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1. Vision, challenges and opportunities for a Plant Cell Atlas.

Author

Plant Cell Atlas Consortium, Jha, Suryatapa Ghosh, Borowsky, Alexander T, Cole, Benjamin J, Fahlgren, Noah, Farmer, Andrew, Huang, Shao-Shan Carol, Karia, Purva, Libault, Marc, Provart, Nicholas J, Rice, Selena L, Saura-Sanchez, Maite, Agarwal, Pinky, Ahkami, Amir H, Anderton, Christopher R, Briggs, Steven P, Brophy, Jennifer An, Denolf, Peter, Di Costanzo, Luigi F, Exposito-Alonso, Moises, Giacomello, Stefania, Gomez-Cano, Fabio, Kaufmann, Kerstin, Ko, Dae Kwan, Kumar, Sagar, Malkovskiy, Andrey V, Nakayama, Naomi, Obata, Toshihiro, Otegui, Marisa S, Palfalvi, Gergo, Quezada-Rodríguez, Elsa H, Singh, Rajveer, Uhrig, R Glen, Waese, Jamie, Van Wijk, Klaas, Wright, R Clay, Ehrhardt, David W, Birnbaum, Kenneth D, and Rhee, Seung Y

Subjects
Plant Cell Atlas Consortium, 4D imaging, A. thaliana, Plant Cell Atlas, cell biology, chlamydomonas reinhardtii, location-to-function, maize, science forum, single-cell omics, translational research, Biochemistry and Cell Biology
Abstract

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

Published
2021

9. A separated vortex ring underlies the flight of the dandelion

Author

Cummins, Cathal, Seale, Madeleine, Macente, Alice, Certini, Daniele, Mastropaolo, Enrico, Viola, Ignazio Maria, and Nakayama, Naomi

Subjects
Dandelion -- Research, Botanical research, Vortex motion -- Research, Seed dispersal -- Research, Plant evolution, Resveratrol, Porosity, Seeds, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Wind-dispersed plants have evolved ingenious ways to lift their seeds.sup.1,2. The common dandelion uses a bundle of drag-enhancing bristles (the pappus) that helps to keep their seeds aloft. This passive flight mechanism is highly effective, enabling seed dispersal over formidable distances.sup.3,4; however, the physics underpinning pappus-mediated flight remains unresolved. Here we visualized the flow around dandelion seeds, uncovering an extraordinary type of vortex. This vortex is a ring of recirculating fluid, which is detached owing to the flow passing through the pappus. We hypothesized that the circular disk-like geometry and the porosity of the pappus are the key design features that enable the formation of the separated vortex ring. The porosity gradient was surveyed using microfabricated disks, and a disk with a similar porosity was found to be able to recapitulate the flow behaviour of the pappus. The porosity of the dandelion pappus appears to be tuned precisely to stabilize the vortex, while maximizing aerodynamic loading and minimizing material requirements. The discovery of the separated vortex ring provides evidence of the existence of a new class of fluid behaviour around fluid-immersed bodies that may underlie locomotion, weight reduction and particle retention in biological and manmade structures.The flight of dandelion seeds is enabled by an extraordinary vortex ring, which was revealed by the visualization of the flow around the seed., Author(s): Cathal Cummins [sup.1] [sup.2] [sup.3] , Madeleine Seale [sup.2] [sup.3] [sup.4] , Alice Macente [sup.2] [sup.4] [sup.5] , Daniele Certini [sup.1] , Enrico Mastropaolo [sup.4] , Ignazio Maria Viola [...]

Published
2018
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18. Environmental morphing enables informed dispersal of the dandelion diaspore

Author

Seale, Madeleine, primary, Zhdanov, Oleksandr, additional, Soons, Merel B, additional, Cummins, Cathal, additional, Kroll, Erika, additional, Blatt, Michael R, additional, Zare-Behtash, Hossein, additional, Busse, Angela, additional, Mastropaolo, Enrico, additional, Bullock, James M, additional, Viola, Ignazio M, additional, and Nakayama, Naomi, additional

Published
2022
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19. Author response: Environmental morphing enables informed dispersal of the dandelion diaspore

Author

Seale, Madeleine, primary, Zhdanov, Oleksandr, additional, Soons, Merel B, additional, Cummins, Cathal, additional, Kroll, Erika, additional, Blatt, Michael R, additional, Zare-Behtash, Hossein, additional, Busse, Angela, additional, Mastropaolo, Enrico, additional, Bullock, James M, additional, Viola, Ignazio M, additional, and Nakayama, Naomi, additional

Published
2022
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23. Technology generation to dissemination: lessons learned from the tef improvement project

Author

Cannarozzi, Gina, Chanyalew, Solomon, Assefa, Kebebew, Bekele, Abate, Blösch, Regula, Weichert, Annett, Klauser, Dominik, Plaza-Wüthrich, Sonia, Esfeld, Korinna, Jöst, Moritz, Rindisbacher, Abiel, Jifar, Habte, Johnson-Chadwick, Victoria, Abate, Ermias, Wang, Wuyan, Kamies, Rizqah, Husein, Negussu, Kebede, Worku, Tolosa, Kidist, Genet, Yazachew, Gebremeskel, Kidu, Ferede, Brikti, Mekbib, Firew, Martinelli, Federico, Pedersen, Hans Christian, Rafudeen, Suhail, Hussein, Shimelis, Tamiru, Muluneh, Nakayama, Naomi, Robinson, Mike, Barker, Ian, Zeeman, Samuel, and Tadele, Zerihun

Published
2018
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27. Morphology, Development and Phenotypic Plasticity in Tef

Author

Wight, Tara, Robinson, Sarah, Kebede, Worku, Assefa, Kebebew, Chanyalew, Solomon, Tadele, Zerihun, and Nakayama, Naomi

Subjects
580 Plants (Botany)
Abstract

Due to the large influence of the environment on plant development and morphology, there is a lot of potential to use a variety of crop management processes to improve tef production. A major benefit of this is that these methods can be used to promote development of desirable traits in tef varieties already preferred by farmers. Initiatives such as Sustainable Rice Intensification (SRI), a basic system of crop management practises for rice, are already improving cereal crop performance around the world (Mishra et al., 2006).

Published
2022
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35. Interleukin-8 and clinical symptoms can be prognostic indicators for advanced cancer patients with cachexia

Author

Murai, Miyo, Higashiguchi, Takashi, Futamura, Akihiko, Ohara, Hiroshi, Tsuzuki, Norimasa, Itani, Yoshinori, Kaneko, Takaaki, Chihara, Takeshi, Shimpo, Kan, and Nakayama, Naomi

Subjects
lcsh:R5-920, Cachexia, Advanced cancer, Cytokines, Original Article, lcsh:Medicine (General), Prognostic factors
Abstract

Objectives: Prognostic prediction is a significant tool for selecting appropriate treatment in advanced cancer patients with cachexia, at a time when it is important to offer high-quality palliative care and improve quality of life until death. In this retrospective study, we investigated the prognostic potential of serum cytokine level and various clinical symptoms by analyzing the pathological conditions and metabolic dynamics of cachexia in advanced cancer patients. Methods: One hundred and fifty-three advanced cancer patients who underwent palliative care and died at the Department of Surgery and Palliative Medicine, Fujita Health University Nanakuri Memorial Hospital between 1 January 2004 and 30 June 2007 were eligible for the study. We simultaneously assessed their blood factors and clinical symptoms at admission. All patients were divided into two groups according to median survival time to analyze the risk factors for prognosis. Results: Multivariate analysis revealed the following independent prognostic factors: interleukin (IL)-8 (odds ratio [OR]=4.17, 95% confidence interval [CI]=1.52–11.41, p=0.002), general fatigue (OR=1.22, 95%CI=1.03–1.45, p=0.019), anorexia (OR=1.19, 95%CI=1.04–1.37, p=0.008), dyspnea (OR=1.19, 95%CI=1.02–1.38, p=0.024), depression (OR=1.28, 95%CI=1.11–1.47, p

Published
2020

39. What is quantitative plant biology?

Author

Autran, Daphné, Bassel, George W., Chae, Eunyoung, Ezer, Daphne, Ferjani, Ali, Fleck, Christian, Hamant, Olivier, Hartmann, Félix P., Jiao, Yuling, Johnston, Iain G., Kwiatkowska, Dorota, Lim, Boon L., Mahönen, Ari Pekka, Morris, Richard J., Mulder, Bela M., Nakayama, Naomi, Sozzani, Ross, Strader, Lucia C., Ten Tusscher, Kirsten, Ueda, Minako, Wolf, Sebastian, Sub Theoretical Biology, Theoretical Biology and Bioinformatics, Sub Theoretical Biology, Theoretical Biology and Bioinformatics, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of Birmingham [Birmingham], National University of Singapore (NUS), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Tokyo Gakugei University, University of Freiburg [Freiburg], Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), University of Chinese Academy of Sciences [Beijing] (UCAS), University of Bergen (UiB), Silesian University in Opava, The University of Hong Kong (HKU), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, John Innes Centre [Norwich], FOM Institute for Atomic and Molecular Physics (AMOLF), Imperial College London, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC), Utrecht University [Utrecht], Tohoku University [Sendai], Universität Heidelberg [Heidelberg], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Biotechnology and Biological Sciences Research Council (BBSRC), and Universität Heidelberg [Heidelberg] = Heidelberg University

Subjects
0106 biological sciences, 0301 basic medicine, Computer science, biology, Ecology (disciplines), Rehabilitation, biomathematics, Physical Therapy, Sports Therapy and Rehabilitation, General Medicine, Plant, Plant biology, 01 natural sciences, Data science, Field (computer science), 03 medical and health sciences, 030104 developmental biology, Robustness (computer science), Citizen science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Noise (video), quantitative plant biology, Topology (chemistry), 010606 plant biology & botany, Interdisciplinarity
Abstract

Quantitative plant biology is an interdisciplinary field that builds on a long history of biomathematics and biophysics. Today, thanks to high spatiotemporal resolution tools and computational modelling, it sets a new standard in plant science. Acquired data, whether molecular, geometric or mechanical, are quantified, statistically assessed and integrated at multiple scales and across fields. They feed testable predictions that, in turn, guide further experimental tests. Quantitative features such as variability, noise, robustness, delays or feedback loops are included to account for the inner dynamics of plants and their interactions with the environment. Here, we present the main features of this ongoing revolution, through new questions around signalling networks, tissue topology, shape plasticity, biomechanics, bioenergetics, ecology and engineering. In the end, quantitative plant biology allows us to question and better understand our interactions with plants. In turn, this field opens the door to transdisciplinary projects with the society, notably through citizen science.

Published
2021

41. Vision, challenges and opportunities for a Plant Cell Atlas

Author

Ahmed, Jahed, Alaba, Oluwafemi, Ameen, Gazala, Arora, Vaishali, Arteaga-Vazquez, Mario A, Arun, Alok, Bailey-Serres, Julia, Bartley, Laura E, Bassel, George W, Bergmann, Dominique C, Bertolini, Edoardo, Bhati, Kaushal Kumar, Blanco-Touriñán, Noel, Briggs, Steven P, Brumos, Javier, Buer, Benjamin, Burlaocot, Adrien, Cervantes-Pérez, Sergio Alan, Chen, Sixue, Contreras-Moreira, Bruno, CORPAS, Francisco J, Cruz-Ramirez, Alfredo, Cuevas-Velazquez, Cesar L, Cuperus, Josh T, David, Lisa I, de Folter, Stefan, Denolf, Peter H, Ding, Pingtao, Dwyer, William P, Evans, Matthew MS, George, Nancy, Handakumbura, Pubudu P, Harrison, Maria J, Haswell, Elizabeth S, Herath, Venura, Jiao, Yuling, Jinkerson, Robert E, John, Uwe, Joshi, Sanjay, Joshi, Abhishek, Joubert, Lydia-Marie, Katam, Ramesh, Kaur, Harmanpreet, Kazachkova, Yana, Raju, Sunil K Kenchanmane, Khan, Mather A, Khangura, Rajdeep, Kumar, Ajay, Kumar, Arun, Kumar, Pankaj, Kumar, Pradeep, Lavania, Dhruv, Lew, Tedrick Thomas Salim, Lewsey, Mathew, Lin, Chien-Yuan, Liu, Dianyi, Liu, Le, Liu, Tie, Lokdarshi, Ansul, Luong, Ai My, Macaulay, Iain C, Mahmud, Sakil, Mähönen, Ari Pekka, Malukani, Kamal Kumar, Marand, Alexandre P, Martin, Carly A, McWhite, Claire D, Mehta, Devang, Martín, Miguel Miñambres, Mortimer, Jenny C, Nikolov, Lachezar A, Nobori, Tatsuya, Nolan, Trevor M, Ogden, Aaron J, Otegui, Marisa S, Ott, Mark-Christoph, Palma, José M, Paul, Puneet, Rehman, Atique U, Romera-Branchat, Maida, Romero, Luis C, Roth, Ronelle, Sah, Saroj K, Shahan, Rachel, Solanki, Shyam, Song, Bao-Hua, Sozzani, Rosangela, Stacey, Gary, Stepanova, Anna N, Taylor, Nicolas L, Tello-Ruiz, Marcela K, Tran, Tuan M, Tripathi, Rajiv Kumar, Vadde, Batthula Vijaya Lakshmi Vadde, Varga, Tamas, Vidovic, Marija, Walley, Justin W, Wang, Zhiyong, Weizbauer, Renate A, Whelan, James, Wijeratne, Asela J, Xiang, Tingting, Xu, Shouling, Yadegari, Ramin, Yu, Houlin, Yuan, Hai Ying, Zanini, Fabio, Zhao, Feng, Zhu, Jie, Zhuang, Xiaohong, Jha, Suryatapa Ghosh, Borowsky, Alexander T, Cole, Benjamin J, Fahlgren, Noah, Farmer, Andrew, Huang, Shao-shan Carol, Karia, Purva, Libault, Marc, Provart, Nicholas J, Rice, Selena L, Saura-Sanchez, Maite, Agarwal, Pinky, Ahkami, Amir H, Anderton, Christopher R, Brophy, Jennifer AN, Denolf, Peter, Di Costanzo, Luigi F, Exposito-Alonso, Moises, Giacomello, Stefania, Gomez-Cano, Fabio, Kaufmann, Kerstin, Ko, Dae Kwan, Kumar, Sagar, Malkovskiy, Andrey V, Nakayama, Naomi, Obata, Toshihiro, Palfalvi, Gergo, Quezada-Rodríguez, Elsa H, Singh, Rajveer, Uhrig, R Glen, Waese, Jamie, Van Wijk, Klaas, Wright, R Clay, Ehrhardt, David W, Birnbaum, Kenneth D, and Rhee, Seung Y

Subjects
Uncategorized
Abstract

Note: for full list of Plant Cell Atlas Consortium, see publication (p17). With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.

Published
2021
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48. Primary osteosarcoma of ovary

Author

Yeasmin, Shamima, Nakayama, Kentaro, Ishibashi, Masako, Katagiri, Atsuko, Iida, Kouji, Manabe, Atsushi, Nabika, Toru, Nakayama, Naomi, and Miyazaki, Kohji

Published
2009
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50. Generating and characterizing single- and multi-gene mutants 1 of the Rubisco small subunit family in Arabidopsis

Author

Khumsupan, Panupon, Kozlowska, Marta A., Orr, Douglas J, Andreou, Andreas, Nakayama, Naomi, Patron, Nicola, Carmo-Silva, Elizabete, and McCormick, Alistair J

Subjects
photosynthesis, chloroplast, protoplasts, fungi, arabidopsis thaliana, T-DNA, food and beverages, rubisco, SpCas9, CRISPR/Cas9
Abstract

The primary CO2-fixing enzyme Rubisco limits the productivity of plants. The small subunit of Rubisco (SSU) can influence overall Rubisco levels and catalytic efficiency, and is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. However, SSUs are encoded for by a family of nuclear rbcS genes in plants, which makes them challenging to engineer and study. Here we have used CRISPR/Cas9 and T DNA insertion lines to generate a suite of single and multiple gene knockout mutants for the four members of the rbcS family in Arabidopsis, including two novel mutants 2b3b and 1a2b3b. 1a2b3b contained very low levels of Rubisco (ca. 3% relative to WT) and is the first example of a mutant with a homogenous Rubisco pool consisting of a single SSU isoform (1B). Growth under near-outdoor levels of light demonstrated Rubisco-limited growth phenotypes for several SSU mutants and the importance of the 1A and 3B isoforms. We also identified 1a1b as a likely lethal mutation, suggesting a key contributory role for the least expressed 1B isoform during early development. The successful use of CRISPR/Cas here suggests this is a viable approach for exploring the functional roles of SSU isoforms in plants.

Published
2020

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