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Genome editing for plant research and crop improvement

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Journal of Integrative Plant Biology 2021年第1期63卷 3-33页

作者： Xiangqiang Zhan Yuming Lu Jian-Kang Zhu jose ramon botella State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticuture Northwest A&F UniversityXianyang 712100 Shanghai Center for Plant Stress Biology CAS Center of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China Department of Horticulture and Landscape Architecture Purdue UniversityWest LafayetteIndiana 47907USA School of Agriculture and Food Sciences University of QueenslandBrisbaneQueensland 4072Australia

The advent of clustered regularly interspaced short palindromic repeat(CRISPR) has had a profound impact on plant biology, and crop improvement. In this review, we summarize the state-of-the-art development of CRISPR technologies and their applications in plants, from the initial introduction of random small indel(insertion or deletion) mutations at target genomic loci to precision editing such as base editing, prime editing and gene targeting. We describe advances in the use of class 2, types II, V, and VI systems for gene disruption as well as for precise sequence alterations, gene transcription, and epigenome control.

关键词： CRISPR/Cas crop improvement genome editing plant research

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Perspectives on the Application of Genome-Editing Technologies in Crop Breeding

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Molecular Plant 2019年第8期12卷 1047-1059页

作者： Kai Hua Jinshan Zhang jose ramon botella Changle Ma Fanjiang Kong Baohui Liu Jian-Kang Zhu Shanghai Center for Plant Stress Biology CAS Center of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China School of Agriculture and Food Sciences University of QueenslandBrisbaneQLD 4072Australia Shandong Provincial Key Lab of Plant Stress School of Life SciencesShandong Normal UniversityJinanChina School of Life Sciences Guangzhou UniversityGuangzhouChina Department of Horticulture and Landscape Architecture Purdue UniversityWest LafayetteIN 47907USA

Most conventional and modern crop-improvement methods exploit natural or artificially induced genetic variations and require laborious characterization of the progenies of multiple generations derived from time-consuming genetic crosses.Genome-editing systems,in contrast,provide the means to rapidly modify genomes in a precise and predictable way,making it possible to introduce improvements directly into elite varieties.Here,we describe the range of applications available to agricultural researchers using existing genome-editing tools.In addition to providing examples of genome-editing applications in crop breeding,we discuss the technical and social challenges faced by breeders using genome-editing tools for crop improvement.

关键词： genome editing crop breeding mutations base editing plants

Gene Targeting by Homology-Directed Repair in Rice Using a Geminivirus-Based CRISPR/Cas9 System

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Molecular Plant 2017年第7期10卷 1007-1010页

作者： Mugui Wang Yuming Lu jose ramon botella Yanfei Mao Kai Hua Jian-kang Zhu Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences Shanghai 201602 China Plant Genetic Engineering Laboratory School of Agriculture and Food Sciences University of Queensland Brisbane QLD 4072 Austraria Department of Horticulture and Landscape Architecture Purdue University West Lafayette IN 47907 USA

Dear Editor, Rice （Oryza sativa） is the staple food for more than half of the world＇s population. Technologies enabling precise and efficient DNA knock-in or replacement, hereinafter referred to as KI, have the pot... 详细信息

关键词： DNA REPLICONS GENOME

A detailed procedure for CRISPR/Cas9-mediated gene editing in Arabidopsis thaliana

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Science Bulletin 2015年第15期60卷 1332-1347页

作者： Wenshan Liu Xiaohong Zhu Mingguang Lei Qingyou Xia jose ramon botella Jian-Kang Zhu Yanfei Mao School of Life Sciences Chongqing University Shanghai Center for Plant Stress Biology Shanghai Institutes of Biological Sciences Chinese Academy of Sciences State Key Laboratory of Silkworm Genome Biology Southwest University Department of Horticulture and Landscape Architecture Purdue University School of Agriculture and Food Sciences University of Queensland

The newly developed CRISPR(Clustered Regularly Interspaced Short Palindromic Repeats)/Cas(CRISPR-associated) system has emerged as an efficient tool for genome-editing, providing an alternative to classical mutagenesis and transgenic methods to study gene function and improve crop traits. CRISPR/Cas facilitates targeted gene editing through RNA-guided DNA cleavage followed by cellular DNA repair mechanisms that introduce sequence changes at the site of cleavage. Here we describe a detailed procedure for our previously developed and highly efficient CRISPR/Cas9 method that allows the generation of heritable-targeted gene mutations andcorrections in Arabidopsis. This protocol describes the strategies and steps for the selection of targets, design of single-guide RNA(sg RNA), vector construction and analysis of transgenic lines. We also offer a method to target two loci simultaneously using vectors containing two different sg RNAs. The principles described in this protocol can be applied to other plant species to generate stably inherited DNA modifications.

关键词： RNA编辑基因组拟南芥转基因载体 DNA裂解介导程序协议描述

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Review of MXenes as a component in smart textiles and an adsorbent for textile wastewater remediation

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Chinese Chemical Letters 2024年第2期35卷 208-222页

作者： Kaniz Farhana Kumaran Kadirgama Abu Shadate Faisal Mahamude Rajan jose Department of Apparel Engineering Bangladesh University of TextilesDhaka 1208Bangladesh Faculty of Mechanical and Automotive Engineering Technology Universiti Malaysia Pahang26600 PekanPahangMalaysia Center of Automotive Engineering Universiti Malaysia PahangMalaysia College of Engineering Universiti Malaysia Pahang26300 GambangPahangMalaysia Faculty of Industrial Sciences & Technology Universiti Malaysia Pahang26300 KuantanMalaysia Center of Intelligent Materials Universiti Malaysia Pahang26300 KuantanMalaysia

Two-dimensional(2D)MXenes have emerged as an archetypical layered material combining the properties of an organic-inorganic hybrid offering materials sustainability for a range of applications.Their surface functional groups and the associated chemical properties'tailorability through functionalizing MXenes with other materials as well as hydrophilicity and high conductivity enable them to be the best successor for various applications in textile industries,especially in the advancement of smart textiles and remediation of textile wastewater.MXene-based textile composite performs superb smartness in high-performance wearables as well as in the reduction of textile dyes from wastewater.This article critically reviews the significance of MXenes in two sectors of the textile industry.Firstly,we review the improvement of textile raw materials such as fiber,yarn,and fabric by using MXene as electrodes in supercapacitors,pressure sensors.Secondly,we review advancements in the removal of dyes from textile wastewater utilizing MXene as an absorbent by the adsorption process.MXene-based textiles demonstrated superior strength through the strong bonding between MXene and textile structures as well as the treatment of adsorbate by adsorbent(MXene in the adsorption process).We identify critical gaps for further research to enable their real-life applications.

关键词： Textile fibers Industrial wastewater treatment MAX phases Hybrid electrodes Adsorption

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Hepatocellular carcinoma-the role of the underlying liver disease in clinical practice

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World Journal of Gastroenterology 2024年第19期30卷 2488-2495页

作者： Angelo Zambam de Mattos Isadora Zanotelli Bombassaro Arndt Vogel jose D Debes Department of Internal Medicine Universidade Federal de Ciências da Saúde de Porto AlegreRSPorto Alegre 90020090Brazil Graduate Program in Medicine:Hepatology Federal University of Health Sciences of Porto AlegreRSPorto Alegre 90050-170Brazil Division of Gastroenterology Hepatology University of TorontoHannover M5R 0A3Canada Department of Medicine University of MinnesotaMinneapolisMN 55455United States

Hepatocellular carcinoma(HCC)is one of the most common causes of cancerrelated mortality.This particular type of cancer has the distinctive characteristic of mostly happening in individuals with an underlying liver disease.This makes the management of patients more challenging,since physicians must take into consideration two different conditions,the chronic liver disease and the tumor.The underlying liver disease has several implications in clinical practice,because different kinds of chronic liver disease can lead to varying degrees of risk of developing HCC,obstacles in surveillance,and differences in the efficacy of the treatment against HCC.A shift in the prevalence of liver diseases has been evident over the last few years,with viral hepatitis gradually losing the leading position as cause of HCC and metabolic dysfunction-associated steatotic liver disease gaining importance.Therefore,in an era of personalized medicine,it is imperative that physicians are aware of the underlying liver disease of individuals with HCC and its impact in the management of their tumors.

关键词： Hepatocellular carcinoma Etiology Epidemiology Surveillance Therapy

Predicting the clothing insulation through machine learning algorithms:A comparative analysis and a practical approach

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Building Simulation 2024年第5期17卷 839-855页

作者： Pablo Aparicio-Ruiz Elena Barbadilla-Martin jose Guadix Jesus Munuzuri Grupo de Ingenieria de Organizacion Escuela Tecnica Superior de IngenieriaUniversidad de SevillaCamino de los Descubrimientos S/N41092SevilleSpain

Since indoor clothing insulation is a key element in thermal comfort models,the aim of the present study is proposing an approach for predicting it,which could assist the occupants of a building in terms of recommendations regarding their ensemble.For that,a systematic analysis of input variables is exposed,and 13 regression and 12 classification machine learning algorithms were developed and compared.The results are based on data from 3352 questionnaires and 21 input variables from a field study in mixed-mode office buildings in Spain.Outdoor temperature at 6 a.m.,indoor air temperature,indoor relative humidity,comfort temperature and gender were the most relevant features for predicting clothing insulation.When comparing machine learning algorithms,decision tree-based algorithms with Boosting techniques achieved the best performance.The proposed model provides an efficient method for forecasting the clothing insulation level and its application would entail optimising thermal comfort and energy efficiency.

关键词： clothing insulation simulation adaptive thermal comfort behavioural adaptive actions machine learning

Examining the“revisability”benefit of hip resurfacing arthroplasty

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World Journal of Orthopedics 2024年第6期15卷 554-559页

作者： jose George Adam J Taylor Thomas P Schmalzried Department of Orthopedics Harbor UCLA Medical CenterTorranceCA 90509United States

BACKGROUND Hip resurfacing arthroplasty(HRA)is an alternative to total hip arthroplasty(THA)that is typically reserved for young active patients because it preserves bone.However,the benefits of HRA only hold true if conversion THA after failed HRA provides acceptable outcomes.AIM To compare patient reported outcomes for conversion THA after HRA failure to primary THA.METHODS A retrospective review of 36 patients(37 hips)that underwent conversion THA for failed HRA between October 2006 and May 2019 by a single surgeon was performed.Patient reported outcomes[modified Harris Hip Score(mHHS),University of California Los Angeles(UCLA)activity score]were obtained via an email-based responder-anonymous survey.Outcomes were compared to normative data of a primary THA cohort with similar demographics.Subgroup analysis was performed comparing outcomes of conversion THA for adverse local tissue reaction(ALTR)vs all other causes for failure.RESULTS The study group had a lower mHHS than the control group(81.7±13.8 vs 90.2±11.6,P<0.01);however,both groups had similar UCLA activity levels(7.5±2.3 vs 7.2±1.6,P=0.51).Patients that underwent conversion for non-ATLR causes had similar mHHS(85.2±11.5 vs 90.2±11.6,P=0.11)and higher UCLA activity levels(8.5±1.8 vs 7.2±1.6,P<0.01)compared to the control group.Patients that underwent conversion for ATLR had worse mHHS(77.1±14.5 vs 90.2±11.6,P<0.01)and UCLA activity levels(6.1±2.3 vs 7.2±1.6,P=0.05)when compared to the control group.CONCLUSION Patient outcomes equivalent to primary THA can be achieved following HRA conversion to THA.However,inferior outcomes were demonstrated for ALTR-related HRA failure.Patient selection and perhaps further studies examining alternative HRA bearing surfaces should be considered.

关键词： Total hip arthroplasty Hip resurfacing arthroplasty Conversion total hip arthroplasty Adverse local tissue reaction Patient reported outcome measures

Task Offloading in Edge Computing Using GNNs and DQN

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Computer Modeling in Engineering & Sciences 2024年第6期139卷 2649-2671页

作者： Asier Garmendia-Orbegozo jose David Nunez-Gonzalez Miguel Angel Anton Department of Applied Mathematics University of the Basque Country UPV/EHUEibar20600Spain TECNALIA Basque Research and Technology Alliance(BRTA)San Sebastian20009Spain

In a network environment composed of different types of computing centers that can be divided into different layers(clod,edge layer,and others),the interconnection between them offers the possibility of peer-to-peer task offloading.For many resource-constrained devices,the computation of many types of tasks is not feasible because they cannot support such computations as they do not have enough available memory and processing capacity.In this scenario,it is worth considering transferring these tasks to resource-rich platforms,such as Edge Data Centers or remote cloud servers.For different reasons,it is more exciting and appropriate to download various tasks to specific download destinations depending on the properties and state of the environment and the nature of the functions.At the same time,establishing an optimal offloading policy,which ensures that all tasks are executed within the required latency and avoids excessive workload on specific computing centers is not easy.This study presents two alternatives to solve the offloading decision paradigm by introducing two well-known algorithms,Graph Neural Networks(GNN)and Deep Q-Network(DQN).It applies the alternatives on a well-known Edge Computing simulator called PureEdgeSimand compares them with the two defaultmethods,Trade-Off and Round Robin.Experiments showed that variants offer a slight improvement in task success rate and workload distribution.In terms of energy efficiency,they provided similar results.Finally,the success rates of different computing centers are tested,and the lack of capacity of remote cloud servers to respond to applications in real-time is demonstrated.These novel ways of finding a download strategy in a local networking environment are unique as they emulate the state and structure of the environment innovatively,considering the quality of its connections and constant updates.The download score defined in this research is a crucial feature for determining the quality of a download path in the GNN training process and has not previous

关键词： Edge computing edge offloading fog computing task offloading