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4. Multi-layered genome defences in bacteria

Author

Agapov, Aleksei, Baker, Kate S, Bedekar, Paritosh, Bhatia, Rama P, Blower, Tim R, Brockhurst, Michael A, Brown, Cooper, Chong, Charlotte E, Fothergill, Joanne L, Graham, Shirley, Hall, James PJ, Maestri, Alice, McQuarrie, Stuart, Olina, Anna, Pagliara, Stefano, Recker, Mario, Richmond, Anna, Shaw, Steven J, Szczelkun, Mark D, Taylor, Tiffany B, van Houte, Stineke, Went, Sam C, Westra, Edze R, White, Malcolm F, and Wright, Rosanna

Published
2024
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5. IAPT chromosome data 33

Author

Marhold, Karol, Kučera, Jaromír, Acuña, Carlos Alberto, Akopian, Janna A., de Almeida, Erton M., Alves, Marccus V., Amorim, Bruno S., An'kova, Tatyana V., Arora, Jaya, Aytaç, Zeki, Baez, Mariana, Cavalcanti, Taciana Barbosa, Calvente, Alice, Catalan, Pilar, Chernyagina, Olga A., Chernysheva, Olga A., Cordeiro, Joel M.P., Daviña, Julio Rubén, Deanna, Rocío, Delgado, Luis, Silva, Yhanndra K. Dias, Elliott, Tammy L., Erst, Andrey S., Felix, Leonardo P., Forni-Martins, Eliana R., Gallego, Francisca, Facco, Marlon Garlet, Aquino, Analía Cecilia Gianini, de Andrade, Maria J. Gomes, Graham, Shirley A., Hojsgaard, Diego Hernán, Honfi, Ana Isabel, Houben, Andreas, Ikeda, Hiroshi, Khalbekova, Khulkar U., Krivenko, Denis A., Lakhanpaul, Suman, Peñas, M. Laura Las, Lavia, Graciela Inés, Leonova, Tatiana V., Lian, Lian, Lomonosova, Maria N., López-González, Beatriz, Martínez, Eric Javier, Matos, Samara S., Melo, André L., Torres, Esteban Meza, Mitrenina, Elizaveta Yu., El Mokni, Ridha, Valls, José Francisco Montenegro, Morero, Rita Ema, de Moura, Clapton Olimpio, de Oliveira, Regina Célia, de Oliveira Maekawa, Vanessa, Olonova, Marina V., Pandit, Maharaj K., Pedrosa-Harand, Andrea, Peruzzi, Lorenzo, Pinzani, Lorenzo, Potseluev, Oleg M., Probatova, Nina S., Pulkina, Svetlana V., Reutemann, Anna Verena, Rico, Enrique, Rua, Gabriel Hugo, Santos, Fabiano J., Santos, Géssica S., dos Santos Sousa, Mayco Werllen, Silva, Marcos C., Silva, Rhuan C., da Silva Santos, Angeline Maria, Silvestri, María Celeste, Singh, Jaswant, Singhal, Vijay Kumar, Souza, Pamela C.S.S., Tashev, Alexander, Thomas, Wayt W., Pozzobon, Marisa Toniolo, Turginov, Orzimat T., Vanzela, André L.L., Berto, Ana Catarina Vasconcelos, Veklich, Tatiana N., and Wang, Wei

Published
2020

10. An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity

Author

Athukoralage, Januka S., McMahon, Stephen A., Zhang, Changyi, Grüschow, Sabine, Graham, Shirley, Krupovic, Mart, and Whitaker, Rachel J.

Subjects
Genetic research, Nucleases -- Genetic aspects, Immunity -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The CRISPR system in bacteria and archaea provides adaptive immunity against mobile genetic elements. Type III CRISPR systems detect viral RNA, resulting in the activation of two regions of the Cas10 protein: an HD nuclease domain (which degrades viral DNA).sup.1,2 and a cyclase domain (which synthesizes cyclic oligoadenylates from ATP).sup.3-5. Cyclic oligoadenylates in turn activate defence enzymes with a CRISPR-associated Rossmann fold domain.sup.6, sculpting a powerful antiviral response.sup.7-10 that can drive viruses to extinction.sup.7,8. Cyclic nucleotides are increasingly implicated in host-pathogen interactions.sup.11-13. Here we identify a new family of viral anti-CRISPR (Acr) enzymes that rapidly degrade cyclic tetra-adenylate (cA.sub.4). The viral ring nuclease AcrIII-1 is widely distributed in archaeal and bacterial viruses and in proviruses. The enzyme uses a previously unknown fold to bind cA.sub.4 specifically, and a conserved active site to rapidly cleave this signalling molecule, allowing viruses to neutralize the type III CRISPR defence system. The AcrIII-1 family has a broad host range, as it targets cA.sub.4 signalling molecules rather than specific CRISPR effector proteins. Our findings highlight the crucial role of cyclic nucleotide signalling in the conflict between viruses and their hosts. Bacteria and archaea use cyclic oligoadenylate molecules as part of the CRISPR system for antiviral defence; here, a family of viral enzymes that rapidly degrades cyclic oligoadenylates is identified and biochemically and structurally described., Author(s): Januka S. Athukoralage [sup.1] , Stephen A. McMahon [sup.1] , Changyi Zhang [sup.3] [sup.4] , Sabine Grüschow [sup.1] , Shirley Graham [sup.1] , Mart Krupovic [sup.2] , Rachel J. [...]

Published
2020
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26. Molecular and genetic analysis of the vha16 gene in Drosophila melanogaster

Author

Graham, Shirley

Subjects
572.8, Vacuolar, Enzymes, ATP hydrolysis, Proteolipid
Abstract

Vacuolar H+-ATPases (V-ATPases) are multi-subunit enzymes which pump protons across cellular membranes via hydrolysis of ATP. They are related, both in structure and function, to FI-FQ ATP synthases and much about the V-ATPase mode of action has been inferred from FI-FQ studies. V-ATPases have been isolated from a broad phylogenetic range of eukaryotes, from single celled organisms to higher plants and animals. In these higher organisms they can play both endomembrane and plasma membrane roles in a large array of cell types. Several genes encoding subunits of the V-ATPase holoenzyme have been cloned from the model genetic organism Drosophila melanogaster. One of the subunits cloned from D. melanogaster, vhal6, encodes the 16 kDa pore forming protein, through which the hydrogen ions pass. Firstly, this project focuses on this proteolipid gene in Drosophila melanogaster, describing the isolation and characterisation of a lethal P-element insert within the originally described gene, and discussing how the insertion of this element disrupts the normal function of the gene. Also discussed is how this P-element can be used to show the spatial and temporal expression of the gene in vivo. Secondly it describes the isolation of four new homologues of this gene in D. melanogaster. It show's their sequence relationship to the original Drosophila protein, and the protein isolated from other organisms and discusses if they are expressed and whether they would function as V-ATPase pores. This study also describes the attempted rescue of the lethal P-element phenotype with a range of proteolipid sequences cloned from Drosophila and also proteolipids of other organisms. Lastly, this project describes the isolation of two other Drosophila V-ATPase membrane associated subunits, one homologous to PPA1 in yeast and the other homologous to M9.7 in Manduca sexta.

Published
2001

29. A comprehensive genus-level phylogeny and biogeographical history of the Lythraceae based on whole plastome sequences

Author

Inglis, Peter, Cavalcanti, Taciana, Facco, Marlon, Bakker, Freek, Graham, Shirley, Inglis, Peter, Cavalcanti, Taciana, Facco, Marlon, Bakker, Freek, and Graham, Shirley

Abstract

Background and AimsThe Lythraceae are a mainly subtropical to tropical family of the order Myrtales with 28 currently accepted genera and approximately 600 species. There is currently no well-supported phylogenetic and biogeographical hypothesis of the Lythraceae incorporating all currently accepted genera, which we sought to provide.MethodsPlastomes of representative species of 18 distinct Lythraceae genera were sequenced and annotated. Together with existing sequences, plastomes of all 28 currently accepted genera in the Lythraceae were brought together for the first time. The plastomes were aligned and a Bayesian phylogenetic hypothesis was produced. We then conducted a time-calibrated Bayesian analysis and a biogeographical analysis.Key ResultsPlastome-based Bayesian and maximum-likelihood phylogenetic trees are generally congruent with recent nuclear phylogenomic data and resolve two deeply branching major clades in the Lythraceae. One major clade concentrates shrubby and arboreal South American and African genera that inhabit seasonally dry environments, with larger, often winged seeds, adapted to dispersal by the wind. The second major clade concentrates North American, Asian, African and several near-cosmopolitan herbaceous, shrubby and arboreal genera, often inhabiting humid or aquatic environments, with smaller seeds possessing structures that facilitate dispersal by water.ConclusionsWe hypothesize that the Lythraceae dispersed early in the Late Cretaceous from South American to North American continents, with subsequent expansion in the Late Cretaceous of a North American lineage through Laurasia to Africa via a boreotropical route. Two later expansions of South American clades to Africa in the Palaeocene and Eocene, respectively, are also hypothesized. Transoceanic dispersal in the family is possibly facilitated by adaptations to aquatic environments that are common to many extant genera of the Lythraceae, where long-distance dispersal and vicariance may

Published
2023

33. Brazilian Flora 2020: Leveraging the power of a collaborative scientific network

Author

Gomes‐da‐silva, Janaína, Filardi, Fabiana L.R., Barbosa, Maria Regina V., Baumgratz, José Fernando A., Bicudo, Carlos E.M., Cavalcanti, Taciana, Coelho, Marcus A.N., Costa, Andrea, Costa, Denise, Dalcin, Eduardo Couto, Labiak, Paulo, Lima, Haroldo, Lohmann, Lúcia, Maia, Leonor, Mansano, Vidal, Menezes, Mariângela, Morim, Marli, Moura, Carlos Wallace N., Lughadha, Eimear Nic, Peralta, Denilson, Prado, Jefferson, Roque, Nádia, Stehmann, João Renato, Sylvestre, Lana, Trierveiler‐pereira, Larissa, Walter, Bruno M.T., Zimbrão, Geraldo, Forzza, Rafaela, Abreu, Fernanda, Abreu, Maria, Abreu, Vanessa H.R., Acuña‐castillo, Rafael, Afonso, Edgar A.L., Agra, Leandro A.N.N., Agra, Maria, Aguiar, Daniel P.P., Aires, Elisa, Almeda, Frank, Almeida, Gracineide S.S., Almeida, Mariana, Almeida, Nicolli B.C., Almeida, Rafael, Almeida, Roberto B.P., Almeida, Thaís, Almeida, Eduardo, Alves, Daniela, Alves, Flávio, Alves, Karina N.L., Alves, Maria B.B., Alves, Rodolfo, Amaral, Maria C.E., Amaral, André L.S., Amélio, Leandro, Amorim, André M.A., Amorim, Bruno, Amorim, Eduardo, Amorim, Vivian, Andrade, Ivanilza, Andrade, Ray, André, Thiago, Andreata, Regina H.P., Andrino, Caroline, Ângulo, María, Anjos, Cassiane, Antar, Guilherme, Antonicelli, Mirian C.A., Antunes, Lorena l.C., Aona, Lidyanne Y.S., Arana, Marcelo, Aranha, João L.M., Araújo, Anderson G.A., Araujo, Andréa, Araújo, Camila, Araujo, Cintia A.T., Araujo, Flávia, Araújo, Mário H.T., Arbo, Maria, Arnou, Emily, Asprino, Renata, Assis, Francine, Assis, Leandro C.S., Assis, Marta, Athayde Filho, Francisco, Athiê‐souza, Sarah, Azevedo, Igor H.F., Bacci, Lucas, Barbosa, Camilo V.O., Barbosa, Juliana, Barbosa‐silva, Rafael, Barcellos, Ian, Barboza, Gloria, Barcelos, Flávia R.B., Barcelos, Laísa, Barreto, Kamilla l., Barros, Fábio, Barros, Thamires l.A., Barros‐barreto, Maria B.B., Bastos, Cid J.P., Bastos, Cláudia, Batista, João A.N., Batista, Marcella M.I., Bautista, Hortencia, Benelli, Adarilda, Berguecio, Nicolás, Bernacci, Luís, Beyer, Maila, Bezerra, Andrea C.C., Bezerra, Luísa M.P.A., Bezerra, Yuri R.L., Bianchetti, Luciano, Bigio, Narcísio, Biral, Leonardo, Bissoli, Vinícius, Bittencourt, Felipe, Bochorny, Thuane, Bohn, Amabily, Bohs, Lynn, Bojacá, Gabriel F.P., Boldorini, Abril, Boldrini, Ilsi, Bolson, Mônica, Bordin, Juçara, Bordon, Natali, Borges, Rafael A.X., Borges, Rodrigo l., Bortoluzzi, Roseli l.C., Bove, Claudia, Bovini, Massimo, Braga, João M.A., Braga, Nayara S.S., Branco, Suema, Brauner, Laiana, Braz, Denise, Bringel, João B.A., Brito, Antonio l.V.T., Brito, Eliete, Bruniera, Carla, Buchoski, Monica, Buck, William, Bueno, Norma, Bueno, Vinicius, Büneker, Henrique, Bünger, Mariana, Buril‐vital, Maria T.A., Burton, George, Cabral, Andressa, Cabral, Elsa l., Cabral, Fernanda, Cabral, Tiara, Caddah, Mayara, Caires, Claudenir, Caires, Taiara, Calazans, Luana S.B., Caldas, Diana K.D., Calió, Maria, Calvo, Joel, Câmara, Paulo E.A.S., Camargo, Rodrigo, Camelo, Mel, Campos‐rocha, Antonio, Cândido, Elisa, Canestraro, Bianca, Canto‐dorow, Thais, Cantuária, Patrick, Cara, Álison l., Cárdenas, Gabriela, Cardoso, Andréia, Cardoso, Domingos B.O.S., Cardoso, Jesiane, Cardoso, Leandro J.T., Cardoso, Pedro, Cardozo, Andrey l., M.D. Cardozo, Nállarett, Carmo, Dimas, Carmo, João A.M., Carneiro, Camila, Carneiro, Cláudia, Carrijo, Tatiana, Caruzo, Maria B.R., Carvalho, Catarina, Carvalho, Dariane A.S., Carvalho, Fernanda, Carvalho, Maria l.S., Carvalho, Jefferson, Carvalho‐silva, Micheline, Castello, Ana C.D., Castro, Márcia, Castro E Silva, Isabella, Catenacci, Fernanda, Cavalcanti, Laise, Cavalheiro, Larissa, Cervi, Armando, Chacon, Roberta, Chagas, Aline, Chagas, Earl C.O., Chautems, Alain, Chauveau, Olivier, Chequín, Renata, Christ, Anderson l., Christ, Jheniffer, Cidrão, Bruno, Clark, Lynn, Coelho, Alexa A.O.P., Coelho, Guilherme, Coelho, Rubens l.G., Colletta, Gabriel, Colli‐silva, Matheus, Conceição, Adilva, Conceição, Tulio, Condack, João P.S., Contro, Fernanda l., Cordeiro, Inês, Cordeiro, Luciana, Cordeiro, Wesley P.F.S., Côrtes, Ana l.A., Costa, Daniel, Costa, Fabiane, Costa, Fernanda S.N., Costa, Francisco C.P., Costa, Géssica A.G., Costa, Isabelle G.C.M., Costa, Itayguara, Costa, Jeferson, Costa, Jorge A.S., Costa, José G.S., Costa, Maria T.R., Costa, Mitchel I.A., Costa, Suzana, Costa, Thiago, Costa, Tiago, Costa E Silva, Maria, Costa‐lima, James l., Cota, Matheus M.T., Couceiro, Yuri S.V., Coutinho, Thales, Couto, Dayvid, Couto, Ricardo, Couvo, Anielly, Cyrillo, Stephany, Dal Molin, Luis, Dalastra, Claudenice, Damasceno, Rafaella G.L., de Lazzari, Lara R.P., Deble, Leonardo, Delfini, Carolina, Delgado Junior, Geadelande, Delgado‐salinas, Alfonso, Della, Aline, Delprete, Piero, Dematteis, Massimiliano, Dettke, Greta, Devecchi, Marcelo, Dewes, Talita, Di Maio, Fernando, Dias, Kauê N.L., Dias, Micheli, Dias, Pedro, Díaz, Yani C.A., Dittrich, Vinícius A.O., Domínguez, Yoannis, Dórea, Marcos, Dorneles, Mariane, Dressler, Stefan, Duarte, Marilia, Duran, Juan D.T., Dutilh, Julie H.A., Dutra, Letícia l., Dutra, Valquíria, Echternacht, Livia, Eggers, Lilian, Erkens, Roy H.J., Eslabão, Marcelo, Espírito Santo, Fábio, Esser, Hans‐joachim, Essi, Liliana, Esteves, Gerleni l., Esteves, Roberto l., Everling, Joel, Ezcurra, Cecilia, Facco, Marlon, Fader, Andrea A.C., Falcão, Marcus J.A., Fantecelle, Laura, Farco, Gabriela, Faria, Allan l.A., Faria, Ana P.G., Faria, Aparecida, Faria, Maria, Faria, Jair, Farias, Sabrina, Farias‐singer, Rosana, Farinaccio, Maria, Fernandes, Ana, Fernandes, Fernando, Fernandes, José, Fernandes, Rozijane, Fernandes, Thiago, Fernandes, Ulisses, Fernandes, Aluisio, Fernando, Emanoel M.P., Ferreira, Carlos D.M., Ferreira, Fabrício, Ferreira, Gabriel, Ferreira, João P.R., Ferreira, Priscila P.A., Ferreira, Silvana, Ferrucci, María, Fiaschi, Pedro, Fidanza, Karina, Filgueiras, Tarciso, Firetti, Fabiana, Fleischmann, Andreas, Florentín, Javier, Florentín, Mariela, Flores, Andréia, Flores, Jerônimo M.M., Flores, Thiago, Fonseca, Luiz H.M., Fontelas, Jean, Fontella‐pereira, Jorge, Forster, Wellington, Fraga, Claudio, Fraga, Fernanda R.M., Fraga, Santiago, França, Flávio, França, Juliana R.K.G., Francisco, Jéssica N.C., Freire‐fierro, Alina, Freitas, Fernanda, Freitas, Joelcio, Freitas, Maria, Fritsch, Peter, Funez, Luís, Furtado, Samyra, Gaem, Paulo, Gaglioti, André l., Gagnon, Edeline, Gama, Beatriz R.A., Garcia, Flávia C.P., Gasper, André l., Gerace, Samuele, Giacomin, Leandro l., Giaretta, Augusto, Gil, André S.B., Gissi, Danilo, Giuffre, Pamela M.W., Giulietti, Ana, Giussani, Liliana, Goebel, Gabriela, Goes, Monique, Góes, Luiz A.A., Goldenberg, Renato, Gomes, Beatriz, Gomes, Fernanda, Gomes, Mario, Gomes‐klein, Vera l., Gonçalez, Victor, Gonçalves, Ana P.S., Gonçalves, Deise J.P., Gonella, Paulo, Gonzaga, Augusto F.N., Gonzaga, Diego, González, Favio, Gonzatti, Felipe, Gouvêa, Yuri, Graham, Shirley A.T., Gregório, Bernarda, Grings, Martin, Groppo, Milton, Grossi, Mariana, Guarçoni, Elidio A.E., Guedes, Felipe, Guedes, Juliana, Guerra, Ethiéne, Guimarães, Elsie, Guimarães, Leonardo R.S., Guimarães, Paulo J.F., Gurgel, Ely S.C., Gutiérrez, Diego, Hall, Climbiê, Harley, Raymond, Hassemer, Gustavo, Hattori, Eric K.O., Hechenleitner, Paulina, Hefler, Sonia, Heiden, Gustavo, Henning, Tilo, Henriques, Diego, Hensold, Nancy, Hinoshita, Lucas K.R., Hirai, Regina, Hirao, Yasmin, Hiriart, Florencia, Hopkins, Michael J.G., Hoyos‐gómez, Saúl, Huamantupa, Isau, Hurbath, Fernanda, Iganci, João R.V., Ilkiu‐borges, Anna l., Imig, Daniela, Inácio, Camila, Indriunas, Alexandre, Jacques, Eliane l., Jacques, Suara S.A., Jaimes, Juliana, Jardim, Jomar, Jesus, Jôane, Jesus, Priscila, Jiménez‐mejías, Pedro, Johnson, David, Jordão, Lucas S.B., Jordão, Valner M.M., Jorge, Taciane, Kaehler, Miriam, Kameyama, Cíntia, Kataoka, Eric, Kessous, Igor, Kilipper, Julia, Kinoshita, Luiza, Klein, Viviane, Klitgaard, Bente, Knapp, Sandra, Koch, Ana, Koch, Ingrid, Kochanovski, Fábio, Kominami, Gabriel F.G., Konno, Tatiana U.P., Koschnitzke, Cristiana, Kotovski, Emília, Kriebel, Ricardo, Külkamp, Josimar, Leal, Brígida, Leal, Eduardo, Leite, Áurea C.F., Leite, Wellerson, Leitman, Paula, Lewis, Gwilym, Lima, Adriana, Lima, Alexandre, Lima, Duane F.S., Lima, Eliene, Lima, Jessica, Lima, Laíce F.G., Lima, Laura C.P., Lima, Letícia, Lima, Lucas, Lima, Luis F.P., Lima, Rita, Lima, Vanessa l., Link‐perez, Melanie, Lirio, Elton, Lobão, Adriana, Loeuille, Benoit F.P., Loiola, Maria I.B., Lombardi, Julio, Longhi‐wagner, Hilda, Lopes, Gabriel S.R., Lopes, Jenifer, Lopes, Letícia, Lopes, Raimundo, Lopes, Rosana, López, Maria, Lorencini, Tiago, Lorenzi, Harri, Lourenço, Ana R.L., Lourenço, Arthur, Louzada, Rafael, Lovo, Juliana, Lozano, Eduardo, Luber, Jaquelini, Lucas, Dióber, Lucas, Eve, Lüdtke, Raquel, Luebert, Federico, Luizi‐ponzo, Andrea, Luna, Bruna, Luna, Naédja K.M., Luz, Cíntia l.S., Machado, Anderson F.P., Machado, Evandro, Machado, Talita, Maciel, Jefferson, Maciel, Sebastião, Magalhães, Rodrigo, Magenta, Mara A.G., Maia, Talita, Mamede, Maria C.H., Marchioretto, Maria, Margalho, Luciano, Marinho, Lucas, Marques, Danilo, Marquete, Ronaldo, Marra, Raquel, Martins, Angela, Martins, Márcio l.L., Martins, Marcos B.S., Martins, Milena, Martins, Renata, Martins, Suzana, Masson, Victória, Matias, Ligia, Matos, Agnes M.M.V., Matos, Andreza, Matos, Fernando, Matozinhos, Carolina, Mattos, Cilene M.J., Mattos, Leticia, Matzenauer, William, Mauad, Anna V.S.R., Maya‐lastra, Carlos, Mayo, Simon, Mazine, Fiorella, Medeiros, Débora, Medeiros, Erika V.S.S., Medeiros, Herison, Medeiros, Maria C.M.P., Meerow, Alan, Meireles, Jose, Meireles, Leonardo, Meirelles, Julia, Melchor‐castro, Briggitthe, Mello, Zelia, Mello‐silva, Renato, Melo, André l., Melo, Caio V.V.D., Melo, Efigenia, Melo, José I.M., Mendes, Jone C.R., Mendes, Maria C.Q., Mendes‐silva, Ingrid, Meneguzzo, Thiago E.C., Menezes, Cristine, Menezes, Felipe G.P., Menini Neto, Luiz, Mentz, Lilian, Mesquita, Antônio l., Messias, Patrícia, Mezzonato‐pires, Ana, Michelangeli, Fabián, Miguel, João, Miguel, Laila, Milward‐de‐azevedo, Michaele, Miotto, Silvia T.S., Miranda, Cecília, Miranda, Vitor F.O., Mitchell, John, Molina, José M.P., Mondin, Cláudio, Monge, Marcelo, Monteiro, Daniele, Monteiro, Fernanda K.S., Monteiro, Raquel, Monteiro, Silvana H.N., Monteiro, Thiago, Monzoli, João V.L., Moore, Paloma G.P., Mora, Martha, Moraes, Marta, Moraes, Mónica, Morales, Juan, Morales, Matías, Moran, Robbin, Moreira, André l.C., Moreira, Andréia D.R., Moreira, Ariane, Moreira, Bianca, Moreira, Giselle l., Moreira, Kassio V.C., Moreira, Pablo F.F., Morokawa, Rosemeri, Moroni, Pablo, Mota, Aline, Mota, Michelle C.A., Mota, Nara F.O., Moura, Beryl E.L., Moura, Ingridy, Moura, Luíza, Moura, Ricardo l., Moura, Tania, Mundim, Júlia, Muniz, Francisca, Muniz, Leticia, Muniz Filho, Eduardo, Mynssen, Claudine, Nakajima, Jimi, Nascimento, Janaina G.A., Nascimento, José, Nascimento, Silvia, Nepomuceno, Francisco A.A., Nervo, Michelle, Nery, Eduardo, Neves, Beatriz, Nóbrega, Giseli, Nogueira, Matheus G.C., Nunes, Annelise, Nunes, Clebiana, Nunes, Teonildes, Oellgaard, Benjamin, O'Leary, Nataly, Oliveira, Adriana l.R., Oliveira, Ana C.S., Oliveira, Andreza G.S., Oliveira, Aron, Oliveira, Bárbara, Oliveira, Caetano, Oliveira, Fernanda M.C., Oliveira, Filipe G.A., Oliveira, Gleison, Oliveira, Gustavo, Oliveira, Hermeson, Oliveira, Iasmin l.C., Oliveira, Joésili C.P., Oliveira, José F.C., Oliveira, Juliana, Oliveira, Juliana R.P.M., Oliveira, Leticia G.R., Oliveira, Lilian F.A., Oliveira, Lorena, Oliveira, Luciana S.D., Oliveira, Marcia C.R., Oliveira, Márcio l.B., Oliveira, Marcos G.M., Oliveira, Marise H.V., Oliveira, Marla I.U., Oliveira, Regina, Oliveira, Renata, Oliveira, Reyjane, Oliveira, Rodrigo C.G., Oliveira, Sylvia, Oliveira, Ykaro, Orlandini, Priscila, Orsolano, Guilherme, Pacífico, Ricardo, Paglia, Isis, Paiva, Gabrielle C.P., Paixão, Liliane, Pastore, José F.B., Pastore, Mayara, Pastori, Tamara, Paucar, Jenny O.A., Paula‐souza, Juliana, Pederneiras, Leandro, Peichoto, Myriam, Peixoto, Ariane l., Pell, Susan, Pellegrini, Marco O.O., Pena, Nelson T.L., Pennington, Richard, Pereira, Amanda P.N., Pereira, Andreza S.S., Pereira, Jovani B.S., Pereira, Maria, Pereira, Paulo E.E., Pereira, Sidney, Pereira‐silva, Rafaela, Perez, Ana P.F., Pessoa, Cleiton, Pessoa, Clenia, Pessoa, Edlley, Pessoa, Maria C.R., Petrongari, Fernanda, Philbrick, Thomas, Pignal, Marc, Pimenta, Karena, Pinto, Rafael, Pioner, Natália, Pirani, José, Pizzardo, Raquel, Plos, Anabela, Ponce, Marta, Pontes, Juliana, Pontes, Ricardo A.S., Pontes, Tiago, Pontes‐pires, Aline, Pott, Vali, Prado, Thainá, Praia, Talita, Prance, Ghillean, Prange, Carolina, Prata, Ana P.N., Prochazka, Luana, Proença, Carolyn E.B., Prudêncio, Renato X.A., Pscheidt, Allan, Quaresma, Aclebia, Quaresma, Aline, Queiroz, George, Queiroz, Luciano, Queiroz, Rubens, Quinet, Alexandre, Ramos, Eliana, Ramos, Geraldo J.P., Rando, Juliana, Rebouças, Natanael, Reginato, Marcelo, Reis, Miguel M.R., Reis, Priscila, Reis‐silva, Genilson, Ribas, Osmar, Ribeiro, André R.O., Ribeiro, Carolina l., Ribeiro, José E.L.S., Ribeiro, Michel, Ribeiro, Pétala, Ribeiro, Rayane T.M., Ribeiro, Ricardo, Ribeiro, Rogério, Riina, Ricarda, Ritter, Mara, Rivadavia, Fernando, Rivera, Vanessa l., Rizzo, Beatriz, Rocha, Antônio E.S., Rocha, Lamarck, Rocha, Maria J.R., Rodrigues, Carine, Rodrigues, Christchellyn, Rodrigues, Izabella M.C., Rodrigues, Marianna, Rodrigues, Rodrigo Sampaio, Rodrigues, Rodrigo Schütz, Rodríguez, Juan F.C., Rodríguez, Pedro, Rollim, Isis, Romanini, Rebeca, Romão, Gerson, Romão, Marcos V.V., Romero, María, Romero, Rosana, Rosa, Bárbara, Rosa, Patrícia, Rosa, Priscila, Rosário, Alessandro, Rossa, Iago, Rossetto, Elson F.S., Rossi, Lucia, Rossini, Josiene, Royer, Carla, Rua, Gabriel, Sá, Cyl F.C., Saavedra, Mariana, Saka, Mariana, Sakuragui, Cassia, Salas, Roberto, Sales, Margareth, Salgado, Vanina, Salimena, Fátima R.G., Salino, Alexandre, Salvador, Rafael, Sampaio, Daniela, Sancho, Gisela, Sano, Paulo, Santana, Jéssica C.O., Santana, Karoline, Santana, Mariana, Santiago, Augusto C.P., Santos, Alessandra, Santos, Amanda P.B., Santos, Ana C.A.S., Santos, Andrea K.A., Santos, Carlos A.G., Santos, Emanuelle l., Santos, Felipe, Santos, Fernanda, Santos, João U.M., Santos, Karin, Santos, Leidiana l., Santos, Matheus, Santos, Otilene, Santos, Rafaela, Santos, Renata G.P., Santos, Thaíla V.A., Santos, Thiago, Santos, Vanessa, Santos‐silva, Fernanda, Santos‐silva, Juliana, São‐mateus, Wallace M.B., Saraiva, Deisy, Sarkinen, Tiina, Sartori, Ângela l.B., Sassone, Agostina, Sauthier, Luana, Scalon, Viviane, Scatigna, André, Schaefer, Juliana, Scheidegger, Najla M.B., Schliewe, Marcos, Schmidt, Eduard D.L., Schneider, Angelo, Schneider, Layla J.C., Schuettpelz, Eric, Schwartsburd, Pedro, Schwarz, Elizabeth, Scudeler, Ana l., Sebastiani, Renata, Secco, Ricardo, Secretti, Elisangela, Segalla, Rosane, Seleme, Elidiene, Semir, João, Senna, Luisa, Setubal, Robberson, Shimizu, Gustavo, Shirasuna, Regina, Silva, Adaíses S.M., Silva, Aline V.M., Silva, Amanda l., Silva, Anádria, Silva, Caroline C.A., Silva, Cassio, Silva, Christian, Silva, Cintia, Silva, Diego, Silva, Dilana, Silva, Fabio, Silva, Fernanda, Silva, Francismeire, Silva, Gabriel, Silva, Gledson, Silva, Guilherme, Silva, Gustavo H.L., Silva, João P.S., Silva, Juliana l., Silva, Juliene F.M., Silva, Leonardo, Silva, Lucas, Silva, Luciana, Silva, Luiza, Silva, Márcio, Silva, Marcio R.P., Silva, Marcos, Silva, Marcus F.O., Silva, Maria l.B., Silva, Maria S.D., Silva, Nilda M.F., Silva, Otávio l.M., Silva, Rafael, Silva, Raphael, Silva, Renata S.A., Silva, Renato, Silva, Ronaldo, Silva, Saura, Silva, Suelma, Silva, Tânia R.S., Silva, Tatiane, Silva, Thaynara, Silva, Wanderson l.S., Silva Filho, Pedro J.S., Silva‐castro, Milene, Silva‐cobra, Gisele, Silva‐gonçalves, Kelly, Silveira, Fernanda, Silveira, João, Silveira, Thamyres, Simão‐bianchini, Rosangela., Simões, Ana, Simões, André, Simon, Marcelo, Siniscalchi, Carolina, Siqueira, Carlos, Smidt, Eric, Smith, Alan, Smith, Nathan, Snak, Cristiane, Soares, Abel E.R., Soares, Arthur, Soares, Edson l.C., Soares, Kelen, Soares, Luanda, Soares, Marcos V.B., Soares, Maria l.C., Soares, Polyana, Soares, Raimundo, Sobrado, Sandra, Sobral, Marcos, Somner, Genise, Sothers, Cynthia, Sousa, Ana A.C., Sousa, Danilo J.L., Sousa, Francisco, Sousa, Gardene, Sousa, Hian C.F., Sousa, Leandro O.F., Sousa, Mayco W.S., Sousa, Valdeci, Souza, Aline, Souza, Bruno, Souza, Elnatan, Souza, Élvia, Souza, Filipe, Souza, Luzia, Souza, Marcelo, Souza, Maria A.D., Souza, Raquel M.B.S., Souza, Vinicius, Souza‐buturi, Fátima, Spina, Andréa, Stadnik, Aline M.S., Staggemeier, Vanessa, Stapf, María N.S., Stefano, Rodrigo, Stern, Stephen, Streher, Nathália, Suchoronczek, Andréia, Sundue, Michael, Takeuchi, Cátia, Tardivo, Rosângela, Taylor, Nigel, Teixeira, Michella D.R., Teles, Aristônio, Temponi, Livia, Thode, Verônica, Thomas, William, Tierno, Lorena, Tissot‐squalli, Mara, Toledo, Cássio A.P., Torke, Benjamin, Torres, Alicia, Torres, Daniela S.C., Torres‐leite, Filipe, Tozzi, Ana M.G.A., Trad, Rafaela, Trevisan, Rafael, Trovó, Marcelo, Tuler, Amélia, Tyrrell, Christopher, Udulutsch, Renata, Uribbe, Fernando, Vahl, Daiane, Valadares, Rodrigo, Valdemarin, Karinne, Valduga, Eduardo, Valente, Emilia, Valls, Jose F.M., van den Berg, Cássio, Vasconcelos, Liziane, Vasconcelos, Thaís N.C., Vasques, Diego, Vaz, Angela M.S.F., Versiane, Ana F.A., Versieux, Leonardo, Via Do Pico, Gisela, Viana, Pedro l., Vianna, Suelen, Vianna Filho, Marcelo D.M., Vidal, Kaio V.A., Vidal, João, Vieira, Fábio C.S., Vieira, Jaqueline, Vieira, João P.S., Vieira, Lucas l.A., Vieira, Tamara A.F., Vieira, Tiago l., Viera‐barreto, Jéssica, Vignoli‐silva, Márcia, Vilas Bôas‐bastos, Silvana, Villarreal, Juan, Vincent, Michael, Vita, Marcela, Vitta, Fabio, Viveros, Raquel, Viviurka, Fernanda, Vogel Ely, Cleusa, Volet, Danilo, Völtz, Rafael, Wallnöfer, Bruno, Wanderley, Maria G.L., Watanabe, Mauricio T.C., Weber, Philipy A.P., Weigend, Maximilian, Welker, Cassiano A.D., Windisch, Paulo, Yoshikawa, Vania, Zamengo, Henrique, Zanatta, Maria R.V., Zannin, Ana, Zappi, Daniela, Zeferino, Laís, Zelenski, Andréia, Zuloaga, Fernando, Zuntini, Alexandre, Maastricht Science Programme, RS: FSE MSP, JANAÍNA GOMES-DA-SILVA, Jardim Botânico do Rio de Janeiro, FABIANA L. R. FILARDI, MARIA REGINA V. BARBOSA, UFPB, JOSÉ FERNANDO A. BAUMGRATZ, CARLOS E. M. BICUDO, TACIANA BARBOSA CAVALCANTI, Cenargen, MARCUS A. N. COELHO, Prefeitura Municipal de Campinas, ANDREA F. COSTA, DENISE P. COSTA, Instituto de Pesquisas Jardim Botanico do Rio de Janeiro, EDUARDO COUTO DALCIN, Rio de Janeiro Botanical Garden Research Institute, PAULO LABIAK, UFPR, HAROLDO C. LIMA, Jardim Botânico do Rio de Janeiro, LÚCIA G. LOHMANN, USP, LEONOR C. MAIA, UFPE, VIDAL F. MANSANO, Jardim Botânico do Rio de Janeiro, MARIÂNGELA MENEZES, UFRJ, MARLI P. MORIM, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, CARLOS WALLACE N. MOURA, EIMEAR NIC LUGHADHA, DENILSON F. PERALTA, JEFFERSON PRADO, Instituto de Botânica de São Paulo, NÁDIA ROQUE, UFBA, JOÃO RENATO STEHMANN, LANA S. SYLVESTRE, UFRJ, LARISSA TRIERVEILER-PEREIRA, Instituto de Botânica, São Paulo, BRUNO MACHADO TELES WALTER, Cenargen, GERALDO ZIMBRÃO, RAFAELA C. FORZZA, Jardim Botânico do Rio de Janeiro., Instituto de Pesquisas Jardim Botanico do Rio de Janeiro (JBRJ), Universidade Federal da Paraiba (UFPB), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Herbier de Guyane - IRD, and Institut de Recherche pour le Développement (IRD [Guyane])

Subjects
Grandes Datos, Natural history collections, natural history collections, América del Sur, Plant Science, Repositories, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Colecciones de Historia Natural, Taxonomic impediment, Biodiversidad, Big data, flora, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, big data, taxonomic impedimen, Repositorios, Ecology, Evolution, Behavior and Systematics, biodiversity, Biodiversity, botany, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Impedimento Taxonómico, South America, collaboration, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, repositories, Brazil
Abstract

The shortage of reliable primary taxonomic data limits the description of biological taxa and the understanding of biodiver sity patterns and processes, complicating biogeographical, ecological, and evolutionary studies. This deficit creates a significant taxo nomic impediment to biodiversity research and conservation planning. The taxonomic impediment and the biodiversity crisis are widely recognized, highlighting the urgent need for reliable taxonomic data. Over the past decade, numerous countries worldwide have devoted considerable effort to Target 1 of the Global Strategy for Plant Conservation (GSPC), which called for the preparation of a working list of all known plant species by 2010 and an online world Flora by 2020. Brazil is a megadiverse country, home to more of the world’s known plant species than any other country. Despite that, Flora Brasiliensis, concluded in 1906, was the last comprehensive treatment of the Brazilian flora. The lack of accurate estimates of the number of species of algae, fungi, and plants occurring in Brazil contributes to the prevailing taxonomic impediment and delays progress towards the GSPC targets. Over the past 12 years, a legion of taxonomists motivated to meet Target 1 of the GSPC, worked together to gather and integrate knowledge on the algal, plant, and fungal diversity of Brazil. Overall, a team of about 980 taxonomists joined efforts in a highly collaborative project that used cybertaxonomy to prepare an updated Flora of Brazil, showing the power of scientific collaboration to reach ambitious goals. This paper presents an overview of the Brazilian Flora 2020 and provides taxonomic and spatial updates on the algae, fungi, and plants found in one of the world’s most biodiverse countries. We further identify collection gaps and summarize future goals that extend be yond 2020. Our results show that Brazil is home to 46,975 native species of algae, fungi, and plants, of which 19,669 are endemic to the country. The data compiled to date suggests that the Atlantic Rainforest might be the most diverse Brazilian domain for all plant groups except gymnosperms, which are most diverse in the Amazon. However, scientific knowledge of Brazilian diversity is still un equally distributed, with the Atlantic Rainforest and the Cerrado being the most intensively sampled and studied biomes in the coun try. In times of “scientific reductionism”, with botanical and mycological sciences suffering pervasive depreciation in recent decades, the first online Flora of Brazil 2020 significantly enhanced the quality and quantity of taxonomic data available for algae, fungi, and plants from Brazil. This project also made all the information freely available online, providing a firm foundation for future research and for the management, conservation, and sustainable use of the Brazilian funga and flora. Fil: Gomes da Silva, Janaina. Jardim Botânico do Rio de Janeiro: Rio de Janeiro, Brasil Fil: Filardi, Fabiana L.R. Jardim Botânico do Rio de Janeiro; Brasil Fil: Barbosa, María Regina de V. Universidade Federal da Paraíba: Joao Pessoa; Brasil Fil: Baumgratz, José Fernando Andrade. Jardim Botânico do Rio de Janeiro; Brasil Fil: de Mattos Bicudo, Carlos Eduardo. Instituto de Botânica. Núcleo de Pesquisa em Ecologia; Brasil Fil: Cavalcanti, Taciana. Empresa Brasileira de Pesquisa Agropecuária Recursos Genéticos e Biotecnologia; Brasil Fil: Coelho, Marcus. Prefeitura Municipal de Campinas; Brasil Fil: Ferreira da Costa, Andrea. Federal University of Rio de Janeiro. Museu Nacional. Department of Botany; Brasil Fil: Costa, Denise. Instituto de Pesquisas Jardim Botanico do Rio de Janeiro; Brasil Fil: Dalcin, Eduardo C. Rio de Janeiro Botanical Garden Research Institute; Brasil Fil: Labiak, Paulo. Universidade Federal do Parana; Brasil Fil: Cavalcante de Lima, Haroldo. Jardim Botânico do Rio de Janeiro; Brasil Fil: Lohmann, Lucia. Universidade de São Paulo; Brasil Fil: Maia, Leonor. Universidade Federal de Pernambuco; Brasil Fil: Mansano, Vidal de Freitas. Instituto de Pesquisas Jardim Botânico do Rio de Janeiro; Brasil. Jardim Botânico do Rio de Janeiro; Brasil Fil: Menezes, Mariângela. Federal University of Rio de Janeiro. Museu Nacional. Department of Botany; Brasil Fil: Morim, Marli. Instituto de Pesquisas Jardim Botânico do Rio de Janeiro; Brasil Fil: Moura, Carlos Wallace do Nascimento. Universidade Estadual de Feira de Santana. Department of Biological Science; Brasil Fil: Lughadha, Eimear NIck. Royal Botanic Gardens; Reino Unido Fil: Peralta, Denilson. Instituto de Pesquisas Ambientais; Brazil Fil: Prado, Jefferson. Instituto de Pesquisas Ambientais; Brasil Fil: Roque, Nádia. Universidade Federal da Bahia; Brasil Fil: Stehmann, Joao. Universidade Federal de Minas Gerais; Brasil Fil: da Silva Sylvestre, Lana. Universidade Federal do Rio de Janeiro; Brasil Fil: Trierveiler-Pereira, Larissa. Universidade Estadual de Maringá. Departamento de Análises Clínicas e Biomedicina; Brasil Fil: Walter, Bruno Machado Teles. EMBRAPA Cenargen Brasília; Brasil Fil: Zimbrão, Geraldo. Universidade Federal do Rio de Janeiro; Brasil Fil: Forzza, Rafaela C. Jardim Botânico do Rio de Janeiro; Brasil Fil: Morales, Matías. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Morón. Facultad de Agronomía y Ciencias Agroalimentarias; Argentina

Published
2021
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38. A comprehensive genus-level phylogeny and biogeographical history of the Lythraceae based on whole plastome sequences.

Author

Inglis, Peter W, Cavalcanti, Taciana B, Facco, Marlon G, Bakker, Freek T, and Graham, Shirley A

Subjects
PHYLOGENY, PARSIMONIOUS models, BAYESIAN analysis, CONTINENTS, EOCENE Epoch, VICARIANCE
Abstract

Background and Aims The Lythraceae are a mainly subtropical to tropical family of the order Myrtales with 28 currently accepted genera and approximately 600 species. There is currently no well-supported phylogenetic and biogeographical hypothesis of the Lythraceae incorporating all currently accepted genera, which we sought to provide. Methods Plastomes of representative species of 18 distinct Lythraceae genera were sequenced and annotated. Together with existing sequences, plastomes of all 28 currently accepted genera in the Lythraceae were brought together for the first time. The plastomes were aligned and a Bayesian phylogenetic hypothesis was produced. We then conducted a time-calibrated Bayesian analysis and a biogeographical analysis. Key Results Plastome-based Bayesian and maximum-likelihood phylogenetic trees are generally congruent with recent nuclear phylogenomic data and resolve two deeply branching major clades in the Lythraceae. One major clade concentrates shrubby and arboreal South American and African genera that inhabit seasonally dry environments, with larger, often winged seeds, adapted to dispersal by the wind. The second major clade concentrates North American, Asian, African and several near-cosmopolitan herbaceous, shrubby and arboreal genera, often inhabiting humid or aquatic environments, with smaller seeds possessing structures that facilitate dispersal by water. Conclusions We hypothesize that the Lythraceae dispersed early in the Late Cretaceous from South American to North American continents, with subsequent expansion in the Late Cretaceous of a North American lineage through Laurasia to Africa via a boreotropical route. Two later expansions of South American clades to Africa in the Palaeocene and Eocene, respectively, are also hypothesized. Transoceanic dispersal in the family is possibly facilitated by adaptations to aquatic environments that are common to many extant genera of the Lythraceae, where long-distance dispersal and vicariance may be invoked to explain several remarkable disjunct distributions in Lythraceae clades. [ABSTRACT FROM AUTHOR]

Published
2023
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39. The Irish defence forces and the silencing of a feminist researcher

Author

Graham, Shirley

Abstract

ABSTRACTAs a feminist researcher undertaking my PhD field research from 2006 to 2009 with officers in the Irish Defence Forces, I experienced the gender discrimination I was endeavouring to make visible. My PhD study, borne out of UNSCR 1325 and the Women, Peace and Security agenda, was testing claims by the United Nations that the inclusion of women peacekeepers brings important benefits to civilian women populations in mission contexts. The study adopted discourse analysis and included equal numbers of interviews with women and men peacekeepers and observation of Irish troops during the UNMIK/KFOR mission in Kosovo. At each stage of my research journey into the Irish Defence Forces I encountered barriers to continuing my study which had negative impacts on me personally and professionally. The culmination of which was them attempting to publicly discredit my research findings. This paper explores the process by which institutions attempt to silence feminist researchers and what we can learn about gender, knowledge and power from these affective experiences and how collective storytelling is key to breaking the silence.

Published
2023
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