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      Fifteen compelling open questions in plant cell biology

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          Abstract

          As scientists, we are at least as excited about the open questions—the things we do not know—as the discoveries. Here, we asked 15 experts to describe the most compelling open questions in plant cell biology. These are their questions: How are organelle identity, domains, and boundaries maintained under the continuous flux of vesicle trafficking and membrane remodeling? Is the plant cortical microtubule cytoskeleton a mechanosensory apparatus? How are the cellular pathways of cell wall synthesis, assembly, modification, and integrity sensing linked in plants? Why do plasmodesmata open and close? Is there retrograde signaling from vacuoles to the nucleus? How do root cells accommodate fungal endosymbionts? What is the role of cell edges in plant morphogenesis? How is the cell division site determined? What are the emergent effects of polyploidy on the biology of the cell, and how are any such “rules” conditioned by cell type? Can mechanical forces trigger new cell fates in plants? How does a single differentiated somatic cell reprogram and gain pluripotency? How does polarity develop de-novo in isolated plant cells? What is the spectrum of cellular functions for membraneless organelles and intrinsically disordered proteins? How do plants deal with internal noise? How does order emerge in cells and propagate to organs and organisms from complex dynamical processes? We hope you find the discussions of these questions thought provoking and inspiring.

          Abstract

          We asked 15 experts to address what they consider to be the most compelling open questions in plant cell biology and these are their questions.

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          Most cited references225

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          Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors.

          Differentiated cells can be reprogrammed to an embryonic-like state by transfer of nuclear contents into oocytes or by fusion with embryonic stem (ES) cells. Little is known about factors that induce this reprogramming. Here, we demonstrate induction of pluripotent stem cells from mouse embryonic or adult fibroblasts by introducing four factors, Oct3/4, Sox2, c-Myc, and Klf4, under ES cell culture conditions. Unexpectedly, Nanog was dispensable. These cells, which we designated iPS (induced pluripotent stem) cells, exhibit the morphology and growth properties of ES cells and express ES cell marker genes. Subcutaneous transplantation of iPS cells into nude mice resulted in tumors containing a variety of tissues from all three germ layers. Following injection into blastocysts, iPS cells contributed to mouse embryonic development. These data demonstrate that pluripotent stem cells can be directly generated from fibroblast cultures by the addition of only a few defined factors.
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            One thousand plant transcriptomes and the phylogenomics of green plants

            Green plants (Viridiplantae) include around 450,000–500,000 species 1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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              Stochastic gene expression in a single cell.

              Clonal populations of cells exhibit substantial phenotypic variation. Such heterogeneity can be essential for many biological processes and is conjectured to arise from stochasticity, or noise, in gene expression. We constructed strains of Escherichia coli that enable detection of noise and discrimination between the two mechanisms by which it is generated. Both stochasticity inherent in the biochemical process of gene expression (intrinsic noise) and fluctuations in other cellular components (extrinsic noise) contribute substantially to overall variation. Transcription rate, regulatory dynamics, and genetic factors control the amplitude of noise. These results establish a quantitative foundation for modeling noise in genetic networks and reveal how low intracellular copy numbers of molecules can fundamentally limit the precision of gene regulation.
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                Author and article information

                Journal
                Plant Cell
                Plant Cell
                plcell
                The Plant Cell
                Oxford University Press
                1040-4651
                1532-298X
                January 2022
                16 September 2021
                16 September 2021
                : 34
                : 1
                : 72-102
                Affiliations
                [1 ] Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University , Ithaca, New York 14853, USA
                [2 ] Department of Botany and Center for Quantitative Cell Imaging, University of Wisconsin-Madison , Wisconsin 53706, USA
                [3 ] Department of Biology and Center for Engineering Mechanobiology, Washington University in St Louis , Missouri 63130, USA
                [4 ] Department of Biology and Center for Lignocellulose Structure and Formation, The Pennsylvania State University, University Park , Pennsylvania 16802, USA
                [5 ] Crop Genetics, John Innes Centre, Norwich Research Park , Norwich NR4 7UH, UK
                [6 ] State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University , Tai’an, China
                [7 ] Boyce Thompson Institute , Ithaca, New York 14853, USA
                [8 ] Department of Plant Sciences, University of Oxford , Oxford OX1 3RB, UK
                [9 ] Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNR S , Lyon Cedex 07, France
                [10 ] Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University , Nagoya, Japan
                [11 ] Department of Biology, Reed College , Portland, Oregon 97202, USA
                [12 ] School of Integrative Plant Science, Section of Plant Biology and Section of Plant Breeding and Genetics, Cornell University , Ithaca, New York 14853, USA
                [13 ] Center for Sustainable Resource Science , RIKEN , Kanagawa 230-0045, Japan
                [14 ] Department of Biological Sciences, Graduate School of Science, The University of Toky o , Tokyo 113-0033, Japan
                [15 ] Gregor Mendel Institute of Molecular Plant Biology GmbH , Vienna 1030, Austria
                [16 ] Department of Plant Biology , Carnegie Institution for Science, Stanford, California 94305, USA
                [17 ] LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Pari s , Palaiseau Cedex 91128 France
                [18 ] Corteva Agriscience , Johnston, Iowa 50310, USA
                Author notes
                Author for correspondence: ahr75@ 123456cornell.edu
                [#]

                Authors are listed in the order in which their questions appear.

                Author information
                https://orcid.org/0000-0001-6685-2984
                https://orcid.org/0000-0003-4699-6950
                https://orcid.org/0000-0001-7881-2859
                https://orcid.org/0000-0001-7481-3571
                https://orcid.org/0000-0003-3905-8077
                https://orcid.org/0000-0002-3501-5857
                https://orcid.org/0000-0001-8716-1875
                https://orcid.org/0000-0001-8448-6906
                https://orcid.org/0000-0001-7524-8770
                https://orcid.org/0000-0002-1619-8643
                https://orcid.org/0000-0003-1579-9380
                https://orcid.org/0000-0001-6906-6620
                https://orcid.org/0000-0002-9209-8230
                https://orcid.org/0000-0003-1206-7096
                https://orcid.org/0000-0002-9991-6312
                https://orcid.org/0000-0001-6522-7722
                https://orcid.org/0000-0002-2780-4717
                https://orcid.org/0000-0002-5501-9281
                Article
                koab225
                10.1093/plcell/koab225
                8774073
                34529074
                165a1968-f069-47ae-b775-e8d28329d0a3
                © The Author(s) 2021. Published by Oxford University Press on behalf of American Society of Plant Biologists.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 2 September 2021
                : 14 June 2021
                : 18 October 2021
                Page count
                Pages: 31
                Funding
                Funded by: National Science Foundation (NSF);
                Award ID: MCB2114603
                Categories
                Focus on Cell Biology
                Reviews
                AcademicSubjects/SCI02286
                AcademicSubjects/SCI02287
                AcademicSubjects/SCI01270
                AcademicSubjects/SCI01280
                AcademicSubjects/SCI02288

                Plant science & Botany
                Plant science & Botany

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