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1. Data Management Plans: the Importance of Data Management in the BIG-MAP Project

Author

Castelli, Ivano E., Arismendi-Arrieta, Daniel J., Bhowmik, Arghya, Cekic-Laskovic, Isidora, Clark, Simon, Dominko, Robert, Flores, Eibar, Flowers, Jackson, Frederiksen, Karina Ulvskov, Friis, Jesper, Grimaud, Alexis, Hansen, Karin Vels, Hardwick, Laurence J., Hermansson, Kersti, Königer, Lukas, Lauritzen, Hanne, Cras, Frédéric Le, Li, Hongjiao, Lyonnard, Sandrine, Lorrmann, Henning, Marzari, Nicola, Niedzicki, Leszek, Pizzi, Giovanni, Rahmanian, Fuzhan, Stein, Helge, Uhrin, Martin, Wenzel, Wolfgang, Winter, Martin, Wölke, Christian, and Vegge, Tejs

Subjects
Condensed Matter - Materials Science
Abstract

Open access to research data is increasingly important for accelerating research. Grant authorities therefore request detailed plans for how data is managed in the projects they finance. We have recently developed such a plan for the EU-H2020 BIG-MAP project - a cross-disciplinary project targeting disruptive battery-material discoveries. Essential for reaching the goal is extensive sharing of research data across scales, disciplines and stakeholders, not limited to BIG-MAP and the European BATTERY 2030+ initiative but within the entire battery community. The key challenges faced in developing the data management plan for such a large and complex project were to generate an overview of the enormous amount of data that will be produced, to build an understanding of the data flow within the project and to agree on a roadmap for making all data FAIR. This paper describes the process we followed and how we structured the plan., Comment: 12 pages, 4 figures; the full DMP is published as Supporting Information

Published
2021

2. Phenolic cross-links: building and de-constructing the plant cell wall

Author

Mnich, Ewelina, Bjarnholt, Nanna, Eudes, Aymerick, Harholt, Jesper, Holland, Claire, Jørgensen, Bodil, Larsen, Flemming Hofmann, Liu, Ming, Manat, Renil, Meyer, Anne S, Mikkelsen, Jørn Dalgaard, Motawia, Mohammed Saddik, Muschiol, Jan, Møller, Birger Lindberg, Møller, Svenning Rune, Perzon, Alixander, Petersen, Bent Larsen, Ravn, Jonas Laukkonen, and Ulvskov, Peter

Subjects
Organic Chemistry, Chemical Sciences, Carbohydrate Sequence, Cell Wall, Phenols, Plants, Biological Sciences, Medical and Health Sciences, Medicinal and biomolecular chemistry, Traditional, complementary and integrative medicine
Abstract

Covering: Up to 2019Phenolic cross-links and phenolic inter-unit linkages result from the oxidative coupling of two hydroxycinnamates or two molecules of tyrosine. Free dimers of hydroxycinnamates, lignans, play important roles in plant defence. Cross-linking of bound phenolics in the plant cell wall affects cell expansion, wall strength, digestibility, degradability, and pathogen resistance. Cross-links mediated by phenolic substituents are particularly important as they confer strength to the wall via the formation of new covalent bonds, and by excluding water from it. Four biopolymer classes are known to be involved in the formation of phenolic cross-links: lignins, extensins, glucuronoarabinoxylans, and side-chains of rhamnogalacturonan-I. Lignins and extensins are ubiquitous in streptophytes whereas aromatic substituents on xylan and pectic side-chains are commonly assumed to be particular features of Poales sensu lato and core Caryophyllales, respectively. Cross-linking of phenolic moieties proceeds via radical formation, is catalyzed by peroxidases and laccases, and involves monolignols, tyrosine in extensins, and ferulate esters on xylan and pectin. Ferulate substituents, on xylan in particular, are thought to be nucleation points for lignin polymerization and are, therefore, of paramount importance to wall architecture in grasses and for the development of technology for wall disassembly, e.g. for the use of grass biomass for production of 2nd generation biofuels. This review summarizes current knowledge on the intra- and extracellular acylation of polysaccharides, and inter- and intra-molecular cross-linking of different constituents. Enzyme mediated lignan in vitro synthesis for pharmaceutical uses are covered as are industrial exploitation of mutant and transgenic approaches to control cell wall cross-linking.

Published
2020

3. Cell walls have a new family

Author

Ulvskov, Peter and Scheller, Henrik V

Subjects
Plant Biology, Biological Sciences, Cell Wall, Glycosyltransferases, Pectins, Plants, Crop and Pasture Production, Ecology, Plant biology
Abstract

Cell walls made mainly of polysaccharides are a distinguishing feature of plants. They play key roles in adaptation today and during pivotal evolutionary events, such as colonization of dry land and development of a water-conducting vascular system. A critical enzyme involved in cell wall biosynthesis has now been identified.

Published
2018

4. Identification of an algal xylan synthase indicates that there is functional orthology between algal and plant cell wall biosynthesis

Author

Jensen, Jacob Krüger, Busse‐Wicher, Marta, Poulsen, Christian Peter, Fangel, Jonatan Ulrik, Smith, Peter James, Yang, Jeong‐Yeh, Peña, Maria‐Jesus, Dinesen, Malene Hessellund, Martens, Helle Juel, Melkonian, Michael, Wong, Gane Ka‐Shu, Moremen, Kelley W, Wilkerson, Curtis Gene, Scheller, Henrik Vibe, Dupree, Paul, Ulvskov, Peter, Urbanowicz, Breeanna Rae, and Harholt, Jesper

Subjects
Plant Biology, Biological Sciences, Amino Acid Motifs, Biosynthetic Pathways, Cell Wall, Charophyceae, Evolution, Molecular, HEK293 Cells, Humans, Pentosyltransferases, Phylogeny, Plant Cells, biosynthesis, cell wall, evolution, IRX10, Klebsormidium flaccidum, Klebsormidium nitens, xylan, XYS1, Agricultural and Veterinary Sciences, Plant Biology & Botany, Plant biology, Climate change impacts and adaptation, Ecological applications
Abstract

Insights into the evolution of plant cell walls have important implications for comprehending these diverse and abundant biological structures. In order to understand the evolving structure-function relationships of the plant cell wall, it is imperative to trace the origin of its different components. The present study is focused on plant 1,4-β-xylan, tracing its evolutionary origin by genome and transcriptome mining followed by phylogenetic analysis, utilizing a large selection of plants and algae. It substantiates the findings by heterologous expression and biochemical characterization of a charophyte alga xylan synthase. Of the 12 known gene classes involved in 1,4-β-xylan formation, XYS1/IRX10 in plants, IRX7, IRX8, IRX9, IRX14 and GUX occurred for the first time in charophyte algae. An XYS1/IRX10 ortholog from Klebsormidium flaccidum, designated K. flaccidumXYLAN SYNTHASE-1 (KfXYS1), possesses 1,4-β-xylan synthase activity, and 1,4-β-xylan occurs in the K. flaccidum cell wall. These data suggest that plant 1,4-β-xylan originated in charophytes and shed light on the origin of one of the key cell wall innovations to occur in charophyte algae, facilitating terrestrialization and emergence of polysaccharide-based plant cell walls.

Published
2018

8. Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution

Author

Schulman, Alan H., Yilmaz, Alper, Kalyanaraman, Anantharaman, Hsia, An-Ping, Oliveira, Antonio Costa de, Schnittger, Arp, Meyers, Blake C., Chalhoub, Boulos, Barbazuk, Brad, Sun, Cheng, Dardick, Christopher D., Sullivan, Christopher M., Cass, Cynthia L., Rokhsar, Dan, Garvin, David F., Laudencia-Chingcuanco, Debbie, O'Connor, Devin, Inzé, Dirk, Idziak, Dominika, Bryant, Douglas W., Chapman, Elisabeth J., Pritham, Ellen, Grotewold, Erich, Lindquist, Erika, Murat, Florent, Harmon, Frank, You, Frank M., Haberer, Georg, Tuskan, Gerald A., Lazo, Gerard R., May, Greg D., Mouille, Gregory, Wu, Haiyan, Belcram, Harry, Gundlach, Heidrun, Scheller, Henrik V., Priest, Henry D., Höfte, Herman, Budak, Hikmet, Tice, Hope, Baxter, Ivan, Tanskanen, Jaakko, Carrington, James C., Schnable, James, Thomson, James, Dvorak, Jan, Buchmann, Jan P., Grimwood, Jane, Higgins, Janet, Chang, Jeff H., Kimbrel, Jeffrey A., Bragg, Jennifer N., Schmutz, Jeremy, Pelloux, Jérome, Salse, Jerome, Harholt, Jesper, Wu, Jiajie, Ma, Jianxin, Lai, Jinsheng, Zhai, Jixian, Messing, Joachim, Rose, Jocelyn K. C., Sedbrook, John C., Vogel, John P., Wright, Jonathan, Lail, Kathleen, Barry, Kerrie, Hematy, Kian, Jung, Ki-Hong, Mayer, Klaus, Bartley, Laura E., Zhu, Liucun, Maia, Luciano da C., Tyler, Ludmila, Mueller, Lukas A., Sharma, Manoj K, Spannagl, Manuel, German, Marcelo, Heese, Maren, Byrne, Mary E., Charles, Mathieu, Ganssmann, Matthias, Wang, Mei, Febrer, Melanie, Abrouk, Michael, Bevan, Michael, Vega-Sanchez, Miguel, Luo, Ming-Cheng, Harmon-Smith, Miranda, Huo, Naxin, McKenzie, Neil, Jiang, Ning, Fahlgren, Noah, Anderson, Olin D., Green, Pamela J., Ronald, Pamela, Schnable, Patrick S., Cao, Peijian, and Ulvskov, Peter

Subjects
Brachypodium distachyon, Ehrhartoideae, Pancioideae, Pooideae, renewable energy
Abstract

Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops

Published
2009

29. Rhamnogalacturonan-I based microcapsules for targeted drug release

Author

Svagan, A. J., Kusic, A., De Gobba, C., Larsen, F. H., Sassene, P., Zhou, Qi, Van De Weert, M., Mullertz, A., Jørgensen, B., Ulvskov, P., Svagan, A. J., Kusic, A., De Gobba, C., Larsen, F. H., Sassene, P., Zhou, Qi, Van De Weert, M., Mullertz, A., Jørgensen, B., and Ulvskov, P.

Abstract

Drug targeting to the colon via the oral administration route for local treatment of e.g. inflammatory bowel disease and colonic cancer has several advantages such as needle-free administration and low infection risk. A new source for delivery is plant-polysaccharide based delivery platforms such as Rhamnogalacturonan-I (RG-I). In the gastro-intestinal tract the RG-I is only degraded by the action of the colonic microflora. For assessment of potential drug delivery properties, RG-I based microcapsules (~1 μm in diameter) were prepared by an interfacial poly-addition reaction. The cross-linked capsules were loaded with a fluorescent dye (model drug). The capsules showed negligible and very little in vitro release when subjected to media simulating gastric and intestinal fluids, respectively. However, upon exposure to a cocktail of commercial RG-I cleaving enzymes, ~ 9 times higher release was observed, demonstrating that the capsules can be opened by enzymatic degradation. The combined results suggest a potential platform for targeted drug delivery in the terminal gastro-intestinal tract., QC 20170210

Published
2016
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31. The Amborella Genome and the Evolution of Flowering Plants

Author

Albert, Va, Barbazuk, Wb, Depamphilis, Cw, Der, Jp, Leebens Mack, J, Ma, H, Palmer, Jd, Rounsley, S, Sankoff, D, Schuster, Sc, Soltis, De, Soltis, Ps, Wessler, Sr, Wing, Ra, Ammiraju, Js, Chamala, S, Chanderbali, As, Determann, R, Ralph, P, Talag, J, Tomsho, L, Walts, B, Wanke, S, Chang, Th, Lan, T, Arikit, S, Axtell, Mj, Ayyampalayam, S, Burnette JM 3rd, DE PAOLI, Emanuele, Estill, Jc, Farrell, Np, Harkess, A, Jiao, Y, Liu, K, Mei, W, Meyers, Bc, Shahid, S, Wafula, E, Zhai, J, Zhang, X, Carretero Paulet, L, Lyons, E, Tang, H, Zheng, C, Altman, Ns, Chen, F, Chen, Jq, Chiang, V, De Paoli, E, Fogliani, B, Guo, C, Harholt, J, Job, C, Job, D, Kim, S, Kong, H, Li, G, Li, L, Liu, J, Park, J, Qi, X, Rajjou, L, Burtet Sarramegna, V, Sederoff, R, Sun, Yh, Ulvskov, P, Villegente, M, Xue, Jy, Yeh, Tf, Yu, X, Acosta, Jj, Bruenn, Ra, de Kochko, A, Herrera Estrella LR, Ibarra Laclette, E, Kirst, M, Pissis, Sp, Poncet, V, Tomsho, L., Department of Biological Sciences, University at Buffalo [SUNY] (SUNY Buffalo), State University of New York (SUNY)-State University of New York (SUNY), Department of Biology, University of Florida [Gainesville], University of Florida Genetics Institute, Huck Institutes of the Life Sciences [University Park], Intercollege Plant Biology Graduate Program, Pennsylvania State University (Penn State), Penn State System-Penn State System, Center for Comparative Genomics and Bioinformatics, Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA, Université Paris Diderot - Paris 7 (UPD7), Department of Plant Biology [Athens], University of Georgia [USA], Penn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA, Penn State Univ, Dept Biol, University Pk, PA 16802 USA, Fudan Univ, Sch Life Sci, State Key Lab Genet Engn, Shanghai 200433, Peoples R China, Fudan Univ, Inst Genet, Inst Plant Biol, Ctr Evolutionary Biol,Inst Biomed Sci, Shanghai 200433, Peoples R China, Indiana Univ, Dept Biol, Bloomington, IN 47405 USA, Univ Arizona, Inst Collaborat Res BIO5, Tucson, AZ 85721 USA, Dow AgroSci, Indianapolis, IN 46268 USA, Univ Arizona, Sch Biol Sci, Tucson, AZ 85721 USA, Department of Mathematics and Statistics, University of Ottawa [Ottawa] (uOttawa), Singapore Ctr Environm Life Sci Engn, Singapore, Singapore, Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA, Florida Museum of Natural History, Department of Botany and Plant Sciences [Riverside], University of California [Riverside] (UCR), University of California-University of California, Univ Arizona, Arizona Genom Inst, Tucson, AZ 85721 USA, Atlanta Bot Garden, Atlanta, GA 30309 USA, Univ Florida, Dept Biol, Gainesville, FL 32611 USA, Tech Univ Dresden, Inst Bot, D-01062 Dresden, Germany, SUNY Buffalo, Dept Biol Sci, Buffalo, NY 14260 USA, Chongqing Univ Sci & Technol, Dept Biol, Chongqing 4000042, Peoples R China, Univ Delaware, Delaware Biotechnol Inst, Newark, DE 19711 USA, Univ Georgia, Dept Plant Biol, Athens, GA 30602 USA, Univ Udine, Dipartimento Sci Agr & Ambientali, I-33100 Udine, Italy, Penn State Univ, Intercoll Plant Biol Grad Program, University Pk, PA 16802 USA, Univ Arizona, iPlant Collaborat, Tucson, AZ 85721 USA, J Craig Venter Inst, Rockville, MD 20850 USA, Univ Ottawa, Dept Math & Stat, Ottawa, ON K1N 6N5, Canada, Penn State Univ, Dept Stat, University Pk, PA 16802 USA, Univ Tennessee, Dept Plant Sci, Knoxville, TN 37996 USA, Nanjing Univ, Sch Life Sci, Nanjing 210093, Jiangsu, Peoples R China, N Carolina State Univ, Dept Forestry & Environm Resources, Raleigh, NC 27695 USA, Institut Agronomique Néo-Calédonien (IAC), Univ New Caledonia, Lab Insulaire Vivant & Environm, Noumea 98851, New Caledonia, Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China, Univ Copenhagen, Dept Plant & Environm Sci, DK-1871 Frederiksberg C, Denmark, Univ Claude Bernard Lyon, Inst Natl Sci Appl Bayer CropSci Joint Lab UMR524, CNRS, Bayer CropSci, F-69263 Lyon 9, France, Sungshin Womens Univ, Basic Sci Res Inst, Seoul 142732, South Korea, Sungshin Womens Univ, Sch Biol Sci & Chem, Seoul 142732, South Korea, Zhejiang Univ, Coll Life Sci, Lab Systemat & Evolutionary Bot & Biodivers, Hangzhou 310058, Zhejiang, Peoples R China, Zhejiang Univ, Coll Life Sci, Key Lab Conservat Biol Endangered Wildlife, Minist Educ, Hangzhou 310058, Zhejiang, Peoples R China, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Natl Chung Hsing Univ, Dept Forestry, Taichung 40227, Taiwan, Natl Taiwan Univ, Sch Forestry & Resource Conservat, Taipei 10617, Taiwan, Univ Florida, Sch Forest Resources & Conservat, Gainesville, FL 32611 USA, Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA, 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), Lab Nacl Genom Biodiversidad, Irapuato 36821, Mexico, Univ Florida, Genet Inst, Gainesville, FL 32610 USA, Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611 USA, Heidelberg Inst Theoret Studies, Sci Comp Grp, D-69118 Heidelberg, Germany, NSF Plant Genome Research Program [0922742], NSF, University of Florida [Gainesville] (UF), University of Florida Genetics Institute (UFGI), Center for Comparative Genomics and Bioinformatics (CCBB), Department of Biology [PennState], State Key Laboratory of Genetic Engineering, Fudan University [Shanghai], Institute of Plant Biology [Shanghai], Department of Biology [Bloomington], Indiana University [Bloomington], Indiana University System-Indiana University System, BIO5 - Institute for Collaborative Bioresearch, University of Arizona, Dow AgroSciences LLC, School of Plant Sciences [Tucson], Department of Mathematics and Statistics [Ottawa], University of Ottawa [Ottawa], Singapore Centre for Environmental Life Sciences Engineering [Singapore] (SCELSE), Nanyang Technological University [Singapour], Department of Biochemistry and Molecular Biology [PennState], Arizona Genomics Institute [Tucson], Atlanta Botanical Garden, Department of Biology [Gainesville] (UF|Biology), Institut für Botanik [Dresden], Technische Universität Dresden = Dresden University of Technology (TU Dresden), Department of Biological Sciences [Buffalo], Department of Biology [Chongqing], Chongqing University of Science & Technology, Plant Genome Mapping Laboratory (PGML), Dipartimento di Scienze Agrarie e Ambientali (DiSA), Università degli Studi di Udine - University of Udine [Italie], iPlant Collaborative, J. Craig Venter Institute, Department of Statistics [PennState], Department of Plant Sciences [Knoxville], The University of Tennessee [Knoxville], School of Life Sciences [Nanjing] (SLiS), Nanjing University (NJU), Department of Forestry and Environmental Resources [Raleigh] (FER), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Université de la Nouvelle-Calédonie (UNC), State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany [Beijing] (IB-CAS), Chinese Academy of Sciences [Beijing] (CAS)-Chinese Academy of Sciences [Beijing] (CAS), Department of Plant and Environmental Sciences [Frederiksberg], University of Copenhagen = Københavns Universitet (KU), Microbiologie, adaptation et pathogénie (MAP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Génomique fonctionnelle des champignons pathogènes des plantes (FungiPath), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Basic Science Research Institute [Seoul], Sungshin Women's University, School of Biological Sciences and Chemistry [Seoul], Laboratory of Systematic & Evolutionary Botany and Biodiversity, Zhejiang University, Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Department of Forestry [Taichung], National Chung Hsing University (NCHU), School of Forestry and Resource Conservation [Taiwan], National Taïwan University (NTU), School of Forest Resources and Conservation [Gainesville] (UF|IFAS|FFGS), Institute of Food and Agricultural Sciences [Gainesville] (UF|IFAS), University of Florida [Gainesville] (UF)-University of Florida [Gainesville] (UF), Department of Plant and Microbial Biology [Berkeley], University of California [Berkeley], Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Florida Museum of Natural History [Gainesville], Heidelberg Institute for Theoretical Studies (HITS ), 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]), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL)

Subjects
0106 biological sciences, Most recent common ancestor, Genetics, Transposable element, 0303 health sciences, education.field_of_study, Multidisciplinary, Lineage (evolution), [SDV]Life Sciences [q-bio], Population, fungi, food and beverages, Biology, 01 natural sciences, Genome, 03 medical and health sciences, Gene duplication, Gene family, education, Gene, 030304 developmental biology, 010606 plant biology & botany
Abstract

Shaping Plant Evolution Amborella trichopoda is understood to be the most basal extant flowering plant and its genome is anticipated to provide insights into the evolution of plant life on Earth (see the Perspective by Adams ). To validate and assemble the sequence, Chamala et al. (p. 1516 ) combined fluorescent in situ hybridization (FISH), genomic mapping, and next-generation sequencing. The Amborella Genome Project (p. 10.1126/science.1241089 ) was able to infer that a whole-genome duplication event preceded the evolution of this ancestral angiosperm, and Rice et al. (p. 1468 ) found that numerous genes in the mitochondrion were acquired by horizontal gene transfer from other plants, including almost four entire mitochondrial genomes from mosses and algae.

Published
2013
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37. Pectic arabinan side chains are essential for pollen cell wall integrity during pollen development

Author

Cankar, K., Kortstee, A., Toonen, M.A.J., Wolters-Arts, M., Houbein, R., Mariani, C., Ulvskov, P., Jorgensen, B., Schols, H.A., Visser, R.G.F., Trindade, L.M., Cankar, K., Kortstee, A., Toonen, M.A.J., Wolters-Arts, M., Houbein, R., Mariani, C., Ulvskov, P., Jorgensen, B., Schols, H.A., Visser, R.G.F., and Trindade, L.M.

Abstract

Contains fulltext : 128101.pdf (publisher's version ) (Open Access)

Published
2014

38. Evidence for land plant cell wall biosynthetic mechanisms in charophyte green algae

Author

Mikkelsen, MD, Harholt, J, Ulvskov, P, Johansen, IE, Fangel, JU, Doblin, MS, Bacic, A, Willats, WGT, Mikkelsen, MD, Harholt, J, Ulvskov, P, Johansen, IE, Fangel, JU, Doblin, MS, Bacic, A, and Willats, WGT

Abstract

BACKGROUND AND AIMS: The charophyte green algae (CGA) are thought to be the closest living relatives to the land plants, and ancestral CGA were unique in giving rise to the land plant lineage. The cell wall has been suggested to be a defining structure that enabled the green algal ancestor to colonize land. These cell walls provide support and protection, are a source of signalling molecules, and provide developmental cues for cell differentiation and elongation. The cell wall of land plants is a highly complex fibre composite, characterized by cellulose cross-linked by non-cellulosic polysaccharides, such as xyloglucan, embedded in a matrix of pectic polysaccharides. How the land plant cell wall evolved is currently unknown: early-divergent chlorophyte and prasinophyte algae genomes contain a low number of glycosyl transferases (GTs), while land plants contain hundreds. The number of GTs in CGA is currently unknown, as no genomes are available, so this study sought to give insight into the evolution of the biosynthetic machinery of CGA through an analysis of available transcriptomes. METHODS: Available CGA transcriptomes were mined for cell wall biosynthesis GTs and compared with GTs characterized in land plants. In addition, gene cloning was employed in two cases to answer important evolutionary questions. KEY RESULTS: Genetic evidence was obtained indicating that many of the most important core cell wall polysaccharides have their evolutionary origins in the CGA, including cellulose, mannan, xyloglucan, xylan and pectin, as well as arabino-galactan protein. Moreover, two putative cellulose synthase-like D family genes (CSLDs) from the CGA species Coleochaete orbicularis and a fragment of a putative CSLA/K-like sequence from a CGA Spirogyra species were cloned, providing the first evidence that all the cellulose synthase/-like genes present in early-divergent land plants were already present in CGA. CONCLUSIONS: The results provide new insights into the evolution

Published
2014

39. Towards unravelling the biological significance of the individual components of pectic hairy regions in plants

Author

Oomen, R.J.F.J., Vincken, J.P., Bush, M.S., Skjot, M., Voragen, C.H.L., Ulvskov, P., Voragen, A.G.J., Mccann, M.C., Visser, R.G.F., Visser, J-P, Schols, null, and Voragen, A G J

Subjects
endocrine system, Food Chemistry, cell walls, galactans, poriëngrootte, EPS-3, fungi, food and beverages, galactanen, pectinen, Plant Breeding, pectins, Laboratorium voor Plantenveredeling, Levensmiddelenchemie, celwanden, pore size, plantenweefsels, plant tissues, VLAG
Abstract

This review compares the results from the developmental studies together with those from mutagenized and genetically modified plants with compositional alterations to the hairy region

Published
2003

40. Nanofibers Produced from Agro-Industrial Plant Waste Using Entirely Enzymatic Pretreatments

Author

Holland, Claire, Perzon, Alixander, Cassland, Pierre R. C., Jensen, John P., Langebeck, Birger, Sørensen, Ole Bandsholm, Whale, Eric, Hepworth, David, Plaice-Inglis, Robyn, Moestrup, Øjvind, Ulvskov, Peter, and Jørgensen, Bodil

Abstract

Cellulose fibers can be freed from the cell-wall skeleton via high-shear homogenization, to produce cellulose nanofibers (CNF) that can be used, for example, as the reinforcing phase in composite materials. Nanofiber production from agro-industrial byproducts normally involves harsh chemical-pretreatments and high temperatures to remove noncellulosic polysaccharides (20–70% of dry weight). However, this is expensive for large-scale processing and environmentally damaging. An enzyme-only pretreatment to obtain CNF from agro-industrial byproducts (potato and sugar beet) was developed with targeted commercial enzyme mixtures. It is hypothesized that cellulose can be isolated from the biomass, using enzymes only, due to the low lignin content, facilitating greater liberation of CNF via high-shear homogenization. Comprehensive Microarray Polymer Profiling (CoMPP) measured remaining extractable polysaccharides, showing that the enzyme-pretreatment was more successful at removing noncellulosic polysaccharides than alkaline- or acid-hydrolysis alone. While effective alone, the effect of the enzyme-pretreatment was bolstered via combination with a mild high-pH pretreatment. Dynamic rheology was used to estimate the proportion of CNF in resultant suspensions. Enzyme-pretreated suspensions showed 4-fold and 10-fold increases in the storage modulus for potato and sugar beet, respectively, compared to untreated samples. A greener yet facile method for producing CNF from vegetable waste is presented here.

Published
2018
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41. A new model describing pectin structure

Author

Vincken, J.P., Oomen, R., Bush, M., Ulvskov, P., Beldman, G., McCann, M., and Schols, H.A.

Subjects
Food Chemistry, Levensmiddelenchemie, Life Science, VLAG
Published
2001

42. Method for remodelling cell wall polysaccharide structures in plants

Author

Ulvskov, P., Schols, H.A., Visser, R.G.F., Borkhardt, B., Sorensen, S.O., Oomen, R.J.F.J., Vincken, J.P., Mc Cann, M., Skjot, M., Bush, M.S., Voragen, C.H.L., and Beldman, G.

Subjects
Plant Breeding, Laboratorium voor Plantenveredeling, Food Chemistry, Levensmiddelenchemie, Life Science, VLAG
Abstract

Methods for providing transgenic plants and parts hereof that, relative to the wild type state, is modified in a complex cell wall polysaccharide structure including pectins and hemicelluloses, the modification being in the overall glycosidic linkage pattern or the monosaccharide profile, comprising transforming a plant cell with a nucleotide sequence that causes an altered production of a complex cell wall polysaccharide-modifying enzyme such as endo-rhamnogalacturonan hydrolase, an endo-rhamnogalacturonan lyase, an endo-galactanase, an endo-arabinanase, an arabinofuranosidase, a galactosidase such as a beta-galactosidase, a xylosidase and an exo-galacturosidase. The modification can occur in vivo or post harvest, in which latter case the modifying enzyme is separated in the growing plant from its substrate, e.g. by targeting the enzyme to the Golgi, the endoplasmic reticulum or a vacuole, or is in a form that is inactive in the plant. After harvest the enzyme is brought into contact with its substrate or it is activated to provide the desired post harvest modification of the cell wall polysaccharide. The transgenic plant materials have improved functionalities and are useful in food and feed manufacturing and as pharmaceutically or medically active substances.

Published
2001

44. Remodelling Pectin Structure in Potato

Author

Vincken, J. P., Borkhardt, B., Bush, M., Doeswijk-Voragen, C., Berta Dopico, Labrador, E., Lange, L., Mccann, M., Morvan, C., Munoz, F., Oomen, R., Peugnet, I., Rudolph, B., Schols, H., Sorensen, S., Ulvskov, P., Voragen, A., Visser, R., de Vries, Gert E, and Metzlaff, Karin

Subjects
Food Chemistry, Levensmiddelenchemie, Life Science, VLAG
Published
2000

45. Physico-chemical characterization and cell behavior influence of surfaces modified by enzymatically-tailored pectic hairy polysaccharides

Author

Ceccone, G., Gilliland, D., Liakos, I., Cascardo, G., Cassinelli, C., Morra, M., Della Volpe, C., Rodriguez-Valverde, M., Siboni, S., Ischia, G., Segatta, G., Verhoef, R., Schols, W., Jorgensen, B., Ulvskov, P., Nagel, M. D., Ceccone, G., Gilliland, D., Liakos, I., Cascardo, G., Cassinelli, C., Morra, M., Della Volpe, C., Rodriguez-Valverde, M., Siboni, S., Ischia, G., Segatta, G., Verhoef, R., Schols, W., Jorgensen, B., Ulvskov, P., and Nagel, M. D.

Published
2008

47. High-throughput screening of monoclonal antibodies against plant cell wall glycans by hierarchical clustering of their carbohydrate microarray binding profiles

Author

Moller, I., Marcus, S.E., Haeger, A., Verhertbruggen, Y., Verhoef, R.P., Schols, H.A., Ulvskov, P., Mikkelsen, J.D., Knox, J.P., Willats, W.G.T., Moller, I., Marcus, S.E., Haeger, A., Verhertbruggen, Y., Verhoef, R.P., Schols, H.A., Ulvskov, P., Mikkelsen, J.D., Knox, J.P., and Willats, W.G.T.

Abstract

Antibody-producing hybridoma cell lines were created following immunisation with a crude extract of cell wall polymers from the plant Arabidopsis thaliana. In order to rapidly screen the specificities of individual monoclonal antibodies (mAbs), their binding to microarrays containing 50 cell wall glycans immobilized on nitrocellulose was assessed. Hierarchical clustering of microarray binding profiles from newly produced mAbs, together with the profiles for mAbs with previously defined specificities allowed the rapid assignments of mAb binding to antigen classes. mAb specificities were further investigated using subsequent immunochemical and biochemical analyses and two novel mAbs are described in detail. mAb LM13 binds to an arabinanase-sensitive pectic epitope and mAb LM14, binds to an epitope occurring on arabinogalactan-proteins. Both mAbs display novel patterns of recognition of cell walls in plant materials. Keywords Carbohydrate microarrays - Plant cell walls - Monoclonal antibodies - Hierarchical clustering

Published
2008

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