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Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the singlecell level

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Molecular Plant 2021年第3期14卷 372-383页

作者： andrew farmer Sandra Thibivilliers Kook Hui Ryu John Schiefelbein Marc Libault National Center for Genome Resources Santa FeNM 87505USA Department of Agronomy and Horticulture Center for Plant Science InnovationUniversity of Nebraska-LincolnBeadle CenterLincolnNE 68503USA Department of Molecular Cellularand Developmental BiologyUniversity of MichiganAnn ArborMI 48109USA

Similar to other complex organisms,plants consist of diverse and specialized cell types.The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-typespecific transcriptional programs.As a necessary step in gaining a deeper understanding of the regulatory mechanisms controlling plant gene expression,we report the use of single-nucleus RNA sequencing(sNucRNA-seq)and single-nucleus assay for transposase accessible chromatin sequencing(sNucATACseq)technologies on Arabidopsis roots.The comparison of our single-nucleus transcriptomes to the published protoplast transcriptomes validated the use of nuclei as biological entities to establish plant cell-type-specific transcriptomes.Furthermore,our sNucRNA-seq results uncovered the transcriptomes of additional cell subtypes not identified by single-cell RNA-seq.Similar to our transcriptomic approach,the sNucATAC-seq approach led to the distribution of the Arabidopsis nuclei into distinct clusters,suggesting the differential accessibility of chromatin between groups of cells according to their identity.To reveal the impact of chromatin accessibility on gene expression,we integrated sNucRNA-seq and sNucATAC-seq data and demonstrated that cell-type-specific marker genes display cell-type-specific patterns of chromatin accessibility.Our data suggest that the differential chromatin accessibility is a critical mechanism to regulate gene activity at the cell-type level.

关键词： single-cell RNA-seq single-nucleus ATAC-seq Arabidopsis root

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Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume

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Molecular Plant 2022年第12期15卷 1868-1888页

作者： Sergio Alan Cervantes-Pérez Sandra Thibivilliers Carole Laffont andrew D.farmer Florian Frugier Marc Libault Department of Agronomy and Horticulture Center for Plant Science InnovationUniversity of Nebraska-LincolnLincolnNE 68503USA Single Cell Genomics Core Facility Center for BiotechnologyUniversity of Nebraska-LincolnLincolnNE 68588USA Institute of Plant Sciences Paris-Saclay(IPS2) UniversitéParis-SaclayCNRSINRAEUniversitéParis-CitéUniversitéd’Evry91190 Gif-sur-YvetteFrance National Center for Genome Resources Santa FeNM 87505USA

Medicago truncatula is a model legume species that has been studied for decades to understand the symbiotic relationship between legumes and soil bacteria collectively named rhizobia.This symbiosis called nodulation is initiated in roots with the infection of root hair cells by the bacteria,as well as the initiation of nodule primordia from root cortical,endodermal,and pericycle cells,leading to the development of a new root organ,the nodule,where bacteria fix and assimilate the atmospheric dinitrogen for the benefit of the plant.Here,we report the isolation and use of the nuclei from mock and rhizobia-inoculated roots for the single nuclei RNA-seq(sNucRNA-seq)profiling to gain a deeper understanding of early responses to rhizobial infection in Medicago roots.A gene expression map of the Medicago root was generated,comprising 25 clusters,which were annotated as specific cell types using 119 Medicago marker genes and orthologs to Arabidopsis cell-type marker genes.A focus on root hair,cortex,endodermis,and pericycle cell types,showing the strongest differential regulation in response to a short-term(48 h)rhizobium inoculation,revealed not only known genes and functional pathways,validating the sNucRNA-seq approach,but also numerous novel genes and pathways,allowing a comprehensive analysis of early root symbiotic responses at a cell type-specific level.

关键词： Medicago root single-cell transcriptomic rhizobium nodule initiation root hair cells cortical cells

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Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume

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Molecular Plant 2023年第2期16卷 481-483页

作者： Sergio Alan Cervantes-Perez Sandra Thibivilliers Carole Laffont andrew D.farmer Florian Frugier Marc Libault 不详

In the originally published version of this work,a mistake appeared in Figure 1A wherein the red circles,meant to highlight differing areas of the two side-by-side UMAPs,were misaligned in the image.The corrected Figure 1,in which the red circles indicate areas of differing density within cluster#2,now appears both in the online article and below.The authors apologize for the confusion.

关键词： Figure circles mistake

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将医疗保健干预措施从试验转化为实践

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英国医学杂志中文版 2010年第6期13卷 361-365页

作者： Paul Glasziou Iain Chalmers Douglas G Altman Hilda Bastian IsabeUe Boutron Anne Brice Gro Jamtvedt andrew farmer Davina Ghersi Trish Groves Carl Heneghan Sophie Hill Simon Lewin Susan Michie Rafael Perera Valerie Pomeroy Julie Tilson Sasha Shepperd John W Williams 周久顺(译) 张孔来(校) Department of Public Health and Primary Care University of Oxford Oxford OX3 7LF James Lind Initiative Oxford OX2 7LG Centre for Statistics in Medicine Oxford OX2 6UD German Institute for Quality and Efficiency in Health Care Cologne Germany INSERM Universite Paris Paris France Norwegian Knowledge Centre for the Health Services Oslo Norway Department of Research Policy and Cooperation World Health Organization Geneva BMJ London Centre for Health Communication and Participation Australian Institute for Primary Care La Trobe University Victoria Australia Division of Psychology and Language Sciences University Coflege London London WC1E 7HB Health and Social Sciences Research Institute Faculty of Health University of East Anglia Norwich Division of Biokinesiology and Physical Therapy University of Southern California Los Angeles CA USA Duke Evidence -based Practice Center Duke University and Durham VA Medical Center Durham NC USA 中国医学科学院基础医学研究所流行病与卫生统计学教研室

成千上万的试验结果从未被用于实践，因为其发表的报告未能详细地描述具体的干预措施。如何才能改进这些报告呢？

关键词：干预措施医疗保健试验转化

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A Comprehensive Transcriptome Assembly of Pigeonpea （Cajanus cajan L.） using Sanger and Second-Generation Sequencing Platforms

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Molecular Plant 2012年第5期5卷 1020-1028页

作者： Himabindu Kudapa Arvind K. Bharti Steven B. Cannon andrew D. farmer Benjamin Mulaosmanovi Robin Kramer Abhishek Bohra Nathan T. Weeks John A. Crow Reetu Tuteja Trushar Shah Sutapa Dutta Deepak K. Gupta Archana Singh Kishor Gaikwad Tilak R. Sharma Gregory D. May Nagendra K. Singh Rajeev K. Varshney International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Patancheru 502324 india National Center for Genome Resources (NCGR) Santa Fe NM 87505 USA United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Corn Insects and Crop Genetics Research Unit Ames IA USA National Research Centre on Plant Biotechnology (NRCPB) Indian Agricultural Research Institute New Delhi 110 012 India Department of Agronomy Iowa State University Amens IA USA CGIAR Generation Challenge Programme (GCP) c/o ClMMYT 06600 Mexico DF Mexico

A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 million single end FLX/454 reads, and 18 353 Sanger expressed sequenced tags from more than 16 genotypes. The resultant transcriptome assembly, referred to as CcTA v2, comprised 21 434 transcript as- sembly contigs （TACs） with an N50 of 1510 bp, the largest one being -8 kb. Of the 21 434 TACs, 16 622 （77.5%） could be mapped on to the soybean genome build 1.0.9 under fairly stringent alignment parameters. Based on knowledge of intron junctions, 10 009 primer pairs were designed from 5033 TACs for amplifying intron spanning regions （ISRs）. By using in silico mapping of BAC-end-derived SSR loci of pigeonpea on the soybean genome as a reference, putative mapping posi- tions at the chromosome level were predicted for 6284 ISR markers, covering all 11 pigeonpea chromosomes. A subset of 128 ISR markers were analyzed on a set of eight genotypes. While 116 markers were validated, 70 markers showed one to three alleles, with an average of 0.16 polymorphism information content （PIC） value. In summary, the CcTA v2 transcript assembly and ISR markers will serve as a useful resource to accelerate genetic research and breeding applications in pigeonpea.

关键词： Cajanus cajan （L.） second-generation sequencing transcriptome assembly intron spanning region （ISR）markers.

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复合胰岛素疗法在2型糖尿病患者中的3年有效性研究

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中国处方药 2009年第12期8卷 59-59页

作者： Rury R. Holman andrew J. farmer Melanie J. Davies

背景及目的：支持给2型糖尿病患者在口服治疗的基础上添加特殊胰岛素方案的证据有限。在这项3年非盲法多中心临床试验中，本试验评估了708例二甲双胍和磺脲类治疗未达到最佳糖化血红蛋白水平的患者，添加特殊胰岛素后的治疗效果。

关键词：胰岛素疗法糖尿病患 2型有效性多中心临床试验复合血红蛋白水平口服治疗

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Connecting supplier and DoD blockchains for transparent part tracking

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Blockchain(Research and Applications) 2021年第3期2卷 17-30页

作者： Francis Asuncion Adam Brinckman Dwayne Cole Jeffrey Curtis Matt Davis Timothy Dunlevy Calvin farmer andrew Harrison Daniel P.Johnson Joshua Joyce Chris Klubertanz Jonathan Lane John Martin Jarek Nabrzyski Joel Neidig Deysi Olivares Gregory Robinson Gabriel Rodriguez Chris Root Karen Rowand Al Salour Jeff Score David Scott Ian Taylor Chandler Thompson Huy Truong Xiqun Wang Dale Warren NAVAIR USA SIMBA Chain PlymouthIN46563USA Center for Research Computing University of Notre DameNotre DameIN46556USA Indiana Technology and Manufacturing Companies(ITAMCO) PlymouthIN46563USA Boeing Company USA Naval Systems Inc.USA

Blockchains have been around for more than ten years,and since 2015,a plethora of systems have been launched to target more flexible use cases.More recently,several enterprise blockchain systems,such as Consensys Quorum and Hyperledger Fabric,have been launched to make blockchain simpler to apply in complex organizational configurations.In this paper,we identify a specific Department of Defense use case,extrapolate requirements,and perform a thorough assessment of the different layers of the blockchain stack to identify the existing state of the art and undertake a gap analysis of the technology for this context.We describe a platform that meets many of these challenges and show how we architected,designed,and implemented a solution for this use case for deployment at NAVAIR.This solution connects transactions from two separate blockchain systems,Consensys Quorum and Hyperledger Fabric,by using a graph-based approach that preserves privacy while enabling full transparency across the military and supplier networks.

关键词： Blockchain Smart contracts Supply chain Department of defense(DoD) GraphQL Enterprise blockchain systems

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Do farmers Respond to Training？--The Case of the Millennium Challenge Account （MCA）-Ghana Programme

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Journal of Food Science and Engineering 2013年第11期3卷 592-608页

作者： Robert Darko Osei Isaac Osei Akoto andrew Agyei-Holmes Hayford Mensah Ayerakwa Institute of Statistical Social and Economic Research University of Ghana Legon Accra Ghana Development Policy and Practice the Open University Milton Keynes MK7 6AA United Kingdom

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Prioritization of Crop Residues for Improving Productivity on Smallholder Dairy Farming Households in the Lake Victoria Crescent, Uganda

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Open Journal of Animal Sciences 2014年第2期4卷 103-111页

作者： andrew Mwebaze Atuhaire Swidiq Mugerwa Samuel Okello Kenneth Okello Lapenga Fred Kabi Jolly Mary Kabirizi Department of Agricultural Production College of Agricultural and Environmental Sciences Makerere University Kampala Uganda Department of Livestock and Industrial Resources College of Veterinary Medicine Animal Resources and Bio-Security Makerere University Kampala Uganda National Agricultural Research Institute (NARO) National Livestock Resources Research Institute (NaLIRRI) Tororo Uganda

Poor nutrition has been identified as a major constraint to productivity in smallholder dairy farming households in Uganda, particularly in Lake Victoria Crescent Agroecological Zone (LVZ). Clarification on nutritional potential of crop residues is central to formulation of sustainable dairy cattle nutrition strategies. Data were collected from 126 randomly selected respondents using structured and semi-structured questionnaires. farmers’ responses on crop residues utilization, handling, limitations, spatial and temporal variability were collected. Kruskal-Wallis test showed significant differences on utilization of available crop residues (X2 = 50.4, df = 4, p = 0.0001) among farmer’s rankings. It was established that maize stovers were major crop residues utilized and inadequate knowledge to process crop residues was ranked as a major limitation. The study provided basic information on the importance of crop residues. Further research studies should focus on improving the nutritive value of maize stover.

关键词： Haulms Stovers Nutritive Value Vine

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