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Improving Plant Genome Editing with High-Fidelity xCas9 and Non-canonical PAM-Targeting Cas9-NG

Molecular Plant 2019年第7期12卷 1027-1036页

作者： Zhaohui Zhong Simon Sretenovic Qiurong Ren Lijia Yang Yu Bao Caiyan Qi Mingzhu Yuan Yao He Shishi Liu Xiaopei Liu Jiaheng Wang Lan Huang Yan Wang Dibin Baby David Wang Tao Zhang Yiping Qi Yong Zhang Department of Biotechnology School of Life Sciences and Technology Center for Informational Biology University of 曰ectronic Science and Technology of China Room 216 Main Building No. 4 Section 2 North Jianshe Road Chengdu 610054 China Department of Plant Science and Landscape Architecture University of Maryland College Park MD 20742 USA Jiangsu key laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain Crops Key Laboratory of Plant Functional Genomics of the Ministry of Education Yangzhou University Yangzhou 225009 China Joint International Research laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China Yangzhou University Yangzhou 225009 China Indian Institute of Science Education and Research Timpati Andhra Pradesh 517507 India Seven Lakes High School Katy TX 77494 USA Institute for Bioscience and Biotechnology Research University of Maryland Rockville MD 20850 USA

Two recently engineered SpCas9 variants, namely xCas9 and Cas9-NG, show promising potential in improving targeting specificity and broadening the targeting range. In this study, we evaluated these Cas9 variants in the model and crop plant, rice. We first tested xCas9-3.7, the most effective xCas9 variant in mammalian cells, for targeted mutagenesis at 16 possible NGN PAM (protospacer adjacent motif) combinations in duplicates. xCas9 exhibited nearly equivalent editing efficiency to wild-type Cas9 (Cas9-WT) at most canonical NGG PAM sites tested, whereas it showed limited activity at non-canonical NGH (H = A, C, T) PAM sites. High editing efficiency of xCas9 at NGG PAMs was further demonstrated with C to T base editing by both rAPOBECI and PmCDAI cytidine deaminases. With mismatched sgRNAs, we found that xCas9 had improved targeting specificity over the Cas9-WT. Furthermore, we tested two Cas9-NG variants, Cas9-NGv1 and Cas9-NG, for targeting NGN PAMs. Both Cas9-NG variants showed higher editing efficiency at most non-canonical NG PAM sites tested, and enabled much more efficient editing than xCas9 at AT-rich PAM sites such as GAT, GAA, and CAA. Nevertheless, we found that Cas9-NG variants showed significant reduced activity at the canonical NGG PAM sites. In stable transgenic rice lines, we demonstrated that Cas9-NG had much higher editing efficiency than Cas9-NGv1 and xCas9 at NG PAM sites. To expand the base-editing scope, we developed an efficient C to T base-editing system by making fusion of Cas9-NG nickase (D10A version), PmCDAI, and UGI. Taken together, our work benchmarked xCas9 as a high-fidelity nuclease for targeting canonical NGG PAMs and Cas9-NG as a preferred variant for targeting relaxed PAMs for plant genome editing.

关键词： xCas9 Cas9-NG high fidelity non-canonical PAM base editing

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production of high-energy neutron beam from deuteron breakup

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Nuclear Science and Techniques 2022年第7期33卷 125-132页

作者： Ren-Sheng Wang Li Ou Zhi-Gang Xiao School of Radiation Medicine and Protection Medical College of Soochow UniversitySuzhou215123China Collaborative innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions Suzhou215123China College of Physics and Technology Guangxi Key Laboratory of Nuclear Physics and TechnologyGuangxi Normal UniversityGuilin541004China Department of Physics Tsinghua UniversityBeijing100084China

The deuteron breakup on heavy targets has been investigated in the framework of an improved quantum molecular dynamics model,focusing on the production of neutrons near zero *** experimental differential cross sections of neutron production in the 102 MeV d+C reactions were reproduced by *** on the consistency between the model prediction and experiment,the feasibility of producing a neutron beam through the breakup of deuteron on a carbon target was *** of the nucleon Fermi motion inside the deuteron,the energy spectrum of the inclusive neutron near 0°in the laboratory exhibits considerable energy broadening in the main peak,whereas the long tail on the low-energy side is *** coincidentally measuring the accompanying deuteron breakup proton,the energy of the neutron can be tagged with an intrinsic uncertainty of approximately 5%(1σ).The tagging efficiency of the accompanying proton on the forward-emitted neutron can reach 90%,which ensures that the differential cross section in the(d,np)channel remains two orders higher than that in(p,n)after considering the measurement of accompanying *** enables the application of a well-defined energy neutron beam in an event-by-event scheme.

关键词： Deuteron breakup Monochromatic neutron High energy Quantum molecular dynamics

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Mechanisms underlying the role of endoplasmic reticulum stress in the placental injury and fetal growth restriction in an ovine gestation model

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Journal of Animal Science and Biotechnology 2024年第1期15卷 201-217页

作者： Hao Zhang Xia Zha Yi Zheng Xiaoyun Liu Mabrouk Elsabagh Hongrong Wang Honghua Jiang Mengzhi Wang laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition College of Animal Science and TechnologyYangzhou UniversityYangzhou 225009P.R.China Joint International Research laboratory of Agriculture and Agri‑Product Safety Ministry of Education of ChinaYangzhou UniversityYangzhou 225009P.R.China Department of Animal production and Technology Faculty of Agricultural Sciences and TechnologiesNiğde Omer Halisdemir UniversityNigde 51240Turkey Department of Nutrition and Clinical Nutrition Faculty of Veterinary MedicineKafrelsheikh UniversityKafrelSheikhEgypt Department of Pediatrics Northern Jiangsu People’s HospitalClinical Medical CollegeYangzhou UniversityYangzhou 225001China State key laboratory of Sheep Genetic Improvement and Healthy production Xinjiang Academy of Agricultural Reclamation ScienceShihezi 832000China

Background Exposure to bisphenol A(BPA),an environmental pollutant known for its endocrine-disrupting properties,during gestation has been reported to increase the risk of fetal growth restriction(FGR)in an ovine model of *** hypothesized that the FGR results from the BPA-induced insufficiency and barrier dysfunction of the placenta,oxidative stress,inflammatory responses,autophagy and endoplasmic reticulum stress(ERS).However,precise mechanisms underlying the BPA-induced placental dysfunction,and subsequently,FGR,as well as the potential involvement of placental ERS in these complications,remain to be *** In vivo experiment,16 twin-pregnant(from d 40 to 130 of gestation)Hu ewes were randomly distributed into two groups(8 ewes each).One group served as a control and received corn oil once a day,whereas the other group received BPA(5 mg/kg/d as a subcutaneous injection).In vitro study,ovine trophoblast cells(OTCs)were exposed to 4 treatments,6 replicates *** OTCs were treated with 400μmol/L BPA,400μmol/L BPA+0.5μg/m L tunicamycin(Tm;ERS activator),400μmol/L BPA+1μmol/L 4-phenyl butyric acid(4-PBA;ERS antagonist)and DMEM/F12 complete medium(control),for 24 *** In vivo experiments,pregnant Hu ewes receiving the BPA from 40 to 130 days of pregnancy experienced a decrease in placental efficiency,progesterone(P4)level and fetal weight,and an increase in placental estrogen(E2)level,together with barrier dysfunctions,OS,inflammatory responses,autophagy and ERS in type A *** vitro experiment,the OTCs exposed to BPA for 24 h showed an increase in the E2 level and related protein and gene expressions of autophagy,ERS,pro-apoptosis and inflammatory response,and a decrease in the P4 level and the related protein and gene expressions of antioxidant,anti-apoptosis and barrier ***,treating the OTCs with Tm aggravated BPA-induced dysfunction of barrier and endocrine(the increased E2 level and decreased P4 level),OS,inflamm

关键词： Autophagy Bisphenol A Endoplasmic reticulum stress Fetal growth restriction Inflammatory responses Sheep

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High-fire-safety thermoplastic polyester constructed by novel sulfonate with benzimidazole structure

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Science China Materials 2021年第8期64卷 2067-2080页

作者： Wan-Shou Wu Ping-Hui Duan Yin-Long Wang Li Chen Xiu-Li Wang Yu-Zhong Wang The Collaborative innovation Center for Eco-Friendly and Fire-Safety Polymeric Materials(MoE) State Key Laboratory of Polymer Materials EngineeringNational Engineering Laboratory of Eco-Friendly Polymeric Materials(Sichuan)College of ChemistrySichuan UniversityChengdu 610064China

The flammability of thermoplastic polyesters and the subsequent heavy smoke and severe melt drips formed after ignition are the main obstacles hindering their widespread application. In this study, a novel ionic monomer containing sulfonate and benzimidazole was synthesized and incorporated into the main chain of poly(ethylene terephthalate)(PET, used as a model thermoplastic polyester) by melt copolymerization. The synergetic effect of ionic aggregation and carbonization endowed the obtained copolyester with high melt viscosity and excellent char-forming ability at high temperatures. The copolyester having a monomer content of 8 mol.% easily achieved the Underwriters Laboratories Inc 94(UL-94) V-0 flammability rating without dripping and the limiting oxygen index value reached 33.0 vol.%.In addition, the total smoke production, peak heat release rate,and maximum CO production decreased by 45.2%, 60.5%, and75.0%, respectively, compared with those of PET. In addition,the copolyester was spinnable, and showed greater adsorption efficiency(99.6%) for a cationic dye from solution compared to PET(6.5%), demonstrating the excellent affinity of the copolyester for the cationic dye. The obtained inherently firesafe PET copolyester has great potential for applications in flame retardant textiles, artwork base materials, and decorative materials for transportation applications.

关键词： fire safety thermoplastic polyester cross-linking network carbonization

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Impacts of climate change and agricultural activities on water quality in the Lower Kaidu River Basin,China

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Journal of Geographical Sciences 2020年第1期30卷 164-176页

作者： BA Wulong DU Pengfei LIU Tie BAO Anming CHEN Xi LIU Jiao QIN Chengxin State key laboratory of Environmental Simulation and Pollution Control School of EnvironmentTsinghua UniversityBeijing 100084China State key laboratory of Desert and Oasis Ecology Xinjiang Institute of Ecology and GeographyCASUrumqi 830011China School of Energy and Power Engineering Xihua UniversityChengdu 610039China

In the context of climate change and over-exploitation of water resources, water shortage and water pollution in arid regions have become major constraints to local sustainable development. In this study, we established a Soil and Water Assessment Tool (SWAT) model for simulating non-point source (NPS) pollution in the irrigation area of the lower reaches of the Kaidu River Basin, based on spatial and attribute data (2010-2014). Four climate change scenarios (2040-2044) and two agricultural management scenarios were input into the SWAT model to quantify the effects of climate change and agricultural management on solvents and solutes of pollutants in the study area. The simulation results show that compared to the reference period (2010-2014), with a decline in streamflow from the Kaidu River, the average annual irrigation water consumption is expected to decrease by 3.84x108 m3 or 8.87% during the period of 2040-2044. Meanwhile, the average annual total nitrogen (TN) and total phosphorus (TP) in agricultural drainage canals will also increase by 10.50% and 30.06%, respectively. Through the implementation of agricultural management measures, the TN and TP in farmland drainage can be reduced by 14.49% and 16.03%, respectively, reaching 661.56 t and 12.99 t, accordingly, and the increasing water efficiency can save irrigation water consumption by 4.41 x108 m3 or 4.77%. The results indicate that although the water environment in the irrigation area in the lower reaches of the Kaidu River Basin is deteriorating, the situation can be improved by implementing appropriate agricultural production methods. The quantitative analysis results of NPS pollutants in the irrigation area under different scenarios provide a scientific basis for water environmental management in the Kaidu River Basin.

关键词： climate change agricultural management non-point pollutants SWAT Kaidu River Basin water quality

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A rapid and accurate direct measurement method of underground coal seam gas content based on dynamic diffusion theory

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International Journal of Mining Science and Technology 2020年第6期30卷 799-810页

作者： Yanwei Liu Yang Du Zhiqiang Li Fajun Zhao Weiqin Zuo Jianping Wei Hani Mitri School of Safety Science and Engineering Henan Polytechnic UniversityJiaozuo 454000China The Collaborative innovation Center of Coal Safety production of Henan Province Jiaozuo 454000China Department of Mining and Materials Engineering McGill UniversityMontreal H3A0E8Canada School of Civil Engineering Henan Polytechnic UniversityJiaozuo 454000China

Coal seam gas content is frequently measured in quantity during underground coal mining operation and coalbed methane(CBM)exploration as a significant basic *** to the calculation error of lost gas and residual gas in the direct method,the efficiency and accuracy of the current methods are not inadequate to the large area multi-point measurement of coal seam gas *** paper firstly deduces a simplified theoretical dynamic model for calculating lost gas based on gas dynamic diffusion ***,the effects of various factors on gas dynamic diffusion from coal particle are experimentally *** sampling procedure of representative coal particle is ***,a new estimation method of residual gas content based on excess adsorption and competitive adsorption theory is *** results showed that the maximum error of calculating the losing gas content by using the new simplified model is only 4%.Considering the influence of particle size on gas diffusion law,the particle size of the collected coal sample is below 0.25 mm,which improves the measurement speed and reflects the safety representativeness of the *** determination time of gas content reduced from 36 to 3 h/***,the absolute error is 0.15–0.50 m^3/t,and the relative error is within 5%.A new engineering method for determining the coal seam gas content is developed according to the above research.

关键词： Coal seam gas content Dynamic diffusion model Determination method Lost gas content Desorption characteristics

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Numerical simulation for the investment casting process of a large-size titanium alloy thin-wall casing

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Progress in Natural Science:Materials International 2018年第4期28卷 520-528页

作者： Pan Tao Heng Shao Zhijun Ji Hai Nan Qingyan Xu key laboratory for Advanced Materials Processing Technology Ministry of Education School of Materials Science and Engineering Tsinghua University Beijing Institute of Aeronautical Materials

To optimize the investment casting process when producing high quality large-size titanium alloy thin-wall components is a time-consuming job due to the complicated metallurgical process. Numerical simulation is a high-efficiency method compared with trial and error, and therefore is introduced to the investment casting process optimization to shorten the new product development cycle and reduce the production cost. In this study, weakly compressible model(WCM) and ununiformed finite difference mesh(UFDM) was developed to reduce the memory consumption and ensure the simulation efficiency. The precision of the WCM and UFDM were verified by numerical simulation of cavity heat convection in a square cavity and hydraulics simulation of centrifugal filling in a transparent cavity. The numerical simulation of the investment casting process of a titanium alloy thin-wall casing under different process conditions was accomplished using a self-developed software, and the distribution characteristics of potential shrinkage defects were predicted. It was found that the predicted defects in the titanium alloy casing matched well with the actual X-ray experimental results. For the components investigated in this paper, more numerical simulation results show that the centrifugal casting process with respect to gravity casting had no obvious improvements in the concentrated shrinkage defects, and the gravity casting process can be more reasonable from the engineering point of view.

关键词： Titanium alloy Investment casting Numerical simulation Finite difference method Non-uniform mesh

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Grain carbon emission transfer and its spatiotemporal shifts based on the increasing supply-demand separation in China over the past three decades

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Science China Earth Sciences 2023年第5期66卷 1087-1107页

作者： Xinxian QI Xianjin HUANG Yaya SONG Danyang WANG Tianze ZHONG Zemiao LIU School of Geography and Ocean Science Nanjing UniversityNanjing210023China key laboratory of Carbon Neutrality and Territory Optimization Ministry of Natural ResourcesNanjing210023China

The food system is one of the major sources of anthropogenic greenhouse gas(GHG)*** impact of emission transfer due to the separation between food production and consumption within the context of carbon neutrality remains *** this study,we constructed an emission inventory for three types of grains at the production stage of their life cycle and then analysed the spatiotemporal evolution characteristics of the grain supply and *** the use of a spatial equilibrium model,we simulated the spatial distribution flow of the different types of grains from 1990 to 2018 and calculated the resulting GHG emission transfer *** main results include the following:(1)The imbalance between the grain supply and demand intensified,which was mainly reflected in the distance between the geographic centre of the grain supply and consumption increasing 3.2 times,and thus,the self-sufficiency decreased.(2)The total emission transfer TET of rice and wheat decreased because of the increase in the intra-regional supply,while that of maize gradually increased due to the increase in the inter-regional supply.(3)Overall,grain trade improved the carbon efficiency of grain production in *** trade efficiency of crops varied,with wheat and maize leading to overall effective carbon reductions,while the carbon transfer efficiency of rice from trade was relatively low.(4)The carbon footprint of grain production in China's provinces exhibited a downward trend,but due to the intensified separation between the grain supply and demand,certain major grain-producing areas achieved inefficient carbon ***,we suggest further optimization of the spatial structure of planting and breeding,strengthening of the grain supply in the region,and enhancement in the optimization of the low-carbon production structure and adjustment of cultivated land use combined with regional governance *** application of these measures could contribute to achieving d

关键词： Grains Life cycle Greenhouse gases Spatial equilibrium Transfer efficiency Spatiotemporal shifts

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Processing Map of C71500 Copper-nickel Alloy and Application in production Practice

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Journal of Wuhan University of Technology(Materials Science) 2020年第6期35卷 1104-1115页

作者： GAO Xin WU Huibin LIU Ming ZHANG Yuanxiang GAO Feng SUN Hui Institute of Engineering Technology University of Science and Technology BeijingBeijing 100083China General Research Institute of Nonferrous Metals Beijing 100088China Collaborative innovation Center of Steel Technology University of Science and Technology BeijingBeijing 100083China State key laboratory for Strength and Vibration of Mechanical Structures Xi'an Jiaotong UniversityXi'an 710049China The State key Lab of Rolling and Automation Northeastern UniversityShenyang 110819China School of Materials Science And Engineering Harbin Institute of TechnologyHarbin 150001China

The isothermal compression tests of C71500 copper-nickel alloy at different temperatures (1 073-1 273 K) and strain rates (0.01-10 s^-1) were carried out on Gleeble-3500 thermo-mechanical *** real stress-strain data were *** the basis of dynamic material model,the power dissipation was *** peak efficiency of the power dissipation is 57%.At the same time,Prasad’s,Murty’s and Babu’s instability criteria based on Ziegler’s expectant rheology theory,and Gegel’s and Malas’s instability criteria based on Lyaponov’s function theory,were used to predict the unstable regions in the processing *** maximum entropy generation rate and large plastic deformation principle are more in line with the hot deformation process of C71500 alloy,so the accuracy of Prasad’s instability criterion is much *** to the obtained macro-crack and micro-metallographic structure morphologies,the temperature range of 1 098-1 156 K and the strain rate range of 2.91-10 s^-1,and the temperature range of 1 171-1 273 K and the strain rate range of 0.01-0.33 s^-1 are more suitable for the processing area of C71500 *** accuracy of the above conclusions were verified by the forging of materials and the analysis of hot piercing *** significance of this paper is to provide theoretical basis and technological conditions for hot-press processing of C71500 alloy.

关键词： copper-nickel alloy processing map instability criteria verification forging hot piercing tubes

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A policy gradient algorithm integrating long and short-term rewards for soft continuum arm control

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Science China(Technological Sciences) 2022年第10期65卷 2409-2419页

作者： DONG Xiang ZHANG Jing CHENG Long XU WenJun SU Hang MEI Tao School of Electrical Engineering and Automation Anhui UniversityHefei 230601China State key laboratory for Control and Management of Complex Systems Institute of AutomationChinese Academy of SciencesBeijing 100190China Robotics Research Center Peng Cheng LaboratoryShenzhen 518055China

The soft continuum arm has extensive application in industrial production and human life due to its superior safety and flexibility. Reinforcement learning is a powerful technique for solving soft arm continuous control problems, which can learn an effective control policy with an unknown system model. However, it is often affected by the high sample complexity and requires huge amounts of data to train, which limits its effectiveness in soft arm control. An improved policy gradient method, policy gradient integrating long and short-term rewards denoted as PGLS, is proposed in this paper to overcome this issue. The shortterm rewards provide more dynamic-aware exploration directions for policy learning and improve the exploration efficiency of the algorithm. PGLS can be integrated into current policy gradient algorithms, such as deep deterministic policy gradient(DDPG). The overall control framework is realized and demonstrated in a dynamics simulation environment. Simulation results show that this approach can effectively control the soft arm to reach and track the targets. Compared with DDPG and other model-free reinforcement learning algorithms, the proposed PGLS algorithm has a great improvement in convergence speed and performance. In addition, a fluid-driven soft manipulator is designed and fabricated in this paper, which can verify the proposed PGLS algorithm in real experiments in the future.

关键词： soft arm control Cosserat rod deep reinforcement learning policy gradient algorithm high sample complexity

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