convolution,low detection sensitivity,a limited number of annotated metabolites,and relatively poor reproducibility.Here,we report a widely targeted volatilomics(WTV)method that involves using a“targeted spectra extraction”algorithm to address spectral convolution,constructing a high-coverage MS2 spectral tag library to expand volatile annotation,adapting a multiple reaction monitoring mode to improve sensitivity,and using regression models to adjust for signal drift.The newly developed method was used to profile the volatilome of rice grains.Compared with the untargeted method,the newly developed WTV method shows higher sensitivity(for example,the signal-to-noise ratio of guaicol increased from 4.1 to 18.8),high annotation coverage(the number of annotated volatiles increased from 43 to 132),and better reproducibility(the number of volatiles in quality control samples with relative standard deviation value below 30.0%increased from 14 to 92 after normalization).Using the WTV method,we studied the metabolic responses of tomato to environmental stimuli and profiled the volatilomes of different rice accessions.The results identified benzothiazole as a potential airborne signal priming tomato plants for enhanced defense and 2-nonanone and 2-heptanone as novel aromatic compounds contributing to rice fragrance.These case studies suggest that the widely targeted volatilomics method is more efficient than those currently used and may considerably promote plant volatilomics studies.

关键词： widely targeted volatilomics GC-MS MS2T library plant volatilome rice tomato

Raising the production of phloretin by alleviation of by-product of chalcone synthase in the engineered yeast

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Science China(Life Sciences) 2020年第11期63卷 1734-1743页

作者： Chunmei Jiang Xiaonan liu xianqing Chen Yi Cai Yibin Zhuang Tian liu Xiaoxi Zhu Hui Wang Yuwan liu Huifeng Jiang Wen Wang Key Laboratory for Space Bioscience and Space Biotechnology School of Life SciencesNorthwestern Polytechnical UniversityXi’an 710072China Key Laboratory of Systems Microbial Biotechnology Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin 300308China University of Chinese Academy of Sciences Beijing 100049China Center for Ecology and Environmental Sciences Northwestern Polytechnical UniversityXi’an 710072China Jiaxing Synbiolab Biotechnology Co. Ltd.Jiaxing 314006China

Phloretin is an important skin-lightening and depigmenting agent from the peel of apples. Although de novo production of phloretin has been realized in microbes using the natural pathway from plants, the efficiency of phloretin production is still not enough for industrial application. Here, we established an artificial pathway in the yeast to produce phloretin via assembling two genes of p-coumaroyl-CoA ligase(4CL) and chalcone synthase(CHS). CHS is a key enzyme which conventionally condenses a CoA-tethered starter with three molecules of malonyl-CoA to form the backbone of flavonoids. However, there was 33% of byproduct generated via CHS by condensing two molecules of malonyl-CoA during the fermentation process. Hence, we introduced a more efficient CHS and improved the supply of malonyl-CoA through two pathways;the by-product ratio was decreased from 33% to 17% and the production of phloretin was improved from 48 to 83.2 mg L^(-1). Finally, a fed-batch fermentation process was optimized and the production of phloretin reached 619.5 mg L^(-1), which was 14-fold higher than that of the previous studies. Our work established a platform for the biosynthesis of phloretin from the low-cost raw material 3-(4-hydroxyphenyl) propanoic acid and also illustrated the potential for industrial scale bio-manufacturing of phloretin.

关键词： phloretin Saccharomyces cerevisiae metabolic engineering microbial cell factories fed-batch fermentation

Integration of rhythmic metabolome and transcriptome provides insights into the transmission of rhythmic fluctuations and temporal diversity of metabolism in rice

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Science China(Life Sciences) 2022年第9期65卷 1794-1810页

作者： Junjie Zhou Chengyuan liu Qiyu Chen Ling liu Shuying Niu Ridong Chen Kang Li Yangyang Sun Yuheng Shi Chenkun Yang Shuangqian Shen Yufei Li Junwei Xing Honglun Yuan Xianqing Liu Chuanying Fang Alisdair R.Fernie Jie Luo College of Tropical Crops Hainan UniversityHaikou 570288China National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(Wuhan) Huazhong Agricultural UniversityWuhan 430070China Sanya Nanfan Research Institute of Hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China Max-Planck-Institute of Molecular Plant Physiology Potsdam-Golm 144776Germany Center of Plant System Biology and Biotechnology Plovdiv 4000Bulgaria

Various aspects of the organisms adapt to cyclically changing environmental conditions via transcriptional regulation.However,the role of rhythmicity in altering the global aspects of metabolism is poorly characterized.Here,we subjected four rice(Oryza sativa)varieties to a range of metabolic profiles and RNA-seq to investigate the temporal relationships of rhythm between transcription and metabolism.More than 40%of the rhythmic genes and a quarter of metabolites conservatively oscillated across four rice accessions.Compared with the metabolome,the transcriptome was more strongly regulated by rhythm;however,the rhythm of metabolites had an obvious opposite trend between day and night.Through association analysis,the time delay of rhythmic transmission from the transcript to the metabolite level was~4 h under long-day conditions,although the transmission was nearly synchronous for carbohydrate and nucleotide metabolism.The rhythmic accumulation of metabolites maintained highly coordinated temporal relationships in the metabolic network,whereas the correlation of some rhythmic metabolites,such as branched-chain amino acids(BCAAs),was significantly different intervariety.We further demonstrated that the cumulative diversity of BCAAs was due to the differential expression of branched-chain aminotransferase 2 at dawn.Our research reveals the flexible pattern of rice metabolic rhythm existing with conservation and diversity.

关键词： Oryza sativa diurnal cycle metabolome time delay rhythmic diversity