1
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Whitlock C. Estella Bergere Leopold (1927-2024), passionate environmentalist who traced changing ecosystems. Nature 2024; 628:32. [PMID: 38532116 DOI: 10.1038/d41586-024-00905-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
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2
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Glausiusz J. Are women in research being led up the garden path? Nature 2024; 628:495-496. [PMID: 38622252 DOI: 10.1038/d41586-024-01093-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
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3
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Cai J, He R, Zhang Y, Zhang P, Zhu Y, Wang D. Protocol for detecting lncRNA-protein interaction in vivo using the yeast three-hybrid assay. STAR Protoc 2024; 5:102856. [PMID: 38285736 PMCID: PMC10839528 DOI: 10.1016/j.xpro.2024.102856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/07/2023] [Accepted: 01/12/2024] [Indexed: 01/31/2024] Open
Abstract
Analyses of long non-coding RNA (lncRNA)-protein interactions provide key clues for understanding the molecular basis of lncRNA-modulated biological processes. Here, we detail a yeast three-hybrid assay to identify the lncRNA-interacting protein. We describe steps for lncRNA bait preparation, screening an RNA-binding proteins (RBPs) cDNA library, and validation of the lncRNA-RBP interaction. The assay can also be further applied to delineate the region of RBP that mediates the RNA-protein interaction. For complete details on the use and execution of this protocol, please refer to Zhang et al.1.
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Affiliation(s)
- Jingjing Cai
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Reqing He
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Yongdi Zhang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Pengxiang Zhang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Youlin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China.
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4
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Jiang L, Yang J, He R, Zhu Y, Wang D. Protocol for detecting lncRNA-protein interactions in vitro by tRSA RNA pull-down assay. STAR Protoc 2024; 5:102818. [PMID: 38183656 PMCID: PMC10789616 DOI: 10.1016/j.xpro.2023.102818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/17/2023] [Accepted: 12/19/2023] [Indexed: 01/08/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) work together with diverse RNA-binding proteins (RBPs) to fulfill key regulations in important cellular functions. Here, we present a protocol to detect lncRNA-RBP interactions in vitro using a tRNA scaffold containing a streptavidin aptamer pull-down assay. We describe steps for preparing both protein and lncRNA transcripts, lncRNA-protein interaction detection with an in vitro binding assay, and western blot analysis. This protocol is applicable to screen for RNA-interacting proteins using cell lysates followed by mass spectrometry analysis. For complete details on the use and execution of this protocol, please refer to Yang et al. (2023).1.
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Affiliation(s)
- Liyun Jiang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Jun Yang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Reqing He
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Youlin Zhu
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China.
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5
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Kumar MN, Kalarikkal SP, Jayaram Y, Narayanan J, Sundaram GM. Protocol to produce plant-based hybrid nanovesicles from fresh turmeric and pepper using polyethylene glycol. STAR Protoc 2024; 5:102924. [PMID: 38430518 PMCID: PMC10918324 DOI: 10.1016/j.xpro.2024.102924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/17/2024] [Accepted: 02/14/2024] [Indexed: 03/04/2024] Open
Abstract
In addition to proteins, microRNAs, and lipids, plant-derived exosome-like nanovesicles (ENVs) are also enriched with host plant bioactives. Both curcumin and piperine are water insoluble, lack bioavailability, and are extracted by non-ecofriendly solvents. Herein, we present an eco-friendly protocol for co-isolating both curcumin and piperine in the form of hybrid ENVs. We describe steps for sample pre-processing, combined homogenization of plant materials, filtration, and differential centrifugation. We then detail procedures for polyethylene glycol-based fusion and precipitation of hybrid ENVs. For complete details on the use and execution of this protocol, please refer to Kumar et al.1.
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Affiliation(s)
- Meghana N Kumar
- Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka 570020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-CFTRI Campus, Mysuru, Karnataka 570020, India.
| | - Sreeram Peringattu Kalarikkal
- Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka 570020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-CFTRI Campus, Mysuru, Karnataka 570020, India
| | - Yashaswini Jayaram
- Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka 570020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-CFTRI Campus, Mysuru, Karnataka 570020, India
| | - Janakiraman Narayanan
- Department of Nanobiotechnology, Vision Research Foundation, Chennai, Tamil Nadu 600006, India
| | - Gopinath M Sundaram
- Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka 570020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-CFTRI Campus, Mysuru, Karnataka 570020, India.
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6
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Blanco-Touriñán N. Quantification of xylem connection defects during lateral root development in Arabidopsis. STAR Protoc 2024; 5:102786. [PMID: 38113142 PMCID: PMC10767186 DOI: 10.1016/j.xpro.2023.102786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/13/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023] Open
Abstract
The cellular and molecular mechanisms underlying the establishment of vascular connections between primary and lateral roots have recently gained significant attention. Here, I present a protocol to visualize and quantify xylem connection defects during lateral root development. I describe steps for employing stains to infer whether the defects observed in xylem bridges are associated with alterations in the xylem differentiation program, including programmed cell death and secondary cell wall deposition. For complete details on the use and execution of this protocol, please refer to Blanco-Touriñán et al. (2023) and Ursache et al. (2018).1,2.
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Affiliation(s)
- Noel Blanco-Touriñán
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland.
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7
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Majumder S, Parida S, Dey N. Protocol for imbibed seed piercing for Agrobacterium-mediated transformation of jute. STAR Protoc 2024; 5:102767. [PMID: 38085641 PMCID: PMC10726289 DOI: 10.1016/j.xpro.2023.102767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023] Open
Abstract
Here, we present a streamlined Agrobacterium-mediated transformation protocol for jute (Corchorus sp.). We describe steps to pierce and vacuum infiltrate imbibed jute seeds with Agrobacterium suspension. We then detail procedures for selecting transformed seeds by using a hygromycin-B-supplemented medium. This approach can achieve transformation efficiencies of 20.44% ± 1.17% and 15.55% ± 0.58% for tossa (C. olitorius) and white (C. capsularis) jute, respectively. Demanding minimal resources and time, this protocol can elevate genetic engineering research in jute fiber crops. For complete details on the use and execution of this protocol, please refer to Majumder et al. (2020).1.
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Affiliation(s)
- Shuvobrata Majumder
- Institute of Life Sciences, Nalco square, Bhubaneswar, Odisha 751023, India.
| | | | - Nrisingha Dey
- Institute of Life Sciences, Nalco square, Bhubaneswar, Odisha 751023, India
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8
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Santhanagopalan I, Netzl A, Mathur T, Smith A, Griffiths H, Holzer A. Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing. STAR Protoc 2024; 5:102764. [PMID: 38236771 PMCID: PMC10828896 DOI: 10.1016/j.xpro.2023.102764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/13/2023] [Accepted: 11/21/2023] [Indexed: 02/03/2024] Open
Abstract
The isolation of sufficient amounts of intact nuclei is essential to obtain high-resolution maps of chromatin accessibility via assay for transposase-accessible chromatin using sequencing (ATAC-seq). Here, we present a protocol for tag-free isolation of nuclei from both cell walled and cell wall-deficient strains of the green model alga Chlamydomonas reinhardtii at a suitable quality for ATAC-seq. We describe steps for nuclei isolation, quantification, and downstream ATAC-seq. This protocol is optimized to shorten the time of isolation and quantification of nuclei.
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Affiliation(s)
- Indu Santhanagopalan
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.
| | - Antonia Netzl
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Tanya Mathur
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Alison Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Andre Holzer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; Center for Bioinformatics and Department of Computer Science, Saarland University, 66123 Saarbrücken, Germany.
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9
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Roychoudhry S, Greenberg JT, Cecchini NM. Protocol for analyzing the movement and uptake of isotopically labeled signaling molecule azelaic acid in Arabidopsis. STAR Protoc 2024; 5:102944. [PMID: 38470913 PMCID: PMC10945267 DOI: 10.1016/j.xpro.2024.102944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/01/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Understanding the generation, movement, uptake, and perception of mobile defense signals is key for unraveling the systemic resistance programs in flowering plants against pathogens. Here, we present a protocol for analyzing the movement and uptake of isotopically labeled signaling molecule azelaic acid (AZA) in Arabidopsis thaliana. We describe steps to assess 14C-AZA uptake into leaf discs and its movement from local to systemic tissues. We also detail the assay for uptake and movement of 2H-AZA from roots to the shoot. For complete details on the use and execution of this protocol, please refer to Cecchini et al.1,2.
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Affiliation(s)
| | - Jean T Greenberg
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 929 East 57th Street GCIS 524W, Chicago, IL 60637, USA.
| | - Nicolás M Cecchini
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Departamento de Química Biológica-Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, Córdoba X5000HUA, Argentina.
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10
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Irwin A. The 'Mother Tree' idea is everywhere - but how much of it is real? Nature 2024; 627:718-721. [PMID: 38531992 DOI: 10.1038/d41586-024-00893-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
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11
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Nordling L. Why I wander with wonder through Lesotho's wetlands. Nature 2024; 627:458. [PMID: 38467882 DOI: 10.1038/d41586-024-00726-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
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12
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Ledford H. CRISPR-edited crops break new ground in Africa. Nature 2024; 626:245-246. [PMID: 38278939 DOI: 10.1038/d41586-024-00176-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
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13
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Bourzac K. Glow way! Bioluminescent houseplant hits US market for first time. Nature 2024; 626:701. [PMID: 38337056 DOI: 10.1038/d41586-024-00383-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
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14
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Blilou I. Unravelling how plant cells divide and differ. Nature 2024; 626:484-485. [PMID: 38297053 DOI: 10.1038/d41586-024-00041-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
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15
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Nogrady B. All arabica coffee is genetically similar: how can beans taste so different? Nature 2024:10.1038/d41586-024-00165-x. [PMID: 38263307 DOI: 10.1038/d41586-024-00165-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
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16
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Gewin V. How I fuse Western science with Traditional Knowledge. Nature 2024; 625:416. [PMID: 38191712 DOI: 10.1038/d41586-024-00018-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
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17
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Marshall M. How CRISPR could yield the next blockbuster crop. Nature 2024; 625:230-232. [PMID: 38195874 DOI: 10.1038/d41586-024-00015-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
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18
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Webster SS, Guerinot ML. How plants iron out the competing interests of growth and defence. Nature 2024; 625:671-672. [PMID: 38200336 DOI: 10.1038/d41586-023-03995-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
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19
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Kemp C, Thompson B. Audio long read: Apple revival - how science is bringing historic varieties back to life. Nature 2023:10.1038/d41586-023-03640-z. [PMID: 38001277 DOI: 10.1038/d41586-023-03640-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2023]
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20
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Gould J. Scientific illustration: striking the balance between creativity and accuracy. Nature 2023:10.1038/d41586-023-03391-x. [PMID: 37978277 DOI: 10.1038/d41586-023-03391-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
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21
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Gould J. The unexpected outcomes of artist-scientist collaborations. Nature 2023:10.1038/d41586-023-03390-y. [PMID: 37949986 DOI: 10.1038/d41586-023-03390-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
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22
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23
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Gewin V. Eavesdropping on plant chatter. Nature 2023; 623:880. [PMID: 37985834 DOI: 10.1038/d41586-023-03613-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
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24
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Monosson E. The plant poisons that shape our daily lives. Nature 2023; 622:689-690. [PMID: 37872288 DOI: 10.1038/d41586-023-03303-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
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25
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Kemp C. Apple revival: how science is bringing historic varieties back to life. Nature 2023; 622:446-449. [PMID: 37848522 DOI: 10.1038/d41586-023-03229-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
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26
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Weerathunga M. My quest for hidden treasures in Sri Lanka's flora. Nature 2023; 622:424. [PMID: 37814015 DOI: 10.1038/d41586-023-03164-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
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27
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Manyukwe C. I train farmers to use plant science in the fight against climate change. Nature 2023:10.1038/d41586-023-02914-w. [PMID: 37714984 DOI: 10.1038/d41586-023-02914-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
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28
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Genetic dissection of plants' airborne defences. Nature 2023. [PMID: 37704842 DOI: 10.1038/d41586-023-02770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
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29
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Beattie GA. Bacteria deliver water channels to infect plants. Nature 2023; 621:478-479. [PMID: 37704843 DOI: 10.1038/d41586-023-02767-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
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30
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Melaku Worede, crop genetics leader (1936-2023). Nature 2023; 621:33. [PMID: 37653262 DOI: 10.1038/d41586-023-02735-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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31
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Coleman J. This moss survived 165 million years - and now it's under threat from climate change. Nature 2023:10.1038/d41586-023-02514-8. [PMID: 37558789 DOI: 10.1038/d41586-023-02514-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
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32
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Venus flytraps shut their traps when flames approach. Nature 2023; 620:925. [PMID: 37620571 DOI: 10.1038/d41586-023-02654-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
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33
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Ferry G. Anna Atkins: pioneering botanical photographer who captured algae and ferns in ghostly blue images. Nature 2023; 620:31-32. [PMID: 37524922 DOI: 10.1038/d41586-023-02446-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
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34
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A picture of plant functional diversity on an oceanic island. Nature 2023. [PMID: 37438624 DOI: 10.1038/d41586-023-01998-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
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35
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Mehta D. EU proposal on CRISPR-edited crops is welcome - but not enough. Nature 2023; 619:437. [PMID: 37464084 DOI: 10.1038/d41586-023-02328-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
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36
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37
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Gewin V. Invasive palms and WWII damaged an island paradise. Could fungi help to restore it? Nature 2023; 618:662-665. [PMID: 37344652 DOI: 10.1038/d41586-023-01932-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
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38
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Monastersky R. Finding the Amazon's tallest trees - an epic quest to reach hidden giants. Nature 2023; 618:228-233. [PMID: 37286657 DOI: 10.1038/d41586-023-01828-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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39
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Jiang H, Yu T, Miao M, Liu H. Protocol for early warning of Diaporthe infection in kiwifruit soft rot by plasmonic dimer-enhanced Raman spectroscopy. STAR Protoc 2023; 4:102339. [PMID: 37243598 DOI: 10.1016/j.xpro.2023.102339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/09/2023] [Accepted: 05/04/2023] [Indexed: 05/29/2023] Open
Abstract
The pathogens of the Diaporthe genus are now considered to be the dominant pathogens of kiwifruit soft rot. Here, we present a protocol to construct nanoprobes for the Diaporthe genus and detect changes of surface-enhanced Raman spectroscopy for samples collected from infected kiwifruit. We describe steps for synthesis of gold nanoparticles, DNA extraction from kiwifruit, and construction of nanoprobes. We then detail classification of nanoparticles with different aggregation states through dark-field microscope (DFM) picture analysis using Fiji-ImageJ software. For complete details on the use and execution of this protocol, please refer to Yu et al. (2022).1.
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Affiliation(s)
- Hao Jiang
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, P.R. China
| | - Ting Yu
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, P.R. China
| | - Min Miao
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, P.R. China
| | - Honglin Liu
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230009, P.R. China.
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Pantazis DA. Clues to how water splits during photosynthesis. Nature 2023; 617:468-469. [PMID: 37138059 DOI: 10.1038/d41586-023-01388-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
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41
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Old and new cannabis compounds are found in an African herb. Nature 2023; 617:226. [PMID: 37142717 DOI: 10.1038/d41586-023-01462-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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42
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Odeny DA, Okoth MA. Africa-led group generates lablab crop genome. Nature 2023; 617:37-38. [PMID: 37069304 DOI: 10.1038/d41586-023-01022-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
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Callaway E. Wheat disease's global spread concerns researchers. Nature 2023:10.1038/d41586-023-01043-8. [PMID: 37041287 DOI: 10.1038/d41586-023-01043-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
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45
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Marris E. Stressed plants 'cry' - and some animals can probably hear them. Nature 2023; 616:229. [PMID: 36997712 DOI: 10.1038/d41586-023-00890-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
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46
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Mathew MM, Shanmukhan AP, Varapparambath V, Prasad K. Protocol for real-time imaging, polar protein quantification, and targeted laser ablation of regenerating shoot progenitors in Arabidopsis. STAR Protoc 2023; 4:102184. [PMID: 36952331 PMCID: PMC10064272 DOI: 10.1016/j.xpro.2023.102184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/20/2023] [Accepted: 02/23/2023] [Indexed: 03/24/2023] Open
Abstract
Here, we provide a protocol for real-time tracking of regenerating shoot progenitors, combined with polar protein quantification and targeted laser ablation of callus cells in Arabidopsis. Using Arabidopsis strains expressing GFP-labeled polar auxin efflux carrier, PINFORMED 1 (PIN1) protein, we detail steps to prepare the callus for time-lapse confocal imaging and track the progenitors expressing PIN1-GFP, followed by mapping and quantifying PIN1 polarity using Fiji/ImageJ. We then describe targeted laser ablation of cells and subsequent time-lapse imaging to study regeneration. For complete details on the use and execution of this protocol, please refer to Varapparambath et al. (2022).1.
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Affiliation(s)
- Mabel Maria Mathew
- Indian Institute of Science Education and Research (IISER), Pune 411008, India; Indian Institute of Science Education and Research (IISER), Thiruvananthapuram 695551, India.
| | - Anju Pallipurath Shanmukhan
- Indian Institute of Science Education and Research (IISER), Pune 411008, India; Indian Institute of Science Education and Research (IISER), Thiruvananthapuram 695551, India
| | - Vijina Varapparambath
- Indian Institute of Science Education and Research (IISER), Pune 411008, India; Indian Institute of Science Education and Research (IISER), Thiruvananthapuram 695551, India
| | - Kalika Prasad
- Indian Institute of Science Education and Research (IISER), Pune 411008, India; Indian Institute of Science Education and Research (IISER), Thiruvananthapuram 695551, India.
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Uranga M, Aragonés V, Daròs JA, Pasin F. Heritable CRISPR-Cas9 editing of plant genomes using RNA virus vectors. STAR Protoc 2023; 4:102091. [PMID: 36853698 PMCID: PMC9943877 DOI: 10.1016/j.xpro.2023.102091] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/05/2022] [Accepted: 01/17/2023] [Indexed: 02/11/2023] Open
Abstract
Viral vectors hold enormous potential for genome editing in plants as transient delivery vehicles of CRISPR-Cas components. Here, we describe a protocol to assemble plant viral vectors for single-guide RNA (sgRNA) delivery. The obtained viral constructs are based on compact T-DNA binary vectors of the pLX series and are delivered into Cas9-expressing plants through agroinoculation. This approach allows rapidly assessing sgRNA design for plant genome targeting, as well as the recovery of progeny with heritable mutations at targeted loci. For complete details on the use and execution of this protocol, please refer to Uranga et al. (2021)1 and Aragonés et al. (2022).2.
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Affiliation(s)
- Mireia Uranga
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022 Valencia, Spain.
| | - Verónica Aragonés
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022 Valencia, Spain.
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022 Valencia, Spain.
| | - Fabio Pasin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022 Valencia, Spain.
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Kumar R, Acharya V. Deep learning based protocol to construct an immune-related gene network of host-pathogen interactions in plants. STAR Protoc 2023; 4:101934. [PMID: 36525344 PMCID: PMC9791427 DOI: 10.1016/j.xpro.2022.101934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/14/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
Investigating network behavior from host-pathogen interactions is challenging. Here, we present the deep-learning-based protocol to construct an immune-related gene network and list the genes involved in the defense response of host to specific biotic stress. The protocol includes the steps to pre-process the interaction pairs and expression profile of plants treated with pathogen/control, feed as input for DLNet algorithm to rank genes based on their contribution to data classification. The top-ranked genes are subjected to module and enrichment analysis. For complete details on the use and execution of this protocol, please refer to Kumar et al. (2022).1.
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Affiliation(s)
- Ravi Kumar
- Functional Genomics and Complex System Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vishal Acharya
- Functional Genomics and Complex System Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Hirashima T, Endo T. Path unveiled for protein entry into chloroplasts. Nature 2023; 615:222-4. [PMID: 36854733 DOI: 10.1038/d41586-023-00539-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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50
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Arnold C. How Latin America's genomics revolution began - and why the field is under threat. Nature 2023; 615:754-756. [PMID: 36941379 DOI: 10.1038/d41586-023-00794-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
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