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    Plant parasitic Asterinaceae and Microthyriaceae from the Neotropics (Panama)

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    Plant parasitic species of Asterinaceae and Microthyriaceae (Dothideomycetes, Ascomycota, Fungi) are inconspicuous foliicolous fungi with a mainly tropical distribution. They form black colonies on the surface of living leaves. Members of Asterinaceae and Microthyriaceae are characterized by shield-shaped, flat ascomata (thyriothecia) which grow completely superficially on the leaf cuticle. Microthyriaceae, Asterinaceae and other families of thyriothecia-forming ascomycetes belong to the class Dothideomycetes due to the presence of bitunicate asci. However, until today no consistent taxonomic concept nor molecular phylogenetic studies exist for the families of thyriothecioid ascomycetes. In the present thesis, 42 species belonging to 13 different anamorphic and teleomorphic genera of Asterinaceae, Microthyriaceae and ‘Pycnothyriales’ recently collected in Western Panama, are identified, described in detail and illustrated with drawings, transmission and scanning electron microscopical photographs. Among the 42 species, 37 species belong to the Asterinaceae, four species to the Microthyriaceae and one species to the from group ‘Pycnothyriales’. Two species of Asterinaceae are new to sience: Asterina gaiadendricola with an Asterostomella anamorph and Asterina schlegeliae with a Mahanteshamyces anamorph. Among the remaining species of Asterinaceae, 28 species represent new records for Panama: Asterina cestricola, A. ciferriana, A. consobrina, A. corallopoda, A. davillae with anamorph, A. diplocarpa, A. diplopoda, A. ekmanii, A. fuchsiae, A. manihotis, A. phenacis, A. radiofissilis with anamorph, A. siphocampyli, A. sponiae, A. stipitipodia with anamorph, A. styracina, A. tonduzii with anamorph, A. weinmanniae, A. zanthoxyli, Asterostomella dilleniicola, Asterolibertia licaniicola, Asterolibertia nodulosa, Cirsosia splendida with its Homalopeltis chrysobalani anamorph and Prillieuxina winteriana with its Leprieurina winteriana anamorph. The remaining 11 species of Asterinaceae probably respresent new species: Asterina spp. 1-8, Asterolibertia sp., Halbanina sp. and Mahanteshamyces sp. The four species of Microthyriaceae are new records for Panama: Maublanica uleana, Platypeltella irregularis, Platypeltella smilacis and Xenostomella tovarensis. The species Hemisphaeropsis magnoliae in the form group ‘Pycnothyriales’ is a new record for Panama. During this study, voucher material of 44 additional species of plant parasitic thyriothecioid ascomycetes was examined. Thereby, the number of species of Asterinaceae known for Panama since 2006 raises from four to 30, for Microthyriaceae respectively from zero to four and for ‘Pycnothyriales’ from zero to one. 21 of the presented species are new records for Central America and two species are new records for the American Continent. The presented 42 species parasitize 47 host plant species in 39 genera belonging to 28 plant families. For 23 fungal species, new host plant species are discovered. From those, seven belong to host plant genera not reported before to be parasitized by a member of Asterinaceae and Microthyriaceae: Burmeistera (Campanulaceae), Curatella and Davilla (Dilleniaceae), Greigia (Bromeliaceae), Hirtella (Chrysobalanaceae), Oxandra and Xylopia (Annonaceae). In this study, the first molecular phylogenetic approach in Asterinaceae is provided. For the first time, DNA was isolated from fresh material of Asterina spp. and their respective anamorphic stages on leaves in Panama. The hypothesis derived from SSU and LSU rDNA neighbour-joining analysis supports the monophyly of the Asterinaceae and suggests a close relationship to Venturiaceae within the class Dothideomycetes. The data obtained from the ppMP project (plant parasitic microfungi of Panama) indicate a constant but low abundance of plant parasitic thyriothecioid ascomycetes in natural plant communities in Panama, with Asterinaceae as the most species-rich and diverse family. Further collection activities in tropical regions worldwide will certainly increase our knowledge about species diversity and ecology of tropical plant parasitic thyriothecioid ascomycetes.Zusammenfassung Pflanzenparasitische Arten der Asterinaceae und Microthyriaceae (Dothideomycetes, Ascomycota, Echte Pilze) sind unscheinbare Blattbewohner mit hauptsĂ€chlich tropischer Verbreitung. Sie bilden schwarze Kolonien auf der OberflĂ€che von lebenden BlĂ€ttern und infizieren das Wirtsgewebe auf vielfĂ€ltige Weise. Vertreter der Asterinaceae und Microthyriaceae sind durch spezielle, schild-förmig abgeflachte Fruchtkörper charakterisiert, die als Thyriothezien bezeichnet werden und komplett oberflĂ€chlich auf der Wirtskutikula wachsen. Die sehr kleinen Ascomata entstehen meist an einem ausgedehnten OberflĂ€chenmyzel, welches ausserdem spezielle Infektionsstrukturen zur Penetration des Wirtsgewebes ausbildet. In den Thyriothezien werden globose oder zylindrische, bitunicate Asci gebildet in denen acht zweizellige Ascosporen (Meiosporen) entstehen. Neben dem sexuellen Entwicklungsgang besitzen viele Vertreter der Asterinaceae auch asexuelle Stadien, welche durch den Thyriothezien morphologisch Ă€hnliche Konidiomata, sogenannte Pyknothyrien, gekennzeichnet sind und in denen Konidien (Mitosporen) gebildet werden. Thyriothecien-bildende Ascomyceten, auch thyriothecioide Ascomyceten genannt, werden mithilfe morphologischer und ökologischer Merkmale unterschiedlichen Familien zugeordnet (Asterinaceae, Aulographaceae, Brefeldiellaceae, Leptopeltidaceae, Micropeltidaceae, Microthyriaceae, Parmulariaceae, Polystomellaceae, Schizothyriaceae und Vizellaceae), deren VerwandtschaftsverhĂ€ltnisse untereinander sowie innerhalb der bitunicaten Ascomyceten noch nicht aufgeklĂ€rt sind. In Panama sind thyriothecioide Ascomyceten nahezu unbekannt und nur sehr sporadisch untersucht. Dies liegt zum einen an der geringen GrĂ¶ĂŸe der Pilze, sowie deren unwesentlicher Bedeutung als SchĂ€dlinge auf wirtschaftlich genutzen Pflanzen, aber auch am Fehlen von Spezialisten fĂŒr die Pilzgruppe. Bis 2006 waren fĂŒr Panama nur 10 Arten von thyriothecioiden Ascomyceten bekannt. Trotz der relativ geringen GrĂ¶ĂŸe Panamas ist die DiversitĂ€t der vaskulĂ€ren Pflanzen mit ca. 9500 Arten etwa dreimal so hoch wie in dem etwa fĂŒnfmal grĂ¶ĂŸeren Deutschland. Da Vertreter der Asterinaceae und Microthyriaceae obligat biotroph sind und dauerhafte, komplexe Interaktionen mit ihrem Wirt eingehen, wird eine WirtspezifitĂ€t zumindest auf Pflanzenfamilienebene vermutet. Wenn man die enorme Vielfalt der potentiellen Wirtspflanzen in Panama in Betracht zieht, kann man von einer hohen DiversitĂ€t dieser Pflanzenpathogene in dem Land ausgehen. FĂŒr diese Studie wurden insgesamt 379 Belege geprĂŒft, die 86 verschiedenen Arten von pflanzenparasitischen Asterinaceae und Microthyriaceae entsprechen. Insgesamt wurden 174 Belege von pflanzenparasitischen thyriothecioiden Ascomyceten im Westen Panamas in den Provinzen ChiriquĂ­ und Bocas del Toro gesammelt. Zwischen 2005 und 2007 wurden 86 Belege von der Autorin selbst und 74 Belege im Rahmen des ppMP Projektes (pflanzenparasitische Mikropilze Panamas) von T.A. Hofmann, R. Mangelsdorff, M. Piepenbring und T. Trampe gesammelt. Jeweils 5 Belege wurden zwischen 2000 und 2005 von M. Piepenbring, sowie von T. Trampe 2008 gesammelt. 3 Belege wurden von R. Mangelsdorff zwischen 2004 und 2006 gesammelt, und 1 Beleg wurde 2004 von Boris Koch gesammelt. ZusĂ€tzlich wurden insgesamt 205 Belege aus Herbarien konsultiert, 163 Belege aus den U.S. National Fungus Collections (BPI), 25 Belege aus dem Swedish Museum of Natural History (S), 10 Belege aus dem CABI Bioscience UK Centre (formerly International Mycological Institute, IMI), 3 Belege aus der Universidad National de la Plata (LPS), 2 Belege vom Biozentrum Klein-Flottbeck (HBG) and jeweils 1 Beleg aus dem Herbarium Bogoriense (BO) und dem Plant Protection Research Institute (PREM). In der vorliegenden Arbeit werden 42 Arten von pflanzenparasitischen thyriothecioiden Ascomyceten identifiziert, detailliert beschrieben und durch Zeichungen sowie transmissions- und rasterelektronenmikroskopische Aufnahmen zum großen Teil erstmals illustriert. Die 42 Arten gehören zu 13 unterschiedlichen Anamorph- und Teleomorphgattungen in den zwei Familien Asterinaceae (37 Arten) und Microthyriaceae (vier Arten) sowie der Fromgruppe ‘Pycnothyriales’ (eine Art). Zwei der vorgestellten Arten der Asterinaceae sind neu fĂŒr die Wissenschaft: Asterina gaiadendricola mit Asterostomella-Anamorph auf Gaiadendron punctatum (Loranthaceae) und Asterina schlegeliae mit Mahanteshamyces-Anamorph auf Schlegelia parviflora (Schegeliaceae). Asterina gaiadendricola unterscheidet sich von anderen Asterina-Arten auf Loranthaceae durch das hypophylle Wachstum, die besondere Morphologie der Appressorien und deren ausschließliches Vorkommen auf den Schließzellen der Spaltöffungen der Wirtspflanze. Asterina schlegeliae ist die einzige bekannte Art von Asterina, die auf einem Vertreter der Schlegeliaeceae parasitiert und unterscheidet sich von Asterina-Arten auf den nahe verwandten Pflanzenfamilien Scrophulariaceae und Bignoniaceae durch das Mahanteshamycesartige Anamorph mit dreieckigen Konidien. Von den res tlichen Arten der Asterinaceae werden 24 Arten bis auf Artebene identifiziert und reprĂ€sentieren ausnahmslos Erstnachweise fĂŒr das Land Panama: Asterina cestricola auf Cestrum rugulosum (Solanaceae), A. ciferriana auf Caesalpinia bonduc (Fabaceae), A. consobrina auf Solanum aphyodendron (Solanaceae), A. corallopoda auf Solanum trizygum (Solanaceae), A. davillae mit Anamorph auf Curatella americana (Dilleniaceae), A. diplocarpa auf Sida acuta und Sida rhombifolia (Malvaceae), A. diplopoda auf Solanum acerifolium (Solanaceae), A. ekmanii auf Gonzalagunia rudis (Rubiaceae), A. fuchsiae auf Fuchsia paniculata (Onagraceae), A. manihotis auf Manihot esculenta (Euphorbiaceae), A. phenacis auf Phenax mexicanus (Urticaceae), A. radiofissilis mit Anamorph auf Acalypha arvensis (Euphorbiaceae), A. siphocampyli auf Burmeistera vulgaris and Burmeistera sp. (Campanulaceae), A. sponiae auf Trema micrantha (Cannabaceae) und einer nicht identifizierten Tiliaceae, A. stipitipodia mit Anamorph auf Davilla kunthii (Dilleniaceae), A. styracina auf Styrax argenteus (Styracaceae), A. tonduzii mit Anamorph auf Xylosma sp. (Salicaceae), A. weinmanniae auf Weinmannia pinnata (Cunoniaceae), A. zanthoxyli auf Zanthoxylum scheryi (Rutaceae), Asterostomella dilleniicola auf Davilla kunthii (Dilleniaceae), Asterolibertia licaniicola auf Licania arborea (Chrysobalanaceae), Asterolibertia nodulosa auf Oxandra venezuelana (Annonaceae), Cirsosia splendida mit Homalopeltis chrysobalani- Anamorph auf Chrysobalanus icaco und Hirtella triandra (Chrysobalanceae) und Prillieuxina winteriana mit Leprieurina winteriana-Anamorph auf Annona montana (Annonaceae). Die restlichen 11 Arten der Asterinaceae konnten nicht bis auf Artebene identifiziert werden und sind möglicherweise neue Arten: Asterina sp. 1 auf Hansteinia reflexiflora (Acanthaceae), Asterina sp. 2 auf Hansteinia ventricosa (Acanthaceae), Asterina sp. 3 auf Desmopsis bibracteata (Annonaceae), Asterina sp. 4 auf Cleome sp. (Cleomaceae), Asterina sp. 5 auf Clusia sp. (Clusiaceae), Asterina sp. 6 auf Alloplectus ichtyoderma (Gesnericaceae), Asterina sp. 7 auf Compsoneura sprucei (Myristicaceae), Asterina sp. 8 auf Casearia commersoniana (Salicaceae), Asterolibertia sp. auf Annonaceae, Halbanina sp. auf Chrysobalanus icaco (Chrysobalanaceae) und Mahanteshamyces sp. auf Schlegelia parviflora (Schlegeliaceae). Die vier vorgestellten, pflanzenparasitischen Arten der Microthyriaceae werden erstmalig fĂŒr Panama dokumentiert: Maublanica uleana auf Myrcia splendens (Myrtaceae), Platypeltella irregularis auf Greigia sylvicola (Bromeliaceae), Platypeltella smilacis auf Smilax sp. (Smilacaceae) und Xenostomella tovarensis auf Monnina xalapensis (Polygalaceae). Die Art der Formgruppe “Pycnothyiales”, Hemisphaeropsis magnoliae mit Teleomorph Stadium auf Magnolia sororum (Magnoliaceae), ist ein Neunachweis fĂŒr Panama. Insgesamt 16 der vorgestellten Arten werden erstmals in dieser Studie illustriert. Weiterhin werden Listen der aus der Literatur bekannten Arten der Gattungen Asterina, Asterostomella, Asterolibertia, Cirsosia, Halbanina, Maublancia, Prillieuxina, Platypeltella und Xenostomella vorgestellt. Neben Wirtsindizes der gĂŒltigen Arten werden ebenfalls alle ungĂŒltigen und synonymisierten Arten aufgelistet. Die Zahl der fĂŒr bis 2006 in Panama bekannten Arten der Asterinaceae erhöht sich mit dieser Arbeit von vier auf 30, fĂŒr Microthyriaceae respektive von null auf vier und fĂŒr ‘Pycnothyriales’ von null auf eins. 21 der vorgestellten Arten reprĂ€sentieren Neunachweise fĂŒr Zentralamerika und zwei Arten werden das erste Mal fĂŒr den Amerikanischen Kontinent dokumentiert. In dieser Studie werden Infektionsmechanismen von ausgewĂ€hlten Arten von Asterinaceae und Microthyriaceae auf ultrastrucktureller Ebene untersucht. Erstmals werden fĂŒr Ascomyceten spezifische Zellorganellen in Arten von Asterinaceae und Microthyriaceae nachgewiesen. Mithilfe lichtmikrokopischer Techniken wird die Ascusentwicklung von Asterina schlegeliae, Asterina sp. 7., Asterolibertia nodulosa, Cirsosia splendida, Halbanina sp., Maublancia uleana, Prillieuxina winteriana, Platypeltella irregularis und P. smilacis erstmalig analysiert und illustriert. Weiterhin werden morphologische und ontogenetische Besonderheiten der Pilzgruppen diskutiert, die fĂŒr Art-, Gattungs- und Familienkonzepte thyriothecioider Ascomyceten von taxonomischer Bedeutung sein können. In der vorliegenden Arbeit wird eine neue Teleomorph-Anamorph Verbindung vorgestellt, das Teleomorph Cirsosia splendida (Asterinaceae) mit dem Anamorphstadium Homalopeltis chyrsobalani auf Chrysobalanus icaco und Hirtella triandra (Chrysobalanaceae). ZusĂ€tzlich werden in der Studie taxonomische VerĂ€nderungen vorgeschlagen. Drei Arten von Asterinaceae werden synonymisiert, Asterina melanomera mit Asterina saginata, Asterina myrciae mit Maublancia uleana, und Leprieurina radiata mit Homalopeltis chrysobalani (Anamorph von Cirsosia splendida), eine Art wird umkombiniert, Asterina nodulifera zu Asterolibertia nodulifera, und eine Art wird neu benannt, Asterina schroeteri var. licaniae zu Asterolibertia minor. Die 42 vorgestellten Arten parasitieren auf insgesamt 47 Wirtspflanzenarten in 39 Gattungen und 28 unterschiedlichen Pflanzenfamilien. FĂŒr 23 der prĂ€sentierten Pilzarten werden neue Wirtsarten genannt. Von diesen gehören sieben zu Gattungen, von denen bisher keine Wirtsarten fĂŒr Asterinaceae und Microthyriaceae bekannt waren: Burmeistera (Campanulaceae) fĂŒr Asterina siphocampyli, Curatella (Dilleniaceae) fĂŒr Asterina davillae mit Asterostomella-Anamorph, Davilla (Dilleniaceae) fĂŒr Asterina stipitipodia mit Asterostomella stipitipodia-Anamorph sowie fĂŒr Asterostomella dilleniicola, Greigia (Bromeliaceae) fĂŒr Platypeltella irregularis, Hirtella (Chrysobalanaceae) fĂŒr Cirsosia splendida mit Homalopeltis chrysobalani-Anamorph, Oxandra und Xylopia (Annonaceae) fĂŒr Asterolibertia nodulosa. In dieser Arbeit wird zum ersten Mal eine molekularphylogenetische Hypothese zur den VerwandschaftsverhĂ€ltnissen der Asterinaceae mit Gruppen anderer bitunicater Ascomyceten innerhalb der Klasse Dothideomycetes vorgestellt. In Panama konnte erstmals DNA von Frischmaterial von Asterina spp. und deren Anamorph-Stadien von BlĂ€ttern isoliert werden. Die von LSU und SSU rDNA-Sequenzen abgeleitete Neighbour-Joining-Analyse unterstĂŒtzt die Monophylie der Asterinaceae mit enger Beziehung zu den Venturiaceae innerhalb der Klasse der bitunicaten Ascomyceten, Dothideomycetes. Die vorgestellte phylogenetische Analyse ist jedoch nur als vorlĂ€ufiges Ergebnis anzusehen. Sequenzendaten von anderen Arten von Asterinaceae und nahe verwandte Familien der thyriothecioiden Ascomyceten sowie erweiterte phylogenetische Untersuchungen sind notwendig, um die Pilzgruppe anhand molekularer Daten klassifizieren zu können. Die im Rahmen des ppMP Projektes (pflanzenparasitische Mikropilze Panamas) untersuchte HĂ€ufigkeitsverteilung von pflanzenparasitischen thyriothecioiden Ascomyceten zeigt die konstante aber geringe Abundanz dieser Pflanzenpathogene in natĂŒrlichen Pflanzengesellschaften im Westen Panamas. Dabei stellen die Asterinaceae mit 61 verschiedenen Arten die artenreichste Gruppe dar, Asterina ist die am hĂ€ufigsten gefunden Gattung der Asterinaceae. Faktoren wie jahreszeitliche Schwankungen von Regen- und Trockenzeit, LichtintensitĂ€t oder Höhenlage sind nicht fĂŒr ein vermehrtes Vorkommen von Arten von Asterinaceae in einer bestimmten Pflanzengesellschaft maßgebend. Vielmehr spielen das Vorhandensein von Waldhabitaten mit Tendenz zu LĂŒckenbildung sowie der damit assoziierte erhöhte Störungsgrad der jeweiligen Pflanzengesellschaft eine entscheidende Rolle fĂŒr die DiversitĂ€t der Asterinaceae. VerstĂ€rkte SammelaktivitĂ€ten in Panama und tropischen Gebieten weltweit werden zur Erweiterung des Kenntnisstandes ĂŒber die Artenvielfalt und Ökologie tropischer thyriothecioider Ascomyceten beitragen. Resumen Especies de Asterinaceae y Microthyriaceae son hongos parĂĄsitos qu e ocurren especialmente en los trĂłpicos del mundo. Estos pequeños hongos forman colonias negras en la superficie de hojas vivas e infectan el tejido de la planta en diversas formas. Son caracterizados por ascomatas escutiformes llamado thiriothecia que se desarrollan superficialmente sobre la cutĂ­cula de la planta. Asterinaceae y Microthyriaceae pertenecen juntos con otras familias de ascomicetos thiriothecioides de la clase Dothideomycetes por la presencia de ascos bitunicados. Hasta ahora los ascomicetos thiriothecioides no tienen un concepto taxonĂłmico uniforme y estudios filogenĂ©ticos extensos estan ausentes. En esta thesis 42 especies de ascomicetos thiriothecioides recientemente colectados en el Oeste de PanamĂĄ, se presentan con descripciones detalladas e illustraciones en forma de dibujos e imĂĄgenes de microscopĂ­o electrĂłnico de barrido y transmisiĂłn. Las 42 especies pertenecen a 13 diferentes gĂ©neros de las familias Asterinaceae (37 especies), Microthyriaceae (cuatro especies) y ‘Pycnothyriales’ (una especie). Dos especies de Asterinaceae son nuevas para la ciencia: Asterina gaiadendricola con Asterostomella anamorfo y Asterina schlegeliae con Mahanteshamyces anamorfo. 28 especies de Asterinaceae se citan por primera vez para PanamĂĄ: Asterina cestricola, A. ciferriana, A. consobrina, A. corallopoda, A. davillae con anamorfo, A. diplocarpa, A. diplopoda, A. ekmanii, A. fuchsiae, A. manihotis, A. phenacis, A. radiofissilis con anamorfo, A. siphocampyli, A. sponiae, A. stipitipodia con anamorfo, A. styracina, A. tonduzii con anamorfo, A. weinmanniae, A. zanthoxyli, Asterostomella dilleniicola, Asterolibertia licaniicola, Asterolibertia nodulosa, Cirsosia splendida con Homalopeltis chrysobalani anamorfo y Prillieuxina winteriana con Leprieurina winteriana anamorfo. Las otras 11 especies de Asterinaceae representan probablemente nuevas especies: Asterina spp. 1-8, Asterolibertia sp., Halbanina sp. y Mahanteshamyces sp. Las cuatros especies de Microthyriaceae son nuevos reportes para PanamĂĄ: Maublanica uleana, Platypeltella irregularis, Platypeltella smilacis y Xenostomella tovarensis. Hemisphaeropsis magnoliae que pertenece al grupo ‘Pycnothyriales’, tambiĂ©n representa un nuevo reporte para PanamĂĄ. AsĂ­ el nĂșmero de especies de Asterinaceae conocidas en PanamĂĄ aumenta de cuatro a 30, para Microthyriaceae de cero a cuatro y para ‘Pycnothyriales’ de cero a una. 21 de las especies presentadas son nuevos reportes para AmĂ©rica Central y dos especies estĂĄn nuevamente reportadas para el continente AmĂ©ricano. Las 42 especies presentadas crecen en 47 especies de plantas hospederas de 39 gĂ©neros que pertenecen a 28 familias de plantas vasculares. Para 23 especies de hongos se descubrieron nuevas especies de plantas hospederas. De estas, siete pertenecen a gĂ©neros de plantas desconicidas antes como hospederos de especies de Asterinaceae y Microthyriaceae: Burmeistera (Campanulaceae), Curatella y Davilla (Dilleniaceae), Greigia (Bromeliaceae), Hirtella (Chrysobalanaceae), Oxandra y Xylopia (Annonaceae). En esta tĂ©sis se presenta el primer estudio filogenĂ©tico de la familia Asterinaceae. Por primera vez, el ADN fue aislado en PanamĂĄ de material fresco de especies de Asterina y sus estados anamorfos. La hipĂłtesis derivada de SSU y LSU rADN neighbour-joining anĂĄlisis soporta la monofilia de la familia Asterinaceae en la clase Dothideomycetes. Los datos del proyecto ppMP (microhongos parĂĄsitos en plantas de PanamĂĄ) indican una constante presencia de ascomicetos thiriothecioides parasitĂ­cos en comunidades naturales de plantas en PanamĂĄ. En el Oeste de PanamĂĄ los Asterinaceae representan el grupo mĂĄs diverso y rico en especies. Amplias colecciones en las ĂĄreas tropicales del mundo seguramente pueden ampliar el conocimiento sobre la diversidad y ecologĂ­a de ascomicetos thiriothecioides parasitĂ­cos

    Subcellular localization and tissue specific expression of amidase 1 from Arabidopsis thaliana

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    Amidase 1 (AMI1) from Arabidopsis thaliana converts indole-3-acetamide (IAM), into indole-3-acetic acid (IAA). AMI1 is part of a small isogene family comprising seven members in A. thaliana encoding proteins which share a conserved glycine- and serine-rich amidase-signature. One member of this family has been characterized as an N-acylethanolamine-cleaving fatty acid amidohydrolase (FAAH) and two other members are part of the preprotein translocon of the outer envelope of chloroplasts (Toc complex) or mitochondria (Tom complex) and presumably lack enzymatic activity. Among the hitherto characterized proteins of this family, AMI1 is the only member with indole-3-acetamide hydrolase activity, and IAM is the preferred substrate while N-acylethanolamines and oleamide are not hydrolyzed significantly, thus suggesting a role of AMI1 in auxin biosynthesis. Whereas the enzymatic function of AMI1 has been determined in vitro, the subcellular localization of the enzyme remained unclear. By using different GFP-fusion constructs and an A. thaliana transient expression system, we show a cytoplasmic localization of AMI1. In addition, RT-PCR and anti-amidase antisera were used to examine tissue specific expression of AMI1 at the transcriptional and translational level, respectively. AMI1-expression is strongest in places of highest IAA content in the plant. Thus, it is concluded that AMI1 may be involved in de novo IAA synthesis in A. thaliana

    The Critical Role of N- and C-Terminal Contact in Protein Stability and Folding of a Family 10 Xylanase under Extreme Conditions

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    Stabilization strategies adopted by proteins under extreme conditions are very complex and involve various kinds of interactions. Recent studies have shown that a large proportion of proteins have their N- and C-terminal elements in close contact and suggested they play a role in protein folding and stability. However, the biological significance of this contact remains elusive.In the present study, we investigate the role of N- and C-terminal residue interaction using a family 10 xylanase (BSX) with a TIM-barrel structure that shows stability under high temperature, alkali pH, and protease and SDS treatment. Based on crystal structure, an aromatic cluster was identified that involves Phe4, Trp6 and Tyr343 holding the N- and C-terminus together; this is a unique and important feature of this protein that might be crucial for folding and stability under poly-extreme conditions. folding and activity. Alanine substitution with Phe4, Trp6 and Tyr343 drastically decreased stability under all parameters studied. Importantly, substitution of Phe4 with Trp increased stability in SDS treatment. Mass spectrometry results of limited proteolysis further demonstrated that the Arg344 residue is highly susceptible to trypsin digestion in sensitive mutants such as ΔF4, W6A and Y343A, suggesting again that disruption of the Phe4-Trp6-Tyr343 (F-W-Y) cluster destabilizes the N- and C-terminal interaction. Our results underscore the importance of N- and C-terminal contact through aromatic interactions in protein folding and stability under extreme conditions, and these results may be useful to improve the stability of other proteins under suboptimal conditions

    Identification of regulatory variants associated with genetic susceptibility to meningococcal disease.

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    Non-coding genetic variants play an important role in driving susceptibility to complex diseases but their characterization remains challenging. Here, we employed a novel approach to interrogate the genetic risk of such polymorphisms in a more systematic way by targeting specific regulatory regions relevant for the phenotype studied. We applied this method to meningococcal disease susceptibility, using the DNA binding pattern of RELA - a NF-kB subunit, master regulator of the response to infection - under bacterial stimuli in nasopharyngeal epithelial cells. We designed a custom panel to cover these RELA binding sites and used it for targeted sequencing in cases and controls. Variant calling and association analysis were performed followed by validation of candidate polymorphisms by genotyping in three independent cohorts. We identified two new polymorphisms, rs4823231 and rs11913168, showing signs of association with meningococcal disease susceptibility. In addition, using our genomic data as well as publicly available resources, we found evidences for these SNPs to have potential regulatory effects on ATXN10 and LIF genes respectively. The variants and related candidate genes are relevant for infectious diseases and may have important contribution for meningococcal disease pathology. Finally, we described a novel genetic association approach that could be applied to other phenotypes

    Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

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    Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

    Ten simple rules for Global North researchers to stop perpetuating helicopter research in the Global South

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    The practice of Global North (i.e., “richer” globalized countries located in the northern hemisphere, except for Australia and New Zealand) researchers making roundtrips to the Global South (i.e., “poorer” developing countries located around the tropics and in the Southern hemisphere) to collect materials and then process, analyze, and publish results with little to no involvement from local collaborators is referred to as “helicopter research” or “parachute research”. At best, local scientists provide logistical help and knowledge of the local community, such as field site guiding, identification of local organisms, translation from and to local languages, and facilitating resources to foreign scientists. However, often, these necessary actors in the scientific process receive little to no retribution for their work and knowledge. For example, a systematic problem in academia is that local scientists and graduate and undergraduate students are often not offered coauthorship in manuscripts for which their contributions were essential (e.g., project planning, logistics, and knowledge of local biodiversity). Even worse is that research remains unavailable for them and others who contributed substantially, since in most cases, peer-review publications are available behind a paywall, and they are written in English, which is the second or third language for many Global South researchers. Furthermore, local communities where Global North scientists come to conduct helicopter research are usually left out of broader impacts and outreach efforts, as these tend to happen in Global North communities. Helicopter research is a way to perpetuate colonization practices, and power imbalances are critical in perpetuating helicopter research. For example, Global North researchers often set the research agenda based on priorities of their funding agencies, which, in many cases, are decided upon by those same researchers sitting in decision-making committees of those very agencies. All too often, proposals are developed without a deep understanding of problems and priorities of Global South countries where the anticipated research will take place. Global South collaborators are rarely invited to brainstorm and set the research agenda for their needs. This opens the door for unequal partnership with research objectives that may be irrelevant for Global South collaborators, who then, are forced to accept an already funded proposal due to lack of research funding within their own countries or institutions. Thus, power and politics behind science are interconnected and are a driving force behind helicopter research. Helicopter research is a problem that also happens within Global North and within Global South countries, where dominating cultures perpetuate abuse on historically marginalized communities, including those of indigenous people, people of color, people from lower socioeconomic status, etc. This is an increasingly complex problem that has been intensely discussed in other papers and for which extensive guidelines exist. Here, we address the problem that exists specifically between researchers from the Global North—often members of the dominating culture—toward people of the Global South who may or may not be members of the dominating culture. We propose 10 simple rules for avoiding helicopter research for better, collaborative, and non-colonial science between the Global North and the Global South

    Panama, a hot spot for Hermatomyces (Hermatomycetaceae, Pleosporales) with five new species, and a critical synopsis of the genus

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    Five new species belonging to Hermatomyces (Hermatomycetaceae, Pleosporales) are described based on morphological investigations of specimens collected on rotten twigs and stems of various plants in Panama as well as phylogenetic analyses of sequence data of nuclear ribosomal and protein coding genes (EF1-α, RPB2, ÎČ-TUB). The new species are described as: Hermatomyces bifurcatus, H. constrictus, H. megasporus, H. sphaericoides, and H. verrucosus spp. nov. Previously described species such as H. sphaericus and H. tucumanensis were identified among the studied specimens. The new combination, H. reticulatus, is made for Subicularium reticulatum based on examination of the holotype and fresh collections. Hermatomyces subiculosus, originally described from Thailand, is reduced to synonymy with H. reticulatus; H. tectonae is synonymized under H. sphaericus based on morphological and molecular evidence; and H. chiangmaiensis and H. thailandicus are considered later synonyms of H. krabiensis and H. indicus, respectively. The type material of Scyphostroma mirum was found to be conspecific with H. tucumanensis and, therefore, the generic name Hermatomyces should be conserved or protected against the older name Scyphostroma and the binomial H. tucumanensis against S. mirum. Sixteen species of Hermatomyces are recognized, their distinctive characteristics are highlighted in line drawings and a key is provided for their identification. The peculiar morphology and consistent phylogeny of new and previously known Hermatomyces species supports the recognition of the recently introduced monotypic family Hermatomycetaceae as a well delimited monophyletic taxon within the order Pleosporales

    Two new species in a new genus and a critical revision of Brachybasidiaceae (Exobasidiales, Basidiomycota) in honor of Franz Oberwinkler

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    The Brachybasidiaceae are a family of 22 known species of plant-parasitic microfungi belonging to Exobasidiales, Basidiomycota. Within this family, species of the largest genus Kordyana develop balls of basidia on top of stomatal openings. Basidial cells originate from fungal stroma filling substomatal chambers. Species of Kordyana typically infect species of Commelinaceae. During fieldwork in the neotropics, fungi morphologically similar to Kordyana spp. were found on Goeppertia spp. (syn. Calathea spp., Marantaceae), namely on G. panamensis in Panama and on G. propinqua in Bolivia. These specimens are proposed as representatives of a genus new to science, Marantokordyana, based on the distinct host family and molecular sequence data of ITS and LSU rDNA regions. The specimens on the two host species represent two species new to science, M. oberwinkleriana on G. panamensis and M. boliviana on G. propinqua. They differ by the size and shape of their basidia, molecular sequence data of ITS and LSU rDNA regions, and host plant species. In the past, the understanding of Brachybasidiaceae at order and family level was significantly improved by investigation realized by Franz Oberwinkler and his collaborators at the University of TĂŒbingen, Germany. On species level, however, our knowledge is still very poor due to incomplete species descriptions of several existing names in literature, scarceness of specimens, as well as sequence data lacking for many taxa and for further barcode regions. Especially species of Kordyana and species of Dicellomyces are in need of revision
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