Publications by authors named "Attila Molnar"

50 Publications

Non-perfectly matching small RNAs can induce stable and heritable epigenetic modifications and can be used as molecular markers to trace the origin and fate of silencing RNAs.

Nucleic Acids Res 2021 02;49(4):1900-1913

University of Edinburgh, Institute of Molecular Plant Sciences, Max Born Crescent, Edinburgh EH9 3BF, UK.

Short non-coding RNA molecules (sRNAs) play a fundamental role in gene regulation and development in higher organisms. They act as molecular postcodes and guide AGO proteins to target nucleic acids. In plants, sRNA-targeted mRNAs are degraded, reducing gene expression. In contrast, sRNA-targeted DNA sequences undergo cytosine methylation referred to as RNA-directed DNA methylation (RdDM). Cytosine methylation can suppress transcription, thus sRNAs are potent regulators of gene expression. sRNA-mediated RdDM is involved in genome stability through transposon silencing, mobile signalling for epigenetic gene control and hybrid vigour. Since cytosine methylation can be passed on to subsequent generations, RdDM contributes to transgenerational inheritance of the epigenome. Using a novel approach, which can differentiate between primary (inducer) and secondary (amplified) sRNAs, we show that initiation of heritable RdDM does not require complete sequence complementarity between the sRNAs and their nuclear target sequences. sRNAs with up to four regularly interspaced mismatches are potent inducers of RdDM, however, the number and disruptive nature of nucleotide polymorphisms negatively correlate with their efficacy. Our findings contribute to understanding how sRNA can directly shape the epigenome and may be used in designing the next generation of RNA silencing constructs.
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http://dx.doi.org/10.1093/nar/gkab023DOI Listing
February 2021

Cutin:cutin-acid endo-transacylase (CCT), a cuticle-remodelling enzyme activity in the plant epidermis.

Biochem J 2021 Feb;478(4):777-798

The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh EH9 3BF, U.K.

Cutin is a polyester matrix mainly composed of hydroxy-fatty acids that occurs in the cuticles of shoots and root-caps. The cuticle, of which cutin is a major component, protects the plant from biotic and abiotic stresses, and cutin has been postulated to constrain organ expansion. We propose that, to allow cutin restructuring, ester bonds in this net-like polymer can be transiently cleaved and then re-formed (transacylation). Here, using pea epicotyl epidermis as the main model, we first detected a cutin:cutin-fatty acid endo-transacylase (CCT) activity. In-situ assays used endogenous cutin as the donor substrate for endogenous enzymes; the exogenous acceptor substrate was a radiolabelled monomeric cutin-acid, 16-hydroxy-[3H]hexadecanoic acid (HHA). High-molecular-weight cutin became ester-bonded to intact [3H]HHA molecules, which thereby became unextractable except by ester-hydrolysing alkalis. In-situ CCT activity correlated with growth rate in Hylotelephium leaves and tomato fruits, suggesting a role in loosening the outer epidermal wall during organ growth. The only well-defined cutin transacylase in the apoplast, CUS1 (a tomato cutin synthase), when produced in transgenic tobacco, lacked CCT activity. This finding provides a reference for future CCT protein identification, which can adopt our sensitive enzyme assay to screen other CUS1-related enzymes.
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http://dx.doi.org/10.1042/BCJ20200835DOI Listing
February 2021

Rapid, high efficiency virus-mediated mutant complementation and gene silencing in .

Plant Methods 2020 27;16:145. Epub 2020 Oct 27.

Institute of Molecular Plant Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF UK.

Background: (snapdragon) species are models for genetic and evolutionary research but recalcitrant to genetic transformation, limiting use of transgenic methods for functional genomics. Transient gene expression from viral vectors and virus-induced gene silencing (VIGS) offer transformation-free alternatives. Here we investigate the utility of Tobacco rattle virus (TRV) for homologous gene expression in and VIGS in and its relative

Results: proved highly susceptible to systemic TRV infection. TRV carrying part of the () gene triggered efficient silencing, visible as tissue bleaching, providing a reporter for the extent and location of VIGS. VIGS was initiated most frequently in young seedlings, persisted into inflorescences and flowers and was not significantly affected by the orientation of the homologous sequence within the TRV genome. Its utility was further demonstrated by reducing expression of two developmental regulators that act either in the protoderm of young leaf primordia or in developing flowers. The effects of co-silencing and the trichome-suppressing () gene from the same TRV genome showed that tissue bleaching provides a useful marker for VIGS of a second target gene acting in a different cell layer. The ability of TRV-encoded H protein to complement the mutant phenotype was also tested. TRV carrying the native coding sequence with to report infection failed to complement mutations and triggered VIGS of in wild-type plants. However, a sequence with 43% synonymous substitutions encoding H protein, was able to complement the mutant phenotype when expressed without a VIGS reporter.

Conclusions: We demonstrate an effective method for VIGS in the model genus and its relative that works in vegetative and reproductive tissues. We also show that TRV can be used for complementation of a loss-of-function mutation in These methods make rapid tests of gene function possible in these species, which are difficult to transform genetically, and opens up the possibility of using additional cell biological and biochemical techniques that depend on transgene expression.
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http://dx.doi.org/10.1186/s13007-020-00683-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7590601PMC
October 2020

Potential for gene editing in antiviral resistance.

Curr Opin Virol 2020 06 5;42:47-52. Epub 2020 Jun 5.

The University of Edinburgh, Institute of Molecular Plant Sciences, Mayfield Road, Edinburgh, EH9 3BF, United Kingdom. Electronic address:

The discovery of CRISPR/Cas systems and their subsequent application in genome modifications and in gene expression control have fundamentally changed both basic and applied research. They have already been employed to generate novel virus resistance traits either by modifying host factors in the plant genome or by directly inducing targeted virus degradation. Here we summarise the latest developments in this field and discuss the potential applications and concerns around this technology.
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http://dx.doi.org/10.1016/j.coviro.2020.04.005DOI Listing
June 2020

Virus-induced Gene Silencing in Streptocarpus rexii (Gesneriaceae).

Mol Biotechnol 2020 Jul;62(6-7):317-325

Institute of Molecular Plant Sciences, University of Edinburgh, King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, Scotland, UK.

Many members of the family Gesneriaceae are cultivated as ornamental plants, including Cape primrose (Streptocarpus) species. The range of plant architecture found in this genus has also made it a model to study leaf and meristem development and their evolution. However, the lack of tools to study gene functions through reverse genetics in Streptocarpus has limited the exploitation of its genetic potential. To aid functional genomic studies in Streptocarpus rexii, we sought to investigate virus-induced gene silencing (VIGS). Using the broad host range Tobacco Rattle Virus (TRV) to target the PHYTOENE DESATURASE (PDS) gene of S. rexii, we show that infection with sap from Nicotiana benthamiana triggered VIGS efficiently. VIGS was most effective in the seedling leaves 8 weeks after sowing, but was limited in duration and systemic spread. This study reports the first successful use of VIGS in Streptocarpus and in the family Gesneriaceae. The inoculation of viral sap derived from N. benthamiana was able to overcome the difficulties of standard Agrobacterium-mediated transformation in this genus. Irrespective of its transient effect, this VIGS system will be useful to assess gene function at the cellular level and represent an important tool for further understanding molecular mechanisms in Streptocarpus.
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http://dx.doi.org/10.1007/s12033-020-00248-wDOI Listing
July 2020

Shared Mutations in a Novel Glutaredoxin Repressor of Multicellular Trichome Fate Underlie Parallel Evolution of Antirrhinum Species.

Curr Biol 2020 04 27;30(8):1357-1366.e4. Epub 2020 Feb 27.

University of Edinburgh, Institute of Molecular Plant Sciences, Max Born Crescent, Edinburgh EH9 3BF, UK. Electronic address:

Most angiosperms produce trichomes-epidermal hairs that have protective or more specialized roles. Trichomes are multicellular in almost all species and, in the majority, secretory. Despite the importance of multicellular trichomes for plant protection and as a source of high-value products, the mechanisms that control their development are only poorly understood. Here, we investigate the control of multicellular trichome patterns using natural variation within the genus Antirrhinum (snapdragons), which has evolved hairy alpine-adapted species or lowland species with a restricted trichome pattern multiple times in parallel. We find that a single gene, Hairy (H), which is needed to repress trichome fate, underlies variation in trichome patterns between all Antirrhinum species except one. We show that H encodes a novel epidermis-specific glutaredoxin and that the pattern of trichome distribution within individuals reflects the location of H expression. Phylogenetic and functional tests suggest that H gained its trichome-repressing role late in the history of eudicots and that the ancestral Antirrhinum had an active H gene and restricted trichome distribution. Loss of H function was involved in an early divergence of alpine and lowland Antirrhinum lineages, and the alleles underlying this split were later reused in parallel evolution of alpines from lowland ancestors, and vice versa. We also find evidence for an evolutionary reversal from a widespread to restricted trichome distribution involving a suppressor mutation and for a pleiotropic effect of H on plant growth that might constrain the evolution of trichome pattern.
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http://dx.doi.org/10.1016/j.cub.2020.01.060DOI Listing
April 2020

TRY plant trait database - enhanced coverage and open access.

Authors:
Jens Kattge Gerhard Bönisch Sandra Díaz Sandra Lavorel Iain Colin Prentice Paul Leadley Susanne Tautenhahn Gijsbert D A Werner Tuomas Aakala Mehdi Abedi Alicia T R Acosta George C Adamidis Kairi Adamson Masahiro Aiba Cécile H Albert Julio M Alcántara Carolina Alcázar C Izabela Aleixo Hamada Ali Bernard Amiaud Christian Ammer Mariano M Amoroso Madhur Anand Carolyn Anderson Niels Anten Joseph Antos Deborah Mattos Guimarães Apgaua Tia-Lynn Ashman Degi Harja Asmara Gregory P Asner Michael Aspinwall Owen Atkin Isabelle Aubin Lars Baastrup-Spohr Khadijeh Bahalkeh Michael Bahn Timothy Baker William J Baker Jan P Bakker Dennis Baldocchi Jennifer Baltzer Arindam Banerjee Anne Baranger Jos Barlow Diego R Barneche Zdravko Baruch Denis Bastianelli John Battles William Bauerle Marijn Bauters Erika Bazzato Michael Beckmann Hans Beeckman Carl Beierkuhnlein Renee Bekker Gavin Belfry Michael Belluau Mirela Beloiu Raquel Benavides Lahcen Benomar Mary Lee Berdugo-Lattke Erika Berenguer Rodrigo Bergamin Joana Bergmann Marcos Bergmann Carlucci Logan Berner Markus Bernhardt-Römermann Christof Bigler Anne D Bjorkman Chris Blackman Carolina Blanco Benjamin Blonder Dana Blumenthal Kelly T Bocanegra-González Pascal Boeckx Stephanie Bohlman Katrin Böhning-Gaese Laura Boisvert-Marsh William Bond Ben Bond-Lamberty Arnoud Boom Coline C F Boonman Kauane Bordin Elizabeth H Boughton Vanessa Boukili David M J S Bowman Sandra Bravo Marco Richard Brendel Martin R Broadley Kerry A Brown Helge Bruelheide Federico Brumnich Hans Henrik Bruun David Bruy Serra W Buchanan Solveig Franziska Bucher Nina Buchmann Robert Buitenwerf Daniel E Bunker Jana Bürger Sabina Burrascano David F R P Burslem Bradley J Butterfield Chaeho Byun Marcia Marques Marina C Scalon Marco Caccianiga Marc Cadotte Maxime Cailleret James Camac Jesús Julio Camarero Courtney Campany Giandiego Campetella Juan Antonio Campos Laura Cano-Arboleda Roberto Canullo Michele Carbognani Fabio Carvalho Fernando Casanoves Bastien Castagneyrol Jane A Catford Jeannine Cavender-Bares Bruno E L Cerabolini Marco Cervellini Eduardo Chacón-Madrigal Kenneth Chapin F Stuart Chapin Stefano Chelli Si-Chong Chen Anping Chen Paolo Cherubini Francesco Chianucci Brendan Choat Kyong-Sook Chung Milan Chytrý Daniela Ciccarelli Lluís Coll Courtney G Collins Luisa Conti David Coomes Johannes H C Cornelissen William K Cornwell Piermaria Corona Marie Coyea Joseph Craine Dylan Craven Joris P G M Cromsigt Anikó Csecserits Katarina Cufar Matthias Cuntz Ana Carolina da Silva Kyla M Dahlin Matteo Dainese Igor Dalke Michele Dalle Fratte Anh Tuan Dang-Le Jirí Danihelka Masako Dannoura Samantha Dawson Arend Jacobus de Beer Angel De Frutos Jonathan R De Long Benjamin Dechant Sylvain Delagrange Nicolas Delpierre Géraldine Derroire Arildo S Dias Milton Hugo Diaz-Toribio Panayiotis G Dimitrakopoulos Mark Dobrowolski Daniel Doktor Pavel Dřevojan Ning Dong John Dransfield Stefan Dressler Leandro Duarte Emilie Ducouret Stefan Dullinger Walter Durka Remko Duursma Olga Dymova Anna E-Vojtkó Rolf Lutz Eckstein Hamid Ejtehadi James Elser Thaise Emilio Kristine Engemann Mohammad Bagher Erfanian Alexandra Erfmeier Adriane Esquivel-Muelbert Gerd Esser Marc Estiarte Tomas F Domingues William F Fagan Jaime Fagúndez Daniel S Falster Ying Fan Jingyun Fang Emmanuele Farris Fatih Fazlioglu Yanhao Feng Fernando Fernandez-Mendez Carlotta Ferrara Joice Ferreira Alessandra Fidelis Bryan Finegan Jennifer Firn Timothy J Flowers Dan F B Flynn Veronika Fontana Estelle Forey Cristiane Forgiarini Louis François Marcelo Frangipani Dorothea Frank Cedric Frenette-Dussault Grégoire T Freschet Ellen L Fry Nikolaos M Fyllas Guilherme G Mazzochini Sophie Gachet Rachael Gallagher Gislene Ganade Francesca Ganga Pablo García-Palacios Verónica Gargaglione Eric Garnier Jose Luis Garrido André Luís de Gasper Guillermo Gea-Izquierdo David Gibson Andrew N Gillison Aelton Giroldo Mary-Claire Glasenhardt Sean Gleason Mariana Gliesch Emma Goldberg Bastian Göldel Erika Gonzalez-Akre Jose L Gonzalez-Andujar Andrés González-Melo Ana González-Robles Bente Jessen Graae Elena Granda Sarah Graves Walton A Green Thomas Gregor Nicolas Gross Greg R Guerin Angela Günther Alvaro G Gutiérrez Lillie Haddock Anna Haines Jefferson Hall Alain Hambuckers Wenxuan Han Sandy P Harrison Wesley Hattingh Joseph E Hawes Tianhua He Pengcheng He Jacob Mason Heberling Aveliina Helm Stefan Hempel Jörn Hentschel Bruno Hérault Ana-Maria Hereş Katharina Herz Myriam Heuertz Thomas Hickler Peter Hietz Pedro Higuchi Andrew L Hipp Andrew Hirons Maria Hock James Aaron Hogan Karen Holl Olivier Honnay Daniel Hornstein Enqing Hou Nate Hough-Snee Knut Anders Hovstad Tomoaki Ichie Boris Igić Estela Illa Marney Isaac Masae Ishihara Leonid Ivanov Larissa Ivanova Colleen M Iversen Jordi Izquierdo Robert B Jackson Benjamin Jackson Hervé Jactel Andrzej M Jagodzinski Ute Jandt Steven Jansen Thomas Jenkins Anke Jentsch Jens Rasmus Plantener Jespersen Guo-Feng Jiang Jesper Liengaard Johansen David Johnson Eric J Jokela Carlos Alfredo Joly Gregory J Jordan Grant Stuart Joseph Decky Junaedi Robert R Junker Eric Justes Richard Kabzems Jeffrey Kane Zdenek Kaplan Teja Kattenborn Lyudmila Kavelenova Elizabeth Kearsley Anne Kempel Tanaka Kenzo Andrew Kerkhoff Mohammed I Khalil Nicole L Kinlock Wilm Daniel Kissling Kaoru Kitajima Thomas Kitzberger Rasmus Kjøller Tamir Klein Michael Kleyer Jitka Klimešová Joice Klipel Brian Kloeppel Stefan Klotz Johannes M H Knops Takashi Kohyama Fumito Koike Johannes Kollmann Benjamin Komac Kimberly Komatsu Christian König Nathan J B Kraft Koen Kramer Holger Kreft Ingolf Kühn Dushan Kumarathunge Jonas Kuppler Hiroko Kurokawa Yoko Kurosawa Shem Kuyah Jean-Paul Laclau Benoit Lafleur Erik Lallai Eric Lamb Andrea Lamprecht Daniel J Larkin Daniel Laughlin Yoann Le Bagousse-Pinguet Guerric le Maire Peter C le Roux Elizabeth le Roux Tali Lee Frederic Lens Simon L Lewis Barbara Lhotsky Yuanzhi Li Xine Li Jeremy W Lichstein Mario Liebergesell Jun Ying Lim Yan-Shih Lin Juan Carlos Linares Chunjiang Liu Daijun Liu Udayangani Liu Stuart Livingstone Joan Llusià Madelon Lohbeck Álvaro López-García Gabriela Lopez-Gonzalez Zdeňka Lososová Frédérique Louault Balázs A Lukács Petr Lukeš Yunjian Luo Michele Lussu Siyan Ma Camilla Maciel Rabelo Pereira Michelle Mack Vincent Maire Annikki Mäkelä Harri Mäkinen Ana Claudia Mendes Malhado Azim Mallik Peter Manning Stefano Manzoni Zuleica Marchetti Luca Marchino Vinicius Marcilio-Silva Eric Marcon Michela Marignani Lars Markesteijn Adam Martin Cristina Martínez-Garza Jordi Martínez-Vilalta Tereza Mašková Kelly Mason Norman Mason Tara Joy Massad Jacynthe Masse Itay Mayrose James McCarthy M Luke McCormack Katherine McCulloh Ian R McFadden Brian J McGill Mara Y McPartland Juliana S Medeiros Belinda Medlyn Pierre Meerts Zia Mehrabi Patrick Meir Felipe P L Melo Maurizio Mencuccini Céline Meredieu Julie Messier Ilona Mészáros Juha Metsaranta Sean T Michaletz Chrysanthi Michelaki Svetlana Migalina Ruben Milla Jesse E D Miller Vanessa Minden Ray Ming Karel Mokany Angela T Moles Attila Molnár Jane Molofsky Martin Molz Rebecca A Montgomery Arnaud Monty Lenka Moravcová Alvaro Moreno-Martínez Marco Moretti Akira S Mori Shigeta Mori Dave Morris Jane Morrison Ladislav Mucina Sandra Mueller Christopher D Muir Sandra Cristina Müller François Munoz Isla H Myers-Smith Randall W Myster Masahiro Nagano Shawna Naidu Ayyappan Narayanan Balachandran Natesan Luka Negoita Andrew S Nelson Eike Lena Neuschulz Jian Ni Georg Niedrist Jhon Nieto Ülo Niinemets Rachael Nolan Henning Nottebrock Yann Nouvellon Alexander Novakovskiy Kristin Odden Nystuen Anthony O'Grady Kevin O'Hara Andrew O'Reilly-Nugent Simon Oakley Walter Oberhuber Toshiyuki Ohtsuka Ricardo Oliveira Kinga Öllerer Mark E Olson Vladimir Onipchenko Yusuke Onoda Renske E Onstein Jenny C Ordonez Noriyuki Osada Ivika Ostonen Gianluigi Ottaviani Sarah Otto Gerhard E Overbeck Wim A Ozinga Anna T Pahl C E Timothy Paine Robin J Pakeman Aristotelis C Papageorgiou Evgeniya Parfionova Meelis Pärtel Marco Patacca Susana Paula Juraj Paule Harald Pauli Juli G Pausas Begoña Peco Josep Penuelas Antonio Perea Pablo Luis Peri Ana Carolina Petisco-Souza Alessandro Petraglia Any Mary Petritan Oliver L Phillips Simon Pierce Valério D Pillar Jan Pisek Alexandr Pomogaybin Hendrik Poorter Angelika Portsmuth Peter Poschlod Catherine Potvin Devon Pounds A Shafer Powell Sally A Power Andreas Prinzing Giacomo Puglielli Petr Pyšek Valerie Raevel Anja Rammig Johannes Ransijn Courtenay A Ray Peter B Reich Markus Reichstein Douglas E B Reid Maxime Réjou-Méchain Victor Resco de Dios Sabina Ribeiro Sarah Richardson Kersti Riibak Matthias C Rillig Fiamma Riviera Elisabeth M R Robert Scott Roberts Bjorn Robroek Adam Roddy Arthur Vinicius Rodrigues Alistair Rogers Emily Rollinson Victor Rolo Christine Römermann Dina Ronzhina Christiane Roscher Julieta A Rosell Milena Fermina Rosenfield Christian Rossi David B Roy Samuel Royer-Tardif Nadja Rüger Ricardo Ruiz-Peinado Sabine B Rumpf Graciela M Rusch Masahiro Ryo Lawren Sack Angela Saldaña Beatriz Salgado-Negret Roberto Salguero-Gomez Ignacio Santa-Regina Ana Carolina Santacruz-García Joaquim Santos Jordi Sardans Brandon Schamp Michael Scherer-Lorenzen Matthias Schleuning Bernhard Schmid Marco Schmidt Sylvain Schmitt Julio V Schneider Simon D Schowanek Julian Schrader Franziska Schrodt Bernhard Schuldt Frank Schurr Galia Selaya Garvizu Marina Semchenko Colleen Seymour Julia C Sfair Joanne M Sharpe Christine S Sheppard Serge Sheremetiev Satomi Shiodera Bill Shipley Tanvir Ahmed Shovon Alrun Siebenkäs Carlos Sierra Vasco Silva Mateus Silva Tommaso Sitzia Henrik Sjöman Martijn Slot Nicholas G Smith Darwin Sodhi Pamela Soltis Douglas Soltis Ben Somers Grégory Sonnier Mia Vedel Sørensen Enio Egon Sosinski Nadejda A Soudzilovskaia Alexandre F Souza Marko Spasojevic Marta Gaia Sperandii Amanda B Stan James Stegen Klaus Steinbauer Jörg G Stephan Frank Sterck Dejan B Stojanovic Tanya Strydom Maria Laura Suarez Jens-Christian Svenning Ivana Svitková Marek Svitok Miroslav Svoboda Emily Swaine Nathan Swenson Marcelo Tabarelli Kentaro Takagi Ulrike Tappeiner Rubén Tarifa Simon Tauugourdeau Cagatay Tavsanoglu Mariska Te Beest Leho Tedersoo Nelson Thiffault Dominik Thom Evert Thomas Ken Thompson Peter E Thornton Wilfried Thuiller Lubomír Tichý David Tissue Mark G Tjoelker David Yue Phin Tng Joseph Tobias Péter Török Tonantzin Tarin José M Torres-Ruiz Béla Tóthmérész Martina Treurnicht Valeria Trivellone Franck Trolliet Volodymyr Trotsiuk James L Tsakalos Ioannis Tsiripidis Niklas Tysklind Toru Umehara Vladimir Usoltsev Matthew Vadeboncoeur Jamil Vaezi Fernando Valladares Jana Vamosi Peter M van Bodegom Michiel van Breugel Elisa Van Cleemput Martine van de Weg Stephni van der Merwe Fons van der Plas Masha T van der Sande Mark van Kleunen Koenraad Van Meerbeek Mark Vanderwel Kim André Vanselow Angelica Vårhammar Laura Varone Maribel Yesenia Vasquez Valderrama Kiril Vassilev Mark Vellend Erik J Veneklaas Hans Verbeeck Kris Verheyen Alexander Vibrans Ima Vieira Jaime Villacís Cyrille Violle Pandi Vivek Katrin Wagner Matthew Waldram Anthony Waldron Anthony P Walker Martyn Waller Gabriel Walther Han Wang Feng Wang Weiqi Wang Harry Watkins James Watkins Ulrich Weber James T Weedon Liping Wei Patrick Weigelt Evan Weiher Aidan W Wells Camilla Wellstein Elizabeth Wenk Mark Westoby Alana Westwood Philip John White Mark Whitten Mathew Williams Daniel E Winkler Klaus Winter Chevonne Womack Ian J Wright S Joseph Wright Justin Wright Bruno X Pinho Fabiano Ximenes Toshihiro Yamada Keiko Yamaji Ruth Yanai Nikolay Yankov Benjamin Yguel Kátia Janaina Zanini Amy E Zanne David Zelený Yun-Peng Zhao Jingming Zheng Ji Zheng Kasia Ziemińska Chad R Zirbel Georg Zizka Irié Casimir Zo-Bi Gerhard Zotz Christian Wirth

Glob Chang Biol 2020 01 31;26(1):119-188. Epub 2019 Dec 31.

Max Planck Institute for Biogeochemistry, Jena, Germany.

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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http://dx.doi.org/10.1111/gcb.14904DOI Listing
January 2020

The effect of gut passage by waterbirds on the seed coat and pericarp of diaspores lacking "external flesh": Evidence for widespread adaptation to endozoochory in angiosperms.

PLoS One 2019 19;14(12):e0226551. Epub 2019 Dec 19.

Wetland Ecology Department, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain.

The widely accepted "endozoochory syndrome" is assigned to angiosperm diaspores with a fleshy, attractive tissue and implies the existence of adaptations for protection against digestion during gut passage. This syndrome has led diaspore fleshiness to be emphasized as the exclusive indicator of endozoochory in much of the ecology and biogeography research. Crucially, however, endozoochory in nature is not limited to frugivory, and diaspores without "external flesh" are commonly dispersed, often over long distances, via birds and mammals by granivory. A key question is: are such diaspores somehow less prepared from an architectural point of view to survive gut passage than fleshy diaspores? To answer this question, we selected 11 European angiosperm taxa that fall outside the classical endozoochory syndrome yet are known to be dispersed via endozoochory. We studied their seed coat/pericarp morphology and anatomy both before and after gut passage through granivorous waterfowl, and determined their seed survival and germinability. We found no fundamental differences in the mechanical architecture of the seed coat and pericarp between these plants dispersed by granivory and others dispersed by frugivory. Neither diaspore traits per se, nor dormancy type, were strong predictors of diaspore survival or degree of damage during gut passage through granivores, or of the influence of gut passage on germinability. Among our 11 taxa, survival of gut passage is enabled by the thick cuticle of the exotesta or epicarp; one or several lignified cell layers; and diverse combinations of other architectural elements. These protection structures are ubiquitous in angiosperms, and likely to have evolved in gymnosperms. Hence, many angiosperm diaspores, dry or fleshy, may be pre-adapted to endozoochory, but with differing degrees of specialization and adaptation to dispersal mechanisms such as frugivory and granivory. Our findings underline the broad ecological importance of "non-classical endozoochory" of diaspores that lack "external flesh".
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0226551PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6922415PMC
March 2020

Light Triggers the miRNA-Biogenetic Inconsistency for De-etiolated Seedling Survivability in Arabidopsis thaliana.

Mol Plant 2020 03 31;13(3):431-445. Epub 2019 Oct 31.

Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea; Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, Copenhagen 1871, Denmark. Electronic address:

The shift of dark-grown seedlings into light causes enormous transcriptome changes followed by a dramatic developmental transition. Here, we show that microRNA (miRNA) biogenesis also undergoes regulatory changes during de-etiolation. Etiolated seedlings maintain low levels of primary miRNAs (pri-miRNAs) and miRNA processing core proteins, such as Dicer-like 1, SERRATE, and HYPONASTIC LEAVES 1, whereas during de-etiolation both pri-miRNAs and the processing components accumulate to high levels. However, the levels of most miRNAs do not notably increase in response to light. To reconcile this inconsistency, we demonstrated that an unknown suppressor decreases miRNA-processing activity and light-induced SMALL RNA DEGRADING NUCLEASE 1 shortens the half-life of several miRNAs in de-etiolated seedlings. Taken together, these data suggest a novel mechanism, miRNA-biogenetic inconsistency, which accounts for the intricacy of miRNA biogenesis during de-etiolation. This mechanism is essential for the survival of de-etiolated seedlings after long-term skotomorphogenesis and their optimal adaptation to ever-changing light conditions.
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http://dx.doi.org/10.1016/j.molp.2019.10.011DOI Listing
March 2020

Distinct roles of Argonaute in the green alga Chlamydomonas reveal evolutionary conserved mode of miRNA-mediated gene expression.

Sci Rep 2019 07 31;9(1):11091. Epub 2019 Jul 31.

Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom.

The unicellular green alga Chlamydomonas reinhardtii is evolutionarily divergent from higher plants, but has a fully functional silencing machinery including microRNA (miRNA)-mediated translation repression and mRNA turnover. However, distinct from the metazoan machinery, repression of gene expression is primarily associated with target sites within coding sequences instead of 3'UTRs. This feature indicates that the miRNA-Argonaute (AGO) machinery is ancient and the primary function is for post transcriptional gene repression and intermediate between the mechanisms in the rest of the plant and animal kingdoms. Here, we characterize AGO2 and 3 in Chlamydomonas, and show that cytoplasmically enriched Cr-AGO3 is responsible for endogenous miRNA-mediated gene repression. Under steady state, mid-log phase conditions, Cr-AGO3 binds predominantly miR-C89, which we previously identified as the predominant miRNA with effects on both translation repression and mRNA turnover. In contrast, the paralogue Cr-AGO2 is nuclear enriched and exclusively binds to 21-nt siRNAs. Further analysis of the highly similar Cr-AGO2 and Cr-AGO 3 sequences (90% amino acid identity) revealed a glycine-arginine rich N-terminal extension of ~100 amino acids that, given previous work on unicellular protists, may associate AGO with the translation machinery. Phylogenetic analysis revealed that this glycine-arginine rich N-terminal extension is present outside the animal kingdom and is highly conserved, consistent with our previous proposal that miRNA-mediated CDS-targeting operates in this green alga.
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http://dx.doi.org/10.1038/s41598-019-47415-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6668577PMC
July 2019

Iterative allogamy-autogamy transitions drive actual and incipient speciation during the ongoing evolutionary radiation within the orchid genus Epipactis (Orchidaceae).

Ann Bot 2019 10;124(3):481-497

Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, UK.

Background And Aims: The terrestrial orchid genus Epipactis has become a model system for the study of speciation via transitions from allogamy to autogamy, but close phylogenetic relationships have proven difficult to resolve through Sanger sequencing.

Methods: We analysed with restriction site-associated sequencing (RAD-seq) 108 plants representing 29 named taxa that together span the genus, focusing on section Epipactis. Our filtered matrix of 12 543 single nucleotide polymorphisms was used to generate an unrooted network and a rooted, well-supported likelihood tree. We further inferred genetic structure through a co-ancestry heat map and admixture analysis, and estimated inbreeding coefficients per sample.

Key Results: The 27 named taxa of the ingroup were resolved as 11 genuine, geographically widespread species: four dominantly allogamous and seven dominantly autogamous. A single comparatively allogamous species, E. helleborine, is the direct ancestor of most of the remaining species, though one of the derived autogams has generated one further autogamous species. An assessment of shared ancestry suggested only sporadic hybridization between the re-circumscribed species. Taxa with the greatest inclination towards autogamy show less, if any, admixture, whereas the gene pools of more allogamous species contain a mixture alleles found in the autogams.

Conclusions: This clade is presently undergoing an evolutionary radiation driven by a wide spectrum of genotypic, phenotypic and environmental factors. Epipactis helleborine has also frequently generated many local variants showing inclinations toward autogamy (and occasionally cleistogamy), best viewed as incipient speciation from within the genetic background provided by E. helleborine, which thus becomes an example of a convincingly paraphyletic species. Autogams are often as widespread and ecologically successful as allogams.
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http://dx.doi.org/10.1093/aob/mcz103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6798847PMC
October 2019

Early high-dose caffeine citrate for extremely preterm infants: Neonatal and neurodevelopmental outcomes.

J Paediatr Child Health 2019 Dec 21;55(12):1451-1457. Epub 2019 Mar 21.

Newborn Services, Mater Mothers' Hospital, Brisbane, Queensland, Australia.

Aim: To examine neonatal morbidities, including the incidence of cerebellar haemorrhage (CBH), and neurodevelopmental outcomes following the administration of high loading dose caffeine citrate compared to standard loading dose caffeine citrate.

Methods: This was a retrospective study of 218 preterm infants <28 weeks' gestation who received a loading dose of caffeine citrate within the first 36 h of life at the Mater Mothers' Hospital over a 3-year period (2011-2013). Two groups were compared, with 158 neonates in the high-dose cohort receiving a median dose of caffeine citrate of 80 mg/kg and 60 neonates in the standard dose cohort receiving a median dose of 20 mg/kg. Routine cranial ultrasound, including mastoid views, was performed during the neonatal period. At 2 years of age, infants presented for follow-up and were assessed with the Neurosensory Motor Developmental Assessment (NSMDA) and the Bayley Scales of Infant and Toddler Development-III (Bayley-III).

Results: There was no difference in the incidence of neonatal morbidities, including CBH, between the two groups. The incidence of CBH in the high-dose group was 2.5% compared to 1.7% in the standard-dose group. There was no difference in the neurodevelopmental follow-up scores as evaluated with the NSMDA and the Bayley-III.

Conclusions: The use of early high loading dose caffeine citrate in extremely preterm infants was not shown to be associated with CBH or abnormal long-term neurodevelopmental outcomes. The overall incidence of CBH, however, was much lower than in studies using magnetic resonance imaging techniques. It is suggested that a large randomised clinical trial is needed to determine the optimal dose of caffeine citrate when given early to very preterm infants.
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http://dx.doi.org/10.1111/jpc.14446DOI Listing
December 2019

Gene Editing of Microalgae: Scientific Progress and Regulatory Challenges in Europe.

Biology (Basel) 2018 Mar 6;7(1). Epub 2018 Mar 6.

Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.

It is abundantly clear that the development of gene editing technologies, represents a potentially powerful force for good with regard to human and animal health and addressing the challenges we continue to face in a growing global population. This now includes the development of approaches to modify microalgal strains for potential improvements in productivity, robustness, harvestability, processability, nutritional composition, and application. The rapid emergence and ongoing developments in this area demand a timely review and revision of the current definitions and regulations around genetically modified organisms (GMOs), particularly within Europe. Current practices within the EU provide exemptions from the GMO directives for organisms, including crop plants and micro-organisms that are produced through chemical or UV/radiation mutagenesis. However, organisms generated through gene editing, including microalgae, where only genetic changes in native genes are made, remain currently under the GMO umbrella; they are, as such, excluded from practical and commercial opportunities in the EU. In this review, we will review the advances that are being made in the area of gene editing in microalgae and the impact of regulation on commercial advances in this area with consideration to the current regulatory framework as it relates to GMOs including GM microalgae in Europe.
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http://dx.doi.org/10.3390/biology7010021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5872047PMC
March 2018

Efficient targeted DNA editing and replacement in using Cpf1 ribonucleoproteins and single-stranded DNA.

Proc Natl Acad Sci U S A 2017 12 5;114(51):13567-13572. Epub 2017 Dec 5.

Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom

The green alga is an invaluable reference organism to research fields including algal, plant, and ciliary biology. Accordingly, decades-long standing inefficiencies in targeted nuclear gene editing broadly hinder research. Here we report that single-step codelivery of CRISPR/Cpf1 ribonucleoproteins with single-stranded DNA repair templates results in precise and targeted DNA replacement with as much as ∼10% efficiency in We demonstrate its use in transgene- and selection-free generation of sequence-specific mutations and epitope tagging at an endogenous locus. As the direct delivery of gene-editing reagents bypasses the use of transgenes, this method is potentially applicable to a wider range of species without the need to develop methods for stable transformation.
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http://dx.doi.org/10.1073/pnas.1710597114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5754772PMC
December 2017

Improved Denaturation of Small RNA Duplexes and Its Application for Northern Blotting.

Methods Mol Biol 2017 ;1580:1-6

School of Biological Sciences, University of Edinburgh, Edinburgh, UK.

Small RNAs (sRNAs) are short (18-30 nucleotide) noncoding RNA molecules, which control gene expression and pathogen response in eukaryotes. They are associated with and guide nucleases to target nucleic acids by nucleotide base pairing. We found that current techniques for small RNA detection are adversely affected by the presence of complementary RNA. Thus we established FDF-PAGE (fully denaturing formaldehyde polyacrylamide gel electrophoresis), which dramatically improves denaturation efficiency and subsequently the detection of sequestered sRNAs.
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http://dx.doi.org/10.1007/978-1-4939-6866-4_1DOI Listing
February 2018

Reply: Escaping a Low-Security Prison.

Plant Cell 2017 03 24;29(3):431. Epub 2017 Feb 24.

Institute of Molecular Plant SciencesUniversity of EdinburghEdinburgh EH9 3BFUnited Kingdom

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http://dx.doi.org/10.1105/tpc.17.00128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5385961PMC
March 2017

Lost in Transit: Long-Distance Trafficking and Phloem Unloading of Protein Signals in Arabidopsis Homografts.

Plant Cell 2016 Sep 6;28(9):2016-2025. Epub 2016 Sep 6.

Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom

In addition to moving sugars and nutrients, the phloem transports many macromolecules. While grafting and aphid stylectomy experiments have identified many macromolecules that move in the phloem, the functional significance of phloem transport of these remains unclear. To gain insight into protein trafficking, we micrografted scions expressing GFP-tagged chloroplast transit peptides under the 35S promoter onto nontransgenic rootstocks. We found that plastids in the root tip became fluorescent 10 d after grafting. We obtained identical results with the companion cell-specific promoter and with signals that target proteins to peroxisomes, actin, and the nucleus. We were unable to detect the respective mRNAs in the rootstock, indicating extensive movement of proteins in the phloem. Outward movement from the root protophloem was restricted to the pericycle-endodermis boundary, identifying plasmodesmata at this interface as control points in the exchange of macromolecules between stele and cortex. Intriguingly, signals directing proteins to the endoplasmic reticulum and Golgi apparatus from membrane-bound ribosomes were not translocated to the root. It appears that many organelle-targeting sequences are insufficient to prevent the loss of their proteins into the translocation stream. Thus, nonspecific loss of proteins from companion cells to sieve elements may explain the plethora of macromolecules identified in phloem sap.
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http://dx.doi.org/10.1105/tpc.16.00249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5059797PMC
September 2016

Engineering of CRISPR/Cas9-mediated potyvirus resistance in transgene-free Arabidopsis plants.

Mol Plant Pathol 2016 10 27;17(8):1276-88. Epub 2016 Jun 27.

Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3JR, UK.

Members of the eukaryotic translation initiation factor (eIF) gene family, including eIF4E and its paralogue eIF(iso)4E, have previously been identified as recessive resistance alleles against various potyviruses in a range of different hosts. However, the identification and introgression of these alleles into important crop species is often limited. In this study, we utilise CRISPR/Cas9 technology to introduce sequence-specific deleterious point mutations at the eIF(iso)4E locus in Arabidopsis thaliana to successfully engineer complete resistance to Turnip mosaic virus (TuMV), a major pathogen in field-grown vegetable crops. By segregating the induced mutation from the CRISPR/Cas9 transgene, we outline a framework for the production of heritable, homozygous mutations in the transgene-free T2 generation in self-pollinating species. Analysis of dry weights and flowering times for four independent T3 lines revealed no differences from wild-type plants under standard growth conditions, suggesting that homozygous mutations in eIF(iso)4E do not affect plant vigour. Thus, the established CRISPR/Cas9 technology provides a new approach for the generation of Potyvirus resistance alleles in important crops without the use of persistent transgenes.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026172PMC
http://dx.doi.org/10.1111/mpp.12417DOI Listing
October 2016

Most microRNAs in the single-cell alga Chlamydomonas reinhardtii are produced by Dicer-like 3-mediated cleavage of introns and untranslated regions of coding RNAs.

Genome Res 2016 Apr 11;26(4):519-29. Epub 2016 Mar 11.

Department of Plant Sciences, University of Cambridge CB2 3EA, Cambridge CB2 3EA, United Kingdom.

We describe here a forward genetic screen to investigate the biogenesis, mode of action, and biological function of miRNA-mediated RNA silencing in the model algal species,Chlamydomonas reinhardtii Among the mutants from this screen, there were three at Dicer-like 3 that failed to produce both miRNAs and siRNAs and others affecting diverse post-biogenesis stages of miRNA-mediated silencing. The DCL3-dependent siRNAs fell into several classes including transposon- and repeat-derived siRNAs as in higher plants. The DCL3-dependent miRNAs differ from those of higher plants, however, in that many of them are derived from mRNAs or from the introns of pre-mRNAs. Transcriptome analysis of the wild-type and dcl3 mutant strains revealed a further difference from higher plants in that the sRNAs are rarely negative switches of mRNA accumulation. The few transcripts that were more abundant in dcl3 mutant strains than in wild-type cells were not due to sRNA-targeted RNA degradation but to direct DCL3 cleavage of miRNA and siRNA precursor structures embedded in the untranslated (and translated) regions of the mRNAs. Our analysis reveals that the miRNA-mediated RNA silencing in C. reinhardtii differs from that of higher plants and informs about the evolution and function of this pathway in eukaryotes.
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http://dx.doi.org/10.1101/gr.199703.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817775PMC
April 2016

Mobile small RNAs regulate genome-wide DNA methylation.

Proc Natl Acad Sci U S A 2016 Feb 19;113(6):E801-10. Epub 2016 Jan 19.

Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037

RNA silencing at the transcriptional and posttranscriptional levels regulates endogenous gene expression, controls invading transposable elements (TEs), and protects the cell against viruses. Key components of the mechanism are small RNAs (sRNAs) of 21-24 nt that guide the silencing machinery to their nucleic acid targets in a nucleotide sequence-specific manner. Transcriptional gene silencing is associated with 24-nt sRNAs and RNA-directed DNA methylation (RdDM) at cytosine residues in three DNA sequence contexts (CG, CHG, and CHH). We previously demonstrated that 24-nt sRNAs are mobile from shoot to root in Arabidopsis thaliana and confirmed that they mediate DNA methylation at three sites in recipient cells. In this study, we extend this finding by demonstrating that RdDM of thousands of loci in root tissues is dependent upon mobile sRNAs from the shoot and that mobile sRNA-dependent DNA methylation occurs predominantly in non-CG contexts. Mobile sRNA-dependent non-CG methylation is largely dependent on the DOMAINS REARRANGED METHYLTRANSFERASES 1/2 (DRM1/DRM2) RdDM pathway but is independent of the CHROMOMETHYLASE (CMT)2/3 DNA methyltransferases. Specific superfamilies of TEs, including those typically found in gene-rich euchromatic regions, lose DNA methylation in a mutant lacking 22- to 24-nt sRNAs (dicer-like 2, 3, 4 triple mutant). Transcriptome analyses identified a small number of genes whose expression in roots is associated with mobile sRNAs and connected to DNA methylation directly or indirectly. Finally, we demonstrate that sRNAs from shoots of one accession move across a graft union and target DNA methylation de novo at normally unmethylated sites in the genomes of root cells from a different accession.
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http://dx.doi.org/10.1073/pnas.1515072113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760824PMC
February 2016

FDF-PAGE: a powerful technique revealing previously undetected small RNAs sequestered by complementary transcripts.

Nucleic Acids Res 2015 Sep 13;43(15):7590-9. Epub 2015 Jun 13.

Plant Sciences Department, Cambridge University, Cambridge, CB2 3EA, UK

Small RNAs, between 18nt and 30nt in length, are a diverse class of non-coding RNAs that mediate a range of cellular processes, from gene regulation to pathogen defense. They guide ribonucleoprotein complexes to their target nucleic acids by Watson-Crick base pairing. We report here that current techniques for small RNA detection and library generation are biased by formation of RNA duplexes. To address this problem, we established FDF-PAGE (fully-denaturing formaldehyde polyacrylamide gel electrophoresis) to prevent annealing of sRNAs to their complement. By applying FDF-PAGE, we provide evidence that both strands of viral small RNA are present in near equimolar ratios, indicating that the predominant precursor is a long double-stranded RNA. Comparing non-denaturing conditions to FDF-PAGE uncovered extensive sequestration of miRNAs in model organisms and allowed us to identify candidate small RNAs under the control of competing endogenous RNAs (ceRNAs). By revealing the full repertoire of small RNAs, we can begin to create a better understanding of small RNA mediated interactions.
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http://dx.doi.org/10.1093/nar/gkv604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551911PMC
September 2015

Going mobile: non-cell-autonomous small RNAs shape the genetic landscape of plants.

Plant Biotechnol J 2015 Apr 10;13(3):306-18. Epub 2015 Mar 10.

Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, UK.

RNA silencing is a form of genetic regulation, which is conserved across eukaryotes and has wide ranging biological functions. Recently, there has been a growing appreciation for the importance of mobility in RNA silencing pathways, particularly in plants. Moreover, in addition to the importance for mobile RNA silencing in an evolutionary context, the potential for utilizing mobile short silencing RNAs in biotechnological applications is becoming apparent. This review aims to set current knowledge of this topic in a historical context and provides examples to illustrate the importance of mobile RNA silencing in both natural and artificially engineered systems in plants.
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http://dx.doi.org/10.1111/pbi.12353DOI Listing
April 2015

Molecular phylogeny and evolutionary history of the Eurasiatic orchid genus Himantoglossum s.l. (Orchidaceae).

Ann Bot 2014 Dec 7;114(8):1609-26. Epub 2014 Oct 7.

Jodrell Laboratory, Royal Botanical Gardens Kew, Richmond, Surrey TW9 3DS, UK.

Background And Aims: Lizard orchids of the genus Himantoglossum include many of Eurasia's most spectacular orchids, producing substantial spikes of showy flowers. However, until recently the genus had received only limited, and entirely traditional, systematic study. The aim of the current work was to provide a more robust molecular phylogeny in order to better understand the evolutionary relationships among species of particular conservation concern.

Methods: All putative species of Himantoglossum s.l. were sampled across its geographical range. A large subsample of the 153 populations studied contributed to an initial survey of nuclear ribosomal internal transcribed spacer (nrITS) ribotypes. Smaller subsets were then sequenced for four plastid regions and the first intron of the low-copy-number nuclear gene LEAFY. Rooted using Steveniella as outgroup, phylogenetic trees were generated using parsimony and Bayesian methods from each of the three datasets, supplemented with a ribotype network.

Key Results: The resulting trees collectively determined the order of branching of the early divergent taxa as Himantoglossum comperianum > H. robertianum group > H. formosum, events that also involved significant morphological divergence. Relaxed molecular clock dating suggested that these divergences preceded the Pleistocene glaciations (the origin of the H. robertianum group may have coincided with the Messinian salinity crisis) and occurred in Asia Minor and/or the Caucasus. Among more controversial taxa of the H. hircinum-jankae clade, which are only subtly morphologically divergent, topological resolution was poorer and topological incongruence between datasets was consequently greater.

Conclusions: Plastid sequence divergence is broadly consistent with prior, morphologically circumscribed taxa and indicates a division between H. hircinum-adriaticum to the west of the Carpathians and H. jankae-caprinum (plus local endemics) to the east, a distinction also suggested by nrITS ribotypes. LEAFY phylogenies are less congruent with prior taxonomic arrangements and include one likely example of paralogy. Himantoglossum metlesicsianum fully merits its IUCN Endangered status. Potentially significant genetic variation was detected within Steveniella satyrioides, H. robertianum and H. hircinum. However, confident circumscription of the more derived species of Himantoglossum s.s., including local endemics of hybrid origin, must await future morphometric and population-genetic analyses.
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http://dx.doi.org/10.1093/aob/mcu179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649687PMC
December 2014

5' isomiR variation is of functional and evolutionary importance.

Nucleic Acids Res 2014 Aug 23;42(14):9424-35. Epub 2014 Jul 23.

Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London W12 ONN, UK

We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3' and/or 5' end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5' differences and in support of this we report that a 5' isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5' isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes.
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http://dx.doi.org/10.1093/nar/gku656DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132760PMC
August 2014

Diterpene alkaloids from the roots of Aconitum moldavicum and assessment of Nav 1.2 sodium channel activity of aconitum alkaloids.

Planta Med 2014 Feb 22;80(2-3):231-6. Epub 2014 Jan 22.

Department of Pharmacognosy, University of Szeged, Szeged, Hungary.

A new aconitane alkaloid, 1-O-demethylswatinine (1), was isolated from the root of Aconitum moldavicum together with the known compounds cammaconine (2), columbianine (3), swatinine (4), gigactonine (5), delcosine (6), lycoctonine (7), and ajacine (8). The structures were established by means of HRESIMS, 1D and 2D NMR spectroscopy, including 1H-1H COSY, NOESY, HSQC, and HMBC experiments, resulting in complete 1H-NMR chemical shift assignments for 1-4. The effects of the isolated compounds 4-8, together with eighteen other Aconitum diterpene and norditerpene alkaloids with different skeletal types and substitution patterns, were studied on Nav 1.2 channels by the whole-cell patch clamp technique, using the QPatch-16 automated patch clamp system. Pyroaconitine, ajacine, septentriodine, and delectinine demonstrated significant Nav 1.2 channel inhibition (57-42 %) at 10 µM concentration; several other compounds (acovulparine, acotoxicine, hetisinone, 14-benzoylaconine-8-O-palmitate, aconitine, and lycoctonine) exerted moderate inhibitory activity (30-22 %), while the rest of the tested alkaloids were considered to be inactive. On the basis of these results and by exhaustive comparison of data of previously published computerized QSAR studies on diterpene alkaloids, certain conclusions on the structure-activity relationships of Aconitum alkaloids concerning Nav 1.2 channel inhibitory activity are proposed.
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http://dx.doi.org/10.1055/s-0033-1360278DOI Listing
February 2014

Plant mobile small RNAs.

Cold Spring Harb Perspect Biol 2013 Jul 1;5(7). Epub 2013 Jul 1.

IBMP-CNRS, 67084 Strasbourg Cedex, France.

In plants, RNA silencing is a fundamental regulator of gene expression, heterochromatin formation, suppression of transposable elements, and defense against viruses. The sequence specificity of these processes relies on small noncoding RNA (sRNA) molecules. Although the spreading of RNA silencing across the plant has been recognized for nearly two decades, only recently have sRNAs been formally demonstrated as the mobile silencing signals. Here, we discuss the various types of mobile sRNA molecules, their short- and long-range movement, and their function in recipient cells.
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http://dx.doi.org/10.1101/cshperspect.a017897DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3685890PMC
July 2013

Bone tuberculosis in Roman Period Pannonia (western Hungary).

Mem Inst Oswaldo Cruz 2012 Dec;107(8):1048-53

Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University, Budapest, Hungary.

The purpose of this study was to analyse a skeleton (adult female, 25-30 years) that presented evidence of tuberculous spondylitis. The skeleton, dated from the Roman Period (III-VI centuries), was excavated near the town of Győr, in western Hungary. The skeleton was examined by gross observation supplemented with mycolic acid and proteomic analyses using MALDI-TOF/TOF tandem mass spectrometry. The biomolecular analyses supported the morphological diagnosis.
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http://dx.doi.org/10.1590/s0074-02762012000800014DOI Listing
December 2012

The frequency of alcohol, illicit and licit drug consumption in the general driving population in South-East Hungary.

Forensic Sci Int 2013 Jan 11;224(1-3):37-43. Epub 2012 Nov 11.

Department of Forensic Medicine, University of Szeged, Kossuth L. sgt. 40., H-6724 Szeged, Hungary.

In the framework of the DRUID (Driving under the Influence of Drugs, Alcohol, and Medicines) EU-6 project, a roadside survey was performed in South-East Hungary to determine the incidence of alcohol and the most frequent illicit and licit drug consumption (amphetamines, THC, illicit and medical opiates, cocaine, ketamine, benzodiazepines, zopiclone and zolpidem) in the general driving population. All 3110 drivers stopped between 01 January 2008 and 31 December 2009 were checked for alcohol, and among them 2738 persons (87.7%) participated in the further examinations, on a voluntary basis. Licit and illicit drugs were determined from their oral fluid samples by GC-MS analysis. Illicit drugs were detected in 27 cases (0.99%), licit drugs in 85 cases (3.14%), and alcohol (cut off: 0.1g/l) was found in 4 (0.13%) cases. Illicit drug consumption was the highest among men of the ages 18-34, during the spring, and on the week-end nights. With respect to licit drugs, the highest incidence was found among women over the age of 50, during the summer, and on the week-days. All alcohol positive cases were men over the age of 35. In comparison to international European averages, the alcohol and illicit drug consumption was low, but the licit drug consumption was over the European average.
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http://dx.doi.org/10.1016/j.forsciint.2012.10.022DOI Listing
January 2013

A PHABULOSA/cytokinin feedback loop controls root growth in Arabidopsis.

Curr Biol 2012 Sep 16;22(18):1699-704. Epub 2012 Aug 16.

Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK.

The hormone cytokinin (CK) controls root length in Arabidopsis thaliana by defining where dividing cells, derived from stem cells of the root meristem, start to differentiate [1-6]. However, the regulatory inputs directing CK to promote differentiation remain poorly understood. Here, we show that the HD-ZIPIII transcription factor PHABULOSA (PHB) directly activates the CK biosynthesis gene ISOPENTENYL TRANSFERASE 7 (IPT7), thus promoting cell differentiation and regulating root length. We further demonstrate that CK feeds back to repress both PHB and microRNA165, a negative regulator of PHB. These interactions comprise an incoherent regulatory loop in which CK represses both its activator and a repressor of its activator. We propose that this regulatory circuit determines the balance of cell division and differentiation during root development and may provide robustness against CK fluctuations.
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http://dx.doi.org/10.1016/j.cub.2012.07.005DOI Listing
September 2012

Artificial microRNA-mediated knockdown of pyruvate formate lyase (PFL1) provides evidence for an active 3-hydroxybutyrate production pathway in the green alga Chlamydomonas reinhardtii.

J Biotechnol 2012 Nov 9;162(1):57-66. Epub 2012 Jun 9.

Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.

Artificial microRNA technology was investigated as a means of down regulating metabolic pathways in the green alga Chlamydomonas reinhardtii, targeting pyruvate formate lyase (PFL1), which catalyzes the conversion of pyruvate to acetyl-CoA and formate during anoxic conditions. Two transformants with an 80-90% reduction in target protein and mRNA levels were identified. Nuclear magnetic resonance spectroscopy confirmed a substantial decrease in the production of formate in the knockdown lines during dark anoxic conditions and a re-routing of metabolism leading to enhanced production of ethanol and lactate. Under microaerobic conditions in the light, induced by sulphur-deprivation, knock-down of PFL1 resulted in reduced formate and ethanol production, increased net consumption of acetate and the excretion of lactate but no increase in the production of hydrogen. In addition the production of 3-hydroxybutyrate was identified in knock-down line cultures during the transition between microaerobic and anoxic conditions. Overall our results indicate that microRNA knock-down is a useful tool to manipulate anaerobic metabolism in C. reinhardtii.
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http://dx.doi.org/10.1016/j.jbiotec.2012.05.010DOI Listing
November 2012