The 13th Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-IV Survey Mapping Nearby Galaxies at Apache Point Observatory

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) began observations in July 2014. It pursues three core programs: APOGEE-2,MaNGA, and eBOSS. In addition, eBOSS contains two major subprograms: TDSS and SPIDERS. This paper describes the first data release from SDSS-IV, Data Release 13 (DR13), which contains new data, reanalysis of existing data sets and, like all SDSS data releases, is inclusive of previously released data. DR13 makes publicly available 1390 spatially resolved integral field unit observations of nearby galaxies from MaNGA,the first data released from this survey. It includes new observations from eBOSS, completing SEQUELS. In addition to targeting galaxies and quasars, SEQUELS also targeted variability-selected objects from TDSS and X-ray selected objects from SPIDERS. DR13 includes new reductions ofthe SDSS-III BOSS data, improving the spectrophotometric calibration and redshift classification. DR13 releases new reductions of the APOGEE-1data from SDSS-III, with abundances of elements not previously included and improved stellar parameters for dwarf stars and cooler stars. For the SDSS imaging data, DR13 provides new, more robust and precise photometric calibrations. Several value-added catalogs are being released in tandem with DR13, in particular target catalogs relevant for eBOSS, TDSS, and SPIDERS, and an updated red-clump catalog for APOGEE.This paper describes the location and format of the data now publicly available, as well as providing references to the important technical papers that describe the targeting, observing, and data reduction. The SDSS website, http://www.sdss.org, provides links to the data, tutorials and examples of data access, and extensive documentation of the reduction and analysis procedures. DR13 is the first of a scheduled set that will contain new data and analyses from the planned ~6-year operations of SDSS-IV.PostprintPeer reviewe

Effect of storage temperature on the lag time of Geobacillus stearothermophilus individual spores

The lag times (lambda) of Geobacillus stearothermophilus single spores were studied at different storage temperatures ranging from 45 to 59 degrees C using the Bioscreen C method. A significant variability of lambda was observed among individual spores at all temperatures tested. The storage temperature affected both the position and the spread of the lambda distributions. The minimum mean value of lambda (i.e. 10.87 h) was observed at 55 degrees C, while moving away from this temperature resulted in an increase for both the mean and standard deviation of lambda, A Cardinal Model with Inflection (CMI) was fitted to the reverse mean lambda, and the estimated values for the cardinal parameters T-min, T-max, T-opt and the optimum mean lambda of G. stearothermophilus were found to be 38.1, 64.2, 53.6 degrees C and 10.3 h, respectively. To interpret the observations, a probabilistic growth model for G. stearothermophilus individual spores, taking into account lambda variability, was developed. The model describes the growth of a population, initially consisting of No spores, over time as the sum of cells in each of the N-0 imminent subpopulations originating from a single spore. Growth simulations for different initial contamination levels showed that for low N-0 the number of cells in the population at any time is highly variable. An increase in N-0 to levels exceeding 100 spores results in a significant decrease of the above variability and a shorter lambda of the population. Considering that the number of G. stearothermophilus surviving spores in the final product is usually very low, the data provided in this work can be used to evaluate the probability distribution of the time-to-spoilage and enable decision-making based on the "acceptable level of risk".Understanding the impact of manufacturing processes in the ecology / European Social Fund (ESF

Quorum sensing network in clinical strains of A. baumannii : AidA is a new quorum quenching enzyme

Acinetobacter baumannii is an important pathogen that causes nosocomial infections generally associated with high mortality and morbidity in Intensive Care Units (ICUs). Currently, little is known about the Quorum Sensing (QS)/Quorum Quenching (QQ) systems of this pathogen. We analyzed these mechanisms in seven clinical isolates of A. baumannii. Microarray analysis of one of these clinical isolates, Ab1 (A. baumannii ST-2-clon-2010), previously cultured in the presence of 3-oxo-C12-HSL (a QS signalling molecule) revealed a putative QQ enzyme (α/β hydrolase gene, AidA). This QQ enzyme was present in all nonmotile clinical isolates (67% of which were isolated from the respiratory tract) cultured in nutrient depleted LB medium. Interestingly, this gene was not located in the genome of the only motile clinical strain growing in this medium (A. baumannii strain Ab421-GEIH-2010 [Ab7], isolated from a blood sample). The AidA protein expressed in E. coli showed QQ activity. Finally, we observed downregulation of the AidA protein (QQ system attenuation) in the presence of HO (ROS stress). In conclusion, most of the A. baumannii clinical strains were not surface motile (84%) and were of respiratory origin (67%). Only the pilT gene was involved in surface motility and related to the QS system. Finally, a new QQ enzyme (α/β hydrolase gene, AidA protein) was detected in these strains

Considerations and consequences of allowing DNA sequence data as types of fungal taxa

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.Peer reviewe

Considerations and consequences of allowing DNA sequence data as types of fungal taxa

Abstract Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.Publisher’s Note A first version of this text was prepared by the first eight authors and the last one, given here. The other listed co-authors in the article PDF support the content, and their actual contributions varied from only support to additions that substantially improved the content. The full details of all co-authors, with their affiliations, are included in Supplementary Table 1 after p.175 of the article for reasons of clarity and space. Slavomír Adamčík Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23 Bratislava, Slovakia Teuvo Ahti Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland M. Catherine Aime Purdue University, 915 W. State St., West Lafayette, Indiana 47907, U.S.A. A. Martyn Ainsworth Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom László Albert Hungarian Mycological Society, 1087 Könyves Kálmán krt. 40, Budapest, Hungary Edgardo Albertó Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, Universidad Nacional de San Martin-Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina Alberto Altés García Facultad de Biología, Ciencias Ambientales y Química, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain Dmitry Ageev SIGNATEC Ltd., 630090, Novosibirsk, Akademgorodok (Novosibirsk Scientific Center), Inzhenernaya str., 22, Russia Reinhard Agerer Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638 München, Germany Begona Aguirre-Hudson Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom Joe Ammirati University of Washington, Seattle, Washington 98195-1800, U.S.A. Harry Andersson Eichhahnweg 29a, 38108 Braunschweig, Germany Claudio Angelini Jardín Botánico Nacional Dr. Rafael Ma. Moscoso, Apartado 21-9, Santo Domingo, Dominican Republic Vladimír Antonín Moravian Museum, Zeny trh 6, 659 37 Brno, Czech Republic Takayuki Aoki Genetic Resources Center, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan André Aptroot ABL Herbarium, G.v.d.Veenstraat 107, 3762 XK Soest, The Netherlands Didier Argaud 40 rue du Justemont, 57290 Fameck, France Blanca Imelda Arguello Sosa Instituto Tecnológico de Ciudad Victoria, Tecnológico Nacional de México, Ciudad Victoria, Tamaulipas, Mexico Arne Aronsen Torødveien 54, 3135 Torød, Norway Ulf Arup Biological Museum, Lund University, Box 117, 221 00 Lund, Sweden Bita Asgari Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization, Tehran, Iran Boris Assyov Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin Str., 1113 Sofia, Bulgaria Violeta Atienza Facultad de Ciencias Biológicas, Universitat de València, C/Dr Moliner 50, 46100, Burjasot, Valencia, Spain Ditte Bandini Panoramastr 47, 69257 Wiesenbach, Germany João Luís Baptista-Ferreira Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal Hans-Otto Baral Blaihofstr. 42, 72074 Tübingen, Germany Tim Baroni The State University of New York, 340 Bowers Hall, P.O. Box 2000, Cortland, New York 13045, U.S.A. Robert Weingart Barreto Universidade Federal de Viçosa, 36570-000, Viçosa, Minas Gerais, Brazil Henry Beker (1) Royal Holloway, University of London, United Kingdom; (2) Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium Ann Bell 45 Gurney Road, Lower Hutt, New Zealand Jean-Michel Bellanger CEFE UMR5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, INSERM, 1919 Route de Mende, 34293 Montpellier Cédex 5, France Francesco Bellù Naturmusem of Bolzano, CP 104, 39100, Bolzano, Italy Martin Bemmann Kleingemünderstraße 111, 69118 Heidelberg, Germany Mika Bendiksby NTNU, University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway Egil Bendiksen Norwegian Institute for Nature Research, Gaustadalleen 21, 0349 Oslo, Norway Katriina Bendiksen Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318 Oslo, Norway Lajos Benedek Szent Istvan University, Hungary Anna Bérešová-Guttová Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23 Bratislava, Slovakia Franz Berger University of Salzburg, Salzburg, Austria Reinhard Berndt Herbaria Z+ZT, ETH Zürich, CHN D37, Universitätstr. 16, 8092 Zürich, Switzerland Annarosa Bernicchia Via A. Guidotti 39, 40134 Bologna, Italy Alona Yu. Biketova Institute of Biochemistry, BRC-HAS, 6726 Szeged, Temesvari krt. 62, 6726 Szeged, Hungary Enrico Bizio Società Veneziana di Micologia, Società Veneziana di Scienze Naturali, Fontego dei Turchi, Santa Croce 1730, 30135 Venice, Italy Curtis Bjork UBC Herbarium, Beaty Biodiversity Museum, University of British Columbia, Canada Teun Boekhout (1) Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands; (2) Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands David Boertmann Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark Tanja Böhning AG Geobotanik Schleswig-Holstein & Hamburg, c/o University of Kiel, Olshausenstraße 75, 24098 Kiel, Germany Florent Boittin Ascomycete.org, 36 rue de la Garde, 69005 Lyon, France Carlos G. Boluda Conservatoire et Jardin botaniques de la Ville de Genève, 1292 Genève, Switzerland Menno W. Boomsluiter T.v.Lohuizenstraat 34, 8172xl, Vaassen, The Netherlands Jan Borovička Institute of Geology, Czech Academy of Sciences, Rozvojova 269, 165 00 Prague 6, Czech Republic Tor Erik Brandrud Norwegian Institute for Nature Research, Gaustadalleen 21, 0349 Oslo, Norway Uwe Braun Martin-Luther-Universität, Institut für Biologie, Bereich Geobotanik, und Botanischer Garten, Herbarium, Neuwerk 21, 06099 Halle, Germany Irwin Brodo Canadian Museum of Nature, 240 McLeod Street, Ottawa, Ontario, Canada Tatiana Bulyonkova A.P. Ershov Institute of Informatics Systems, Russian Academy of Sciences, Siberian Branch, 6 Acad. Lavrentjev pr., Novosibirsk 630090, Russia Harold H. Burdsall Jr. Fungal & Decay Diagnostics, LLC, 9350 Union Valley Road, Black Earth, Wisconsin 53515, U.S.A. Bart Buyck Muséum National d’Histoire Naturelle, CP 39, ISYEB, UMR 7205 CNRS MNHN UPMC EPHE, 12 rue Buffon, 75005 Paris, France Ana Rosa Burgaz Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain Vicent Calatayud Fundación CEAM, c/ Charles R. Darwin, 14, Parque Tecnológico, 46980 Paterna, Valencia, Spain Philippe Callac INRA, MycSA, CS 20032, 33882 Villenave d’Ornon, France Emanuele Campo Associazione Micologica Bresadola, Via Alessandro Volta 46, 38123 Trento, Italy Massimo Candusso Via Ottone Primo 90, 17021, Alassio, Savona, Italy Brigitte Capoen Queffioec, rue de Saint Gonval, 22710 Penvenan, France Joaquim Carbó Roser, 60, 17257 Torroella de Montgrí, Girona, Spain Matteo Carbone Via Don Luigi Sturzo 173 16148 Genova, Italy Rafael F. Castañeda-Ruiz Instituto de Investigaciones Fundamentales en Agricultura, Tropical ‘Alejandro de Humboldt’, OSDE, Grupo Agrícola, Calle 1 Esq. 2, Santiago de Las Vegas, C. Habana 17200, Cuba Michael A. Castellano USDA, Forest Service, Northern Research Station, Corvallis, Oregon 97330, U.S.A. Jie Chen Mae Fah Luang University, Chang Wat Chiang Rai 57100, Thailand Philippe Clerc Conservatoire et Jardin botaniques de la Ville de Genève, 1292 Genève, Switzerland Giovanni Consiglio Via C. Ronzani 61, 40033 Casalecchio Bologna, Italy Gilles Corriol National Botanical Conservatory for Pyrenees and Midi-Pyrénées Region of France and BBF Herbarium, Vallon de Salut. B.P. 315. 65203 Bagnères-de-Bigorre, France Régis Courtecuisse Université Lille, Fac. Pharma. Lille, EA4483 IMPECS, 59000 Lille, France Ana Crespo Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain Cathy Cripps Plant Sciences & Plant Pathology, 119 Plant Biosciences Building, Montana State University, Bozeman, Montana 59717, U.S.A. Pedro W. Crous Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands Gladstone Alves da Silva Universidade Federal de Pernambuco, Centro de Biociências, Avenida da Engenharia, S/N, Cidade Universitária, Recife, Pernambuco, Brazil Meiriele da Silva Universidade Federal de Viçosa, 36570-000, Viçosa, Minas Gerais, Brazil Marjo Dam Hooischelf 13, 6581 SL Malden, The Netherlands Nico Dam Hooischelf 13, 6581 SL Malden, The Netherlands Frank Dämmrich The Bavarian Natural History Collections (SNSB Munich), Menzinger Strasse 71, 80638, München, Germany Kanad Das Botanical Survey of India, Cryptogamic Unit, P.O. Botanic Garden, Howrah 711103, W.B., India Linda Davies Centre for Environmental Policy, Imperial College London, SW7 2AZ, United Kingdom Eske De Crop Ghent University K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Andre De Kesel Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium Ruben De Lange Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium Bárbara De Madrignac Bonzi Instituto de Botánica del Nordeste, Universidad Nacional de Nordeste-Consejo Nacional de Investigaciones Científicas y Técnicas, Sargento Cabral 2131, CC 209, Corrientes Capital, Argentina Thomas Edison E. dela Cruz University of Santo Tomas, Espana 1008 Manila, Philippines Lynn Delgat Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium Vincent Demoulin Institut de Botanique, B.22, Université de Liège, 4000 Liège I, Belgium Dennis E. Desjardin HD Thiers Herbarium (SFSU), San Francisco State University, 1600 Holloway Ave, San Francisco, California 94132, U.S.A. Paul Diederich Musée national d’histoire naturelle, 25 rue Münster, 2160 Luxembourg, Luxembourg Bálint Dima (1) Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117 Budapest, Hungary; (2) Viikki Plant Science Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland Maria Martha Dios Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Catamarca, Av Belgrano 300, 4700 San Fernando del Valle de Catamarca, Argentina Pradeep Kumar Divakar Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain Clovis Douanla-Meli Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for National and International Plant Health, Messeweg 11-12, 38104 Braunschweig, Germany Brian Douglas Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom Elisandro Ricardo Drechsler-Santos Universidade Federal de Santa Catarina, Campus Universitário Reitor João David Ferreira Lima, Trindade, Florianópolis, Santa Catarina CEP 88040-900, Brazil Paul S. Dyer School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom Ursula Eberhardt Abt. Botanik, Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany Damien Ertz Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium Fernando Esteve-Raventós Facultad de Biología, Ciencias Ambientales y Química, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain Javier Angel Etayo Salazar Navarro Villoslada 16, 3º dcha., 31003 Pamplona, Navarra, Spain Vera Evenson Sam Mitchel Herbarium of Fungi, Denver Botanic Gardens, 1007 York Street, Denver, Colorado 80206, U.S.A. Guillaume Eyssartier Muséum national d’histoire naturelle, Jardin des plantes, 57 rue Cuvier, 75005 Paris, France Edit Farkas Institute of Ecology and Botany, MTA Centre for Ecological Research, 2163 Vácrátót, Hungary Alain Favre Fédération Mycologique et Botanique Dauphiné Savoie, Le Prieuré, 144 Place de l’Eglise, 74320 Sevrier, France Anna G. Fedosova Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia Mario Filippa Regione Monsarinero 36, 14041 Agliano Terme, Italy Péter Finy 8000 Székesfehérvár, Zsombolyai u. 56, Hungary Adam Flakus W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Krakow, Poland Simón Fos Facultad de Ciencias Biológicas, Universitat de València, C/Dr Moliner 50, 46100, Burjasot, Valencia, Spain Jacques Fournier Las Muros, F. 09420 Rimont, France André Fraiture Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium Paolo Franchi Associazione Micologica Bresadola, Via Alessandro Volta 46, 38123 Trento, Italy Ana Esperanza Franco Molano Escuela de Microbiología, Universidad de Antioquia, AA1226, Fundación Biodiversa Colombia, Medellín, Colombia Gernot Friebes Centre of Natural History, Botany & Mycology, Universalmuseum Joanneum, Weinzöttlstraße 16, 8045 Graz, Austria Andreas Frisch NTNU, University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway Alan Fryday Michigan State University, East Lansing, Michigan 48824, U.S.A. Giuliana Furci The Fungi Foundation, Paseo Bulnes 79 of. 112A, Santiago, Chile Ricardo Galán Márquez Facultad de Biología, Ciencias Ambientales y Química, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain Matteo Garbelotto University of California, 130 Mulford Hall #3114 Berkeley, California 94720, U.S.A. Joaquina Maria Garcia-Martin Real Jardín Botánico-CSIC, Plaza de Murillo 2, 28014, Madrid, Spain Mónica A. García Otálora Herbaria Z+ZT, ETH Zürich, CHN D37, Universitätstr. 16, 8092 Zürich, Switzerland Dania García Sánchez Universitat Rovira i Virgili, C/ Sant Llorenç 21, 43201 Reus, Tarragona, Spain Alain Gardiennet 14 rue Roulette, 21260 Véronnes, France Sigisfredo Garnica Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Isla Teja Campus, Casilla 567, Valdivia, Chile Isaac Garrido Benavent Real Jardín Botánico-CSIC, Plaza de Murillo 2, 28014, Madrid, Spain Genevieve Gates Tasmanian Institute of Agriculture, Private Bag 54, Hobart, Tasmania 7001, Australia Alice da Cruz Lima Gerlach Conservatoire et Jardin Botaniques de la ville de Genève, Genève, Switzerland Masoomeh Ghobad-Nejhad Iranian Research Organization for Science and Technology, P.O. Box 15815-3538, Tehran 15819, Iran Tatiana B. Gibertoni Universidade Federal de Pernambuco, Centro de Biociências, Avenida da Engenharia, S/N, Cidade Universitária, Recife, Pernambuco, Brazil Tine Grebenc Slovenian Forestry Institute, Vecna pot 2, 100 Ljubljana, Slovenia Irmgard Greilhuber University of Vienna, Rennweg 14, 1030 Vienna, Austria Bella Grishkan Institute of Evolution, University of Haifa, Aba Khoushi Ave. 199, Mt. Carmel, Haifa 3498838, Israel Johannes Z. Groenewald Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands Martin Grube Institute of Biology, University of Graz, Holteiasse 6, 8010 Graz, Austria Gérald Gruhn Office National des Forêts, 2 Avenue de Saint-Mandé, 75570 Paris Cedex 12, France Cécile Gueidan CSIRO — Australian National Herbarium, Clunies Ross Street, Canberra ACT 2601, Australia Gro Gulden Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318 Oslo, Norway Luis FP Gusmão Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Bairro Novo Horizonte, CEP:44036-900, Feira de Santana, Bahia, Brazil Josef Hafellner Institute of Biology, University of Graz, Holteiasse 6, 8010 Graz, Austria Michel Hairaud 2 Impasse des Marronniers, 79360 Poivendre de Marigny, France Marek Halama Museum of Natural History, Wrocław University, ul. H. Sienkiewicza 5, 50-335 Wrocław, Poland Nils Hallenberg University of Gothenburg, Box 461, 40530 Göteborg, Sweden Roy E. Halling Institute of Systematic Botany, New York Botanical Garden, 2900 Southern Blvd, Bronx, New York 10458-5126, U.S.A. Karen Hansen Swedish Museum of Natural History, P.O. Box 50007, 104 05 Stockholm, Sweden Christoffer Bugge Harder Texas Tech University, Box 42122, Lubbock, Texas 79409, U.S.A. Jacob Heilmann-Clausen Natural History Museum of Denmark, Universitetsparken 15, 2100 København, Denmark Stip Helleman Sweelinck 78, 5831KT Boxmeer, The Netherlands Alain Henriot Mycological Society of France, 20 rue Rottembourg, 12th arrondissement, Paris, France Margarita Hernandez-Restrepo Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands Raphaël Herve 24 rue des Fougères, 86550 Mignaloux-Beauvoir, France Caroline Hobart 84 Stafford Road, Sheffield, South Yorkshire S2 2SF, United Kingdom Mascha Hoffmeister Julius Kühn-Institut, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany Klaus Høiland University of Oslo, P.O.Box 1066, Blindern, 0316 Oslo, Norway Jan Holec National Museum, Herbarium PRM, Cirkusová 1740, 193 00 Praha 9, Czech Republic Håkon Holien Faculty of Bioscience and Aquaculture, NORD University, P.O. Box 2501, 7729 Steinkjer, Norway Karen Hughes University of Tennessee, Knoxville, Tennessee 37996, U.S.A. Vit Hubka Faculty of Science, Charles University, Benátská 2, 128 01 Praha 2, Czech Republic Seppo Huhtinen Herbarium TUR, Biodiversity Unit, University of Turku, 20014 Turku, Finland Boris Ivančević Natural History Museum, Njegoševa 51, P.O. Box 401, 11000 Belgrade, Serbia Marian Jagers Reelaan 13, 7522 LR Enschede, The Netherlands Walter Jaklitsch Institute of Forest Entomology, Forest Pathology and Forest Protection, University of Natural Resources and Life Sciences Vienna, Vienna, Austria AnnaElise Jansen Stationsstraat 10, 6701 AM Wageningen, the Netherlands Ruvishika S. Jayawardena Mae Fah Luang University, Chang Wat Chiang Rai 57100, Thailand Thomas Stjernegaard Jeppesen Global Biodiversity Information Facility, Universitetsparken 15, 2100 København Ø, Denmark Mikael Jeppson Lilla Håjumsgatan 4, 46135 Trollhättan, Sweden Peter Johnston Manaaki Whenua Landcare Research, Private Bag 92170, Auckland 1072, New Zealand Per Magnus Jørgensen University of Bergen, Allégaten 41, P.O. Box 7800, 5020 Bergen, Norway Ingvar Kärnefelt Biological Museum, Lund University, Box 117, 221 00 Lund, Sweden Liudmila B. Kalinina Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia Gintaras Kantvilas Tasmanian Herbarium (HO), Tasmanian Museum and Art Gallery, P.O. Box 5058, UTAS LP.O., Sandy Bay, Tasmania 7005, Australia Mitko Karadelev Institute of Biology, Faculty of Natural Science and Mathematics, Ss. Cyril and Methodius University, Arhimedova 5, 1000 Skopje, Republic of Macedonia Taiga Kasuya Faculty of Risk and Crisis Management, Chiba Institute of Science, 3 Shiomi-cho, Choshi, Chiba 288-0025, Japan Ivona Kautmanová Natural History Museum, Slovak National Museum, Bratislava, Slovakia Richard W. Kerrigan RWK Research, Kittanning, Pennsylvania 16201, U.S.A. Martin Kirchmair Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria Anna Kiyashko Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia Dániel G. Knapp Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117 Budapest, Hungary Henning Knudsen Natural History Museum of Denmark, Universitetsparken 15, 2100 København, Denmark Kerry Knudsen Faculty of Environmental Sciences, University of Life Sciences at Prague, Prague, Czech Republic Tommy Knutsson Nedra Västerstad 111, 380 62 Mörbylånga, Sweden Miroslav Kolařík Institute of Microbiology ASCR, Videnska 1083, 142 20 Prague 4, Czech Republic Urmas Kõljalg Institute of Ecology and Earth Sciences, 40 Lai Street, Tartu 51005, Estonia Alica Košuthová Swedish Museum of Natural History, P.O. Box 50007, 104 05 Stockholm, Sweden Attila Koszka Faculty of Agricultural and Environmental Sciences, Kaposvar University, 7400 Kaposvar, Hungary Heikki Kotiranta Finnish Environment Institute, P.O. Box 140, 00251 Helsinki, Finland Vera Kotkova Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia Ondřej Koukol Faculty of Science, Charles University, Benátská 2, 128 01 Praha 2,

Neotropical freshwater fisheries : A dataset of occurrence and abundance of freshwater fishes in the Neotropics

The Neotropical region hosts 4225 freshwater fish species, ranking first among the world's most diverse regions for freshwater fishes. Our NEOTROPICAL FRESHWATER FISHES data set is the first to produce a large-scale Neotropical freshwater fish inventory, covering the entire Neotropical region from Mexico and the Caribbean in the north to the southern limits in Argentina, Paraguay, Chile, and Uruguay. We compiled 185,787 distribution records, with unique georeferenced coordinates, for the 4225 species, represented by occurrence and abundance data. The number of species for the most numerous orders are as follows: Characiformes (1289), Siluriformes (1384), Cichliformes (354), Cyprinodontiformes (245), and Gymnotiformes (135). The most recorded species was the characid Astyanax fasciatus (4696 records). We registered 116,802 distribution records for native species, compared to 1802 distribution records for nonnative species. The main aim of the NEOTROPICAL FRESHWATER FISHES data set was to make these occurrence and abundance data accessible for international researchers to develop ecological and macroecological studies, from local to regional scales, with focal fish species, families, or orders. We anticipate that the NEOTROPICAL FRESHWATER FISHES data set will be valuable for studies on a wide range of ecological processes, such as trophic cascades, fishery pressure, the effects of habitat loss and fragmentation, and the impacts of species invasion and climate change. There are no copyright restrictions on the data, and please cite this data paper when using the data in publications

Guidelines for the use and interpretation of assays for monitoring autophagy

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field