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2. VarLOCK: sequencing-independent, rapid detection of SARS-CoV-2 variants of concern for point-of-care testing, qPCR pipelines and national wastewater surveillance

Author

Nan, Xinsheng, Hardinge, Patrick, Hoehn, Sven, Dighe, Shrinivas Nivrutti, Ukeri, John, Pease, Darius F., Griffin, Joshua, Warrington, Jessica I., Saud, Zack, Hottinger, Emma, Webster, Gordon, Jones, Davey, Kille, Peter, Weightman, Andrew, Stanton, Richard, Castell, Oliver K., Murray, James A. H., and Jurkowski, Tomasz P.

Published
2023
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4. Amazonian earthworm biodiversity is heavily impacted by ancient and recent human disturbance

Author

Conrado, Ana C., Demetrio, Wilian C., Stanton, David W.G., Bartz, Marie L.C., James, Samuel W., Santos, Alessandra, da Silva, Elodie, Ferreira, Talita, Acioli, Agno N.S., Ferreira, Alexandre C., Maia, Lilianne S., Silva, Telma A.C., Lavelle, Patrick, Velasquez, Elena, Tapia-Coral, Sandra C., Muniz, Aleksander W., Segalla, Rodrigo F., Decaëns, Thibaud, Nadolny, Herlon S., Peña-Venegas, Clara P., Pasini, Amarildo, de Oliveira Júnior, Raimundo C., Kille, Peter, Brown, George G., and Cunha, Luís

Published
2023
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9. Micronutrient availability in amazonian dark earths and adjacent soils

Author

Sátiro, José Nivaldo de Oliveira, Motta, Antônio Carlos V., Demetrio, Wilian C., Segalla, Rodrigo F., Cremonesi, Marcus Vinicius, Araújo, Eloá Moura, Falcão, Newton Paulo de Souza, Martins, Gilvan C., Muniz, Aleksander W., Taube, Paulo Sérgio, Rebellato, Lilian, de Oliveira Júnior, Raimundo C., Teixeira, Wenceslau G., Neves, Eduardo G., Lima, Helena P., Shock, Myrtle P., Kille, Peter, Cunha, Luís, TPI Network, and Brown, George G.

Published
2021
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12. Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

Author

Nobu, Masaru K, Dodsworth, Jeremy A, Murugapiran, Senthil K, Rinke, Christian, Gies, Esther A, Webster, Gordon, Schwientek, Patrick, Kille, Peter, Parkes, R John, Sass, Henrik, Jørgensen, Bo B, Weightman, Andrew J, Liu, Wen-Tso, Hallam, Steven J, Tsiamis, George, Woyke, Tanja, and Hedlund, Brian P

Subjects
Microbiology, Biological Sciences, Ecology, Genetics, Human Genome, Bacteria, Genomics, Geologic Sediments, Lakes, Molecular Sequence Data, Phylogeny, Environmental Sciences, Technology, Biological sciences, Environmental sciences
Abstract

The 'Atribacteria' is a candidate phylum in the Bacteria recently proposed to include members of the OP9 and JS1 lineages. OP9 and JS1 are globally distributed, and in some cases abundant, in anaerobic marine sediments, geothermal environments, anaerobic digesters and reactors and petroleum reservoirs. However, the monophyly of OP9 and JS1 has been questioned and their physiology and ecology remain largely enigmatic due to a lack of cultivated representatives. Here cultivation-independent genomic approaches were used to provide a first comprehensive view of the phylogeny, conserved genomic features and metabolic potential of members of this ubiquitous candidate phylum. Previously available and heretofore unpublished OP9 and JS1 single-cell genomic data sets were used as recruitment platforms for the reconstruction of atribacterial metagenome bins from a terephthalate-degrading reactor biofilm and from the monimolimnion of meromictic Sakinaw Lake. The single-cell genomes and metagenome bins together comprise six species- to genus-level groups that represent most major lineages within OP9 and JS1. Phylogenomic analyses of these combined data sets confirmed the monophyly of the 'Atribacteria' inclusive of OP9 and JS1. Additional conserved features within the 'Atribacteria' were identified, including a gene cluster encoding putative bacterial microcompartments that may be involved in aldehyde and sugar metabolism, energy conservation and carbon storage. Comparative analysis of the metabolic potential inferred from these data sets revealed that members of the 'Atribacteria' are likely to be heterotrophic anaerobes that lack respiratory capacity, with some lineages predicted to specialize in either primary fermentation of carbohydrates or secondary fermentation of organic acids, such as propionate.

Published
2016

18. The genome sequence of the common earthworm, Lumbricus terrestris (Linnaeus, 1758)

Author

Blaxter, Mark L., Spurgeon, David, Kille, Peter, Blaxter, Mark L., Spurgeon, David, and Kille, Peter

Abstract

We present a genome assembly from an individual Lumbricus terrestris (the common earthworm; Annelida; Clitellata; Haplotaxida; Lumbricidae). The genome sequence is 1,056.5 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.93 kilobases in length.

Published
2023

19. A novel Lepidoptera bioassay analysed using a reduced GUTS model

Author

Badder, Claire, Bart, Sylvain, Robinson, Alex, Hesketh, Helen, Kille, Peter, Spurgeon, David J., Badder, Claire, Bart, Sylvain, Robinson, Alex, Hesketh, Helen, Kille, Peter, and Spurgeon, David J.

Abstract

Lepidopteran species can be both pests and also beneficial pollinators for agricultural crops. However, despite these important roles, the effects of pesticides on this diverse taxa are relatively understudied. To facilitate the assessment of pesticides and other chemical hazards on this taxa, we present a novel bioassay capable of testing chemical sensitivity to lepidopteran larvae through dietary exposure. We used Mamestra brassicae caterpillars as a model lepidopteran and tested their sensitivity for the organophosphate insecticide chlorpyrifos. We exposed larvae to an artificial diet spiked with chlorpyrifos and monitored survival over time, as well as weight change over a 96-hour exposure period. To test the repeatability and reliability of the developed bioassay, the experiment was repeated three times. The survival in time data collected enabled analysis with the General Unified Threshold of Survival (GUTS) model, recently recognized by EFSA as a ready-to-use tool for regulatory purposes. The GUTS modelling was used to derive a set of relevant toxicokinetic and toxicodynamic parameters relating to the larval response to exposure over time. We found that across the three repeats studies there was no more than a threefold difference in LC₅₀ values (13.1, 18.7 and 8.1 mg/Kg) at 48 h and fourfold difference at 96 h, highlighting the repeatability of the bioassay. We also highlighted the potential of the method to observe sub-lethal effects such as changes in weight. Finally, we discuss the applications of this new bioassay method to chemical risk assessments and its potential for use in other scenarios, such as mixture or pulsed exposure testing.

Published
2023

20. The genome sequence of the red compost earthworm, Lumbricus rubellus (Hoffmeister, 1843)

Author

Short, Stephen, Green Etxabe, Amaia, Robinson, Alex, Spurgeon, David, Kille, Peter, Short, Stephen, Green Etxabe, Amaia, Robinson, Alex, Spurgeon, David, and Kille, Peter

Abstract

We present a genome assembly from an individual Lumbricus rubellus (the red compost earthworm; Annelida; Clitellata; Haplotaxida; Lumbricidae). The genome sequence is 787.5 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.81 kilobases in length. Gene annotation of this assembly on Ensembl identified 33,426 protein coding genes.

Published
2023

22. Identifying knowledge gaps in understanding the effects of selective serotonin reuptake inhibitors (SSRIs) on fish behaviour

Author

Ferreira, Carla S. S., Soares, Sandra C., Kille, Peter, and Oliveira, Miguel

Subjects
Aquatic pollution, Behaviour, Antidepressants, Personality
Abstract

Selective serotonin reuptake inhibitors (SSRIs) are a class of antidepressants increasingly prescribed to treat patients with clinical depression. As a result of the significant negative impact of the COVID-19 pandemic on the population's mental health, its consumption is expected to increase even more. The high consumption of these substances leads to their environmental dissemination, with evidence of their ability to compromise molecular, biochemical, physiological, and behavioural endpoints in non-target organisms. This study aimed to provide a critical review of the current knowledge regarding the effects of SSRI antidepressants on fish ecologically relevant behaviours and personality-dependent traits. A literature review shows limited data concerning the impact of fish personality on their responses to contaminants and how such responses could be influenced by SSRIs. This lack of information may be attributable to a lack of widely adopted standardized protocols for evaluating behavioural responses in fish. The existing studies examining the effects of SSRIs across various biological levels overlook the intra-specific variations in behaviour and physiology associated with different personality patterns or coping styles. Consequently, some effects may remain undetected, such as variations in coping styles and the capacity to handle environmental stressors. This oversight could potentially result in long-term effects with ecological implications. Data support the need for more studies to understand the impact of SSRIs on personality-dependent traits and how they may impair fitness-related behaviours. Given the considerable cross-species similarity in the personality dimensions, the collected data may allow new insights into the correlation between personality and animal fitness. published

Published
2023

23. Earthworm communities in long-term no-tillage systems and secondary forest fragments in Paraná, Southern Brazil

Author

DUDAS, RAFAELA T., primary, DEMETRIO, WILIAN C., additional, MAIA, LILIANE S., additional, SÁTIRO, JOSÉ N.O., additional, SILVA, KARLO A., additional, NICOLA, VITORIA B., additional, KILLE, PETER, additional, OLIVEIRA, CINTÍA M.R., additional, AFONSO, RITA O., additional, RUSSELL, GEORGINA, additional, FERREIRA, NUNO G. C., additional, CUNHA, LUIS, additional, BROWN, GEORGE G., additional, and BARTZ, MARIE L.C, additional

Published
2023
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25. How Do Recent and Historic Anthropic Changes Affect the Diversity of Earthworms in Amazonian Soils?

Author

Conrado, Ana Carol, primary, Demetrio, Wilian, additional, Stanton, David, additional, Bartz, Marie, additional, Kille, Peter, additional, James, Samuel, additional, Peña-Venegas, Clara, additional, Santos, Alessandra, additional, da Silva, Elodie, additional, Maia, Lilianne, additional, Silva, Telma, additional, Ferreira, Talita, additional, Acioli, Agno, additional, Ferreira, Alexandre, additional, Lavelle, Patrick, additional, Velasquez, Elena, additional, Tapia-Coral, Sandra, additional, Muniz, Aleksander, additional, Segalla, Rodrigo, additional, Decaens, Thibaud, additional, Nadolny, Herlon, additional, Pasini, Amarildo, additional, Oliveira-Junior, Raimundo, additional, Brown, George, additional, and Cunha, Luis, additional

Published
2023
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26. Fimoscolex undetermined

Author

Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis, and Brown, George G.

Subjects
Fimoscolex, Annelida, Glossoscolecidae, Animalia, Clitellata, Fimoscolex undetermined, Biodiversity, Haplotaxida, Taxonomy
Abstract

Fimoscolex sp. 21 BRPR1200, 1 individual with DNA analysis (GAN: OQ077058), BRPR1199, 1 individual (juvenile) with DNA analysis (GAN: OQ077056), BRPR1956, 1 individual (juvenile) with DNA analysis (GAN: OQ077062), BRPR1957, 1 individual (juvenile) with DNA analysis (GAN: OQ077070), in Secondary Forest in Mauá da Serra – PR, - 23.89658°S, - 51.20898°W, 1022 msnm, June 2018, R. T. Dudas, K.A. da Silva, W.C. Demetrio, L.S. Maia, V. B. Nicola, A. Pasini, C.M. R. de Oliveira, G.G. Brown, M.L.C. Bartz colls. BRPR1212, 1 individual, in annual crop under No-Tillage System in Palmeira – PR, - 25.38990°S, - 49.97696°W, 897 msnm, June 2018, R. T. Dudas, K.A. da Silva, W.C. Demetrio, L.S. Maia, V. B. Nicola, A. Pasini, C.M. R. de Oliveira, G.G. Brown, M.L.C. Bartz colls., Published as part of Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis & Brown, George G., 2023, Earthworm communities in long-term no-tillage systems and secondary forest fragments in Paraná, Southern Brazil, pp. 347-361 in Zootaxa 5255 (1) on page 352, DOI: 10.11646/zootaxa.5255.1.28, http://zenodo.org/record/7745029

Published
2023
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27. Benhamiidae

Author

Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis, and Brown, George G.

Subjects
Annelida, Crassiclitellata, Animalia, Clitellata, Biodiversity, Benhamiidae, Taxonomy
Abstract

Benhamiidae (juveniles) BRPR1194, 8 individuals, in annual crop under No-Tillage in Faxinal – PR, - 23.89199°S - 51.21379°W, 768 msnm, May 2019, R. T. Dudas, W.C. Demetrio, J.N.O. Sátiro, G.G. Brown, M.L.C. Bartz colls. BRPR1193, 7 individuals, in Secondary Forest in Faxinal – PR, - 23.97425°S, - 51.39393°W, 786 msnm, May 2019, R. T. Dudas, W.C. Demetrio, J.N.O. Sátiro, G.G. Brown, M.L.C. Bartz colls.

Published
2023
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28. Megascolecidae

Author

Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis, and Brown, George G.

Subjects
Annelida, Megascolecidae, Animalia, Clitellata, Biodiversity, Opisthopora, Taxonomy
Abstract

Megascolecidae (juveniles) BRPR1220, 1 individual with DNA analysis (GAN: OQ077063), BRPR1954, 1 individual with DNA analysis (GAN: OQ077065), in annual crop under No-Tillage System in Palmeira – PR, - 25.38990°S, - 49.97696°W, 897 msnm, June 2018 R. T. Dudas, K.A. da Silva, W.C. Demetrio, L.S. Maia, A. Pasini, C.M. R. Oliveira, G.G. Brown, M.L.C. Bartz colls.

Published
2023
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29. Glossoscolecidae

Author

Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis, and Brown, George G.

Subjects
Annelida, Glossoscolecidae, Crassiclitellata, Animalia, Clitellata, Biodiversity, Taxonomy
Abstract

Glossoscolecidae (juveniles) BRPR1186, 1 individual, in Secondary Forest in Faxinal – PR, - 23.97425°S, - 51.39393°W, 786 msnm, June 2018, R. T. Dudas, K.A. da Silva, W.C. Demetrio, L.S Maia, V. B. Nicola, A. Pasini, C.M. R. de Oliveira, G.G. Brown, M.L.C. Bartz colls. BRPR1202, 1 individual, in Secondary Forest in Mauá da Serra – PR, - 23.89658°S - 51.20898°W, 1022 msnm, June 2018, R. T. Dudas, K.A. da Silva, W.C. Demetrio, L.S. Maia, V. B. Nicola, A. Pasini, C.M. R. de Oliveira, G.G. Brown, M.L.C. Bartz colls. BRPR1219, 2 individuals, in annual crop under No-Tillage System in Palmeira – PR, - 25.3899°S, - 49.97696°W, 897 msnm, June 2018, R. T. Dudas, K.A. da Silva, W.C. Demetrio, L.S. Maia, V. B. Nicola, A. Pasini, C.M. R. de Oliveira, G.G. Brown, M.L.C. Bartz colls.

Published
2023
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30. Pontoscolex corethrurus Müller

Author

Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis, and Brown, George G.

Subjects
Pontoscolex corethrurus, Annelida, Glossoscolecidae, Crassiclitellata, Animalia, Clitellata, Biodiversity, Taxonomy, Pontoscolex
Abstract

Pontoscolex corethrurus Müller BRPR1184, 47 individuals, in annual crop under No-Tillage in Faxinal – PR, - 23.89199°S, - 51.21379°W, 768 msnm, June 2018, R. T. Dudas, K.A. da Silva, W.C. Demetrio, L.S. Maia, V. B. Nicola, A. Pasini, C.M. R. de Oliveira, G.G. Brown, M.L.C. Bartz colls. BRPR1196, 27 individuals, in Secondary Forest in Mauá da Serra - PR - 23.89658°S, - 51.20898°W, 1022 msnm, June 2018, R. T. Dudas, K.A. da Silva, W.C. Demetrio, L.S. Maia, V. B. Nicola, A. Pasini, C.M. R. de Oliveira, G.G. Brown, M.L.C. Bartz colls. BRPR1197, 1 individual, in annual crop under No-Tillage System in Mauá da Serra – PR, - 23.89199°S, - 51.21379°W, 979 msnm, June 2018, R. T. Dudas, K.A. da Silva, W.C. Demetrio, L.S. Maia, V. B. Nicola, A. Pasini, C.M. R. de Oliveira, G.G. Brown, M.L.C. Bartz colls. BRPR1189, 36 individuals, in Secondary Forest in Faxinal – PR, - 23.97425°S, - 51.39393°W, 786 msnm, May 2019, R. T. Dudas, W.C. Demetrio, J.N.O. Sátiro, G.G. Brown, M.L.C. Bartz colls. BRPR1190, 12 individuals, in annual crop under No-Tillage in Faxinal – PR, - 23.89199°S, - 51.21379°W, 768 msnm, May 2019, R. T. Dudas, W.C. Demetrio, J.N.O. Sátiro, G.G. Brown, M.L.C. Bartz colls. BRPR1205, 16 individuals, in Secondary Forest in Mauá da Serra – PR, - 23.89658°S, - 51.20898°W, 1022 msnm, May 2019, R. T. Dudas, W.C. Demetrio, J.N.O. Sátiro, G.G. Brown, M.L.C. Bartz colls. BRPR1206, 4 individuals, in annual crop under No-Tillage System in Mauá da Serra – PR, - 23.89199°S, - 51.21379°W, 979 msnm, May 2019, R. T. Dudas, W.C. Demetrio, J.N.O. Sátiro, G.G. Brown, M.L.C. Bartz colls., Published as part of Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis & Brown, George G., 2023, Earthworm communities in long-term no-tillage systems and secondary forest fragments in Paraná, Southern Brazil, pp. 347-361 in Zootaxa 5255 (1) on page 353, DOI: 10.11646/zootaxa.5255.1.28, http://zenodo.org/record/7745029

Published
2023
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31. Urobenus brasiliensis Benham 1886

Author

Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis, and Brown, George G.

Subjects
Annelida, Glossoscolecidae, Animalia, Clitellata, Urobenus, Biodiversity, Haplotaxida, Urobenus brasiliensis, Taxonomy
Abstract

Urobenus brasiliensis Benham BRPR1198, 6 individuals, in Secondary Forest in Mauá da Serra – PR, - 23.89658°S, - 51.20898°W, 1022 msnm, June 2018, R. T. Dudas, K.A. da Silva, W.C. Demetrio, L.S. Maia, V. B. Nicola, A. Pasini, C.M. R. de Oliveira, G.G. Brown, M.L.C. Bartz colls. BRPR1191, 1 individual, in Secondary Forest in Faxinal – PR, - 23.97425°S, - 51.39393°W, 786 msnm, May 2019, R. T. Dudas, W.C. Demetrio, J.N.O. Sátiro, G.G. Brown, M.L.C. Bartz colls., Published as part of Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis & Brown, George G., 2023, Earthworm communities in long-term no-tillage systems and secondary forest fragments in Paraná, Southern Brazil, pp. 347-361 in Zootaxa 5255 (1) on page 354, DOI: 10.11646/zootaxa.5255.1.28, http://zenodo.org/record/7745029

Published
2023
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32. Metaphire californica Kinberg

Author

Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis, and Brown, George G.

Subjects
Annelida, Megascolecidae, Metaphire, Animalia, Clitellata, Biodiversity, Metaphire californica, Haplotaxida, Taxonomy
Abstract

Metaphire californica Kinberg BRPR1224, 1 individual, in Secondary Forest in Palmeira – PR, - 25.39284°S, - 49.96545°W, 885 msnm, May 2019, R. T. Dudas, W.C. Demetrio, J.N.O. Sátiro, G.G. Brown, M.L.C. Bartz colls., Published as part of Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis & Brown, George G., 2023, Earthworm communities in long-term no-tillage systems and secondary forest fragments in Paraná, Southern Brazil, pp. 347-361 in Zootaxa 5255 (1) on page 355, DOI: 10.11646/zootaxa.5255.1.28, http://zenodo.org/record/7745029

Published
2023
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33. Ocnerodrilidae

Author

Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis, and Brown, George G.

Subjects
Annelida, Animalia, Clitellata, Biodiversity, Ocnerodrilidae, Haplotaxida, Taxonomy
Abstract

Ocnerodrilidae (juveniles) BRPR1187, 1 individual, BRPR1950, 1 individual with DNA analysis (GAN: OQ077048), BRPR1951, 1 individual with DNA analysis (GAN: OQ077052), BRPR1952, 1 individual with DNA analysis (GAN: OQ077067), BRPR1953, 1 individual with DNA analysis (GAN: OQ077068) in annual crop under No-Tillage in Faxinal – PR, - 23.89199°S, - 51.21379°W, 768 msnm, June 2018, R. T. Dudas, K.A. da Silva, W.C. Demetrio, L.S. Maia, V. B. Nicola, A. Pasini, C.M. R. de Oliveira, G.G. Brown, M.L.C. Bartz colls. BRPR1209, 1 individual, in annual crop under No-Tillage System in Mauá da Serra – PR, - 23.89199°S, - 51.21379°W, 979 msnm, May 2019, R. T. Dudas, W.C. Demetrio, J.N.O. Sátiro, G.G. Brown, M.L.C. Bartz colls. BRPR1204, 1 individual with DNA analysis (GAN: OQ077049), BRPR1948, 1 individual with DNA analysis (GAN: OQ077061), in annual crop under No-Tillage System in Mauá da Serra – PR, - 23.89199°S, - 51.21379°W, 979 msnm, June 2018, R. T. Dudas, K.A. da Silva, W.C. Demetrio, L.S. Maia, V. B. Nicola, A. Pasini, C.M. R. de Oliveira, G.G. Brown, M.L.C. Bartz colls., Published as part of Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis & Brown, George G., 2023, Earthworm communities in long-term no-tillage systems and secondary forest fragments in Paraná, Southern Brazil, pp. 347-361 in Zootaxa 5255 (1) on page 354, DOI: 10.11646/zootaxa.5255.1.28, http://zenodo.org/record/7745029

Published
2023
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34. Glossoscolex undetermined

Author

Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis, and Brown, George G.

Subjects
Annelida, Glossoscolecidae, Glossoscolex, Animalia, Clitellata, Biodiversity, Haplotaxida, Glossoscolex undetermined, Taxonomy
Abstract

Glossoscolex sp. 22 BRPR1214, 1 individual with DNA analysis (GAN: OQ077055), BRPR1215, 1 individual with DNA analysis (GAN: OQ077054), BRPR1216, 1 individual with DNA analysis (GAN: OQ077051), BRPR1218, 1 individual juvenile with DNA analysis, BRPR1958, 1 individual juvenile with DNA analysis (GAN: OQ077066), BRPR1959, 1 individual with DNA analysis (GAN: OQ077059), BRPR1960, 1 one individual with DNA analysis (GAN: OQ077057), BRPR1961, 1 individual juvenile with DNA analysis in Secondary Forest in Palmeira – PR, - 25.39284°S, - 49.96545W °, 885 msnm, June 2018, R. T. Dudas, K.A. da Silva, W.C. Demetrio, L.S. Maia, A. Pasini, C.M. R. Oliveira, G.G. Brown, M.L.C. Bartz colls. BRPR1223, 4 individuals, in Secondary Forest in Palmeira – PR, - 25.39284°S, - 49.96545°W, 885 msnm, May 2019, R. T. Dudas, W.C. Demetrio, J.N. O. Sátiro, G.G. Brown, M.L.C. Bartz colls., Published as part of Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis & Brown, George G., 2023, Earthworm communities in long-term no-tillage systems and secondary forest fragments in Paraná, Southern Brazil, pp. 347-361 in Zootaxa 5255 (1) on page 352, DOI: 10.11646/zootaxa.5255.1.28, http://zenodo.org/record/7745029

Published
2023
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35. Earthworm communities in long-term no-tillage systems and secondary forest fragments in Paraná, Southern Brazil

Author

Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N.O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M.R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis, and Brown, George G.

Subjects
Annelida, Megascolecidae, Glossoscolecidae, Octochaetidae, Crassiclitellata, Animalia, Clitellata, Biodiversity, Opisthopora, Ocnerodrilidae, Benhamiidae, Haplotaxida, Taxonomy
Abstract

Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N.O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M.R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis, Brown, George G. (2023): Earthworm communities in long-term no-tillage systems and secondary forest fragments in Paraná, Southern Brazil. Zootaxa 5255 (1): 347-361, DOI: 10.11646/zootaxa.5255.1.28, URL: http://dx.doi.org/10.11646/zootaxa.5255.1.28

Published
2023

36. Amynthas gracilis Kinberg

Author

Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis, and Brown, George G.

Subjects
Amynthas, Annelida, Megascolecidae, Animalia, Clitellata, Biodiversity, Opisthopora, Taxonomy, Amynthas gracilis
Abstract

Amynthas gracilis Kinberg BRPR1208, 1 individual, in Secondary Forest in Mauá da Serra – PR, - 23.89658°S - 51.20898°W, 1022 msnm, May 2019, R. T. Dudas, W.C. Demetrio, J.N.O. Sátiro, G.G. Brown, M.L.C. Bartz colls., Published as part of Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis & Brown, George G., 2023, Earthworm communities in long-term no-tillage systems and secondary forest fragments in Paraná, Southern Brazil, pp. 347-361 in Zootaxa 5255 (1) on page 354, DOI: 10.11646/zootaxa.5255.1.28, http://zenodo.org/record/7745029

Published
2023
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37. Andiorrhinus duseni Michaelsen

Author

Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis, and Brown, George G.

Subjects
Andiorrhinus duseni, Annelida, Glossoscolecidae, Andiorrhinus, Animalia, Clitellata, Biodiversity, Haplotaxida, Taxonomy
Abstract

Andiorrhinus duseni Michaelsen BRPR1201, 1 individual, BRPR1944, 1 individual with DNA analysis (GAN: OQ067381), BRPR1945, 1 individual with DNA analysis (GAN: OQ067382), in annual crop under No-Tillage System in Mauá da Serra - PR - 23.89199°S, - 51.21379°W, 979 msnm, June 2018, R. T. Dudas, K.A. da Silva, W.C. Demetrio, L.S. Maia, V. B. Nicola, A. Pasini, C.M. R. de Oliveira, G.G. Brown, M.L.C. Bartz colls. BRPR1207, 2 individuals, in annual crop under No-Tillage System in Mauá da Serra – PR, - 23.89199°S, - 51.21379°W, 979 msnm, May 2019, R. T. Dudas, W.C. Demetrio, J.N.O. Sátiro, G.G. Brown, M.L.C. Bartz colls., Published as part of Dudas, Rafaela T., Demetrio, Wilian C., Maia, Liliane S., Sátiro, José N. O., Silva, Karlo A., Nicola, Vitoria B., Kille, Peter, Oliveira, Cintía M. R., Afonso, Rita O., Russell, Georgina, Ferreira, Nuno G. C., Cunha, Luis & Brown, George G., 2023, Earthworm communities in long-term no-tillage systems and secondary forest fragments in Paraná, Southern Brazil, pp. 347-361 in Zootaxa 5255 (1) on page 353, DOI: 10.11646/zootaxa.5255.1.28, http://zenodo.org/record/7745029

Published
2023
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40. Is fish response to nanoplastics exposure modulated by neuropharmaceuticals pre-exposure? A case study with zebrafish (Danio rerio)s

Author

Ferreira De Melo, Carla, Venâncio, Cátia, Almeida, Mónica, Lopes, Isabel, Kille, Peter, and Oliveira, Miguel

Subjects
long, term exposure, antidepressants, emergent contaminants, nanoplastics
Abstract

Knowledge on the effects of nanoplastics (NPLs) on freshwater biota has progressed greatly in recent years. However, most of the studies have focused on NPLs individual exposures, a condition that lacks environmental relevance as NPLs do not exist alone in the environment. Other environmental contaminants may modulate their behaviour and biological effects. In this sense, it becomes highly relevant to understand how biologically active molecules like neuropharmaceuticals can influence the effects of NPLs, particularly at environmentally and ecologically relevant sub-lethal endpoints, such as behaviour. Accordingly, in this study, the effects of 96h exposure to 1 and 10 µg/L of 50 nm polymethylmethacrylate NPLs (PMMA-NPLs) on zebrafish behaviour (basal swimming activity and response to stressful conditions) was assessed in organisms previously chronically exposed (21 days) to 0, 40, and 400 µg/L of the antidepressant paroxetine (PAR). Overall, chronic exposure to PAR decreased fish basal locomotor activity during both light and dark periods and interfered with stress response. The same pattern was observed in an acute exposure to PMMA-NPLs, with exposed fish swimming less than control, except for 1 µg/L PMMA-NPLs under dark conditions. Finally, when considering fish that were pre-exposed to PAR and then subjected to PMMA acute exposure, a significant interaction between PAR and PMMA-NPLs was found to interfere with fish swimming behaviour under light conditions. These results highlight that effects of NPLs can be modulated by other emerging contaminants and organisms' previous contamination history. Also see: https://micro2022.sciencesconf.org/424495/document, In MICRO 2022, Online Atlas Edition: Plastic Pollution from MACRO to nano

Published
2022
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45. Investigation of Semantic Similarity as a Tool for Comparative Genomics

Author

Welter, Danielle, Gray, W. Alexander, Kille, Peter, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Wagner, Roland, editor, Revell, Norman, editor, and Pernul, Günther, editor

Published
2007
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46. Bioinformatics Data Source Integration Based on Semantic Relationships Across Species

Author

Al-Daihani, Badr, Gray, Alex, Kille, Peter, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Dalkilic, Mehmet M., editor, Kim, Sun, editor, and Yang, Jiong, editor

Published
2006
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49. Molecular insights into high-altitude adaption and acclimatisation of Aporrectodea caliginosa

Author

Perry, Iain, Hernadi, Szabolcs Balazs, Cunha, Luis, Short, Stephen, Marchbank, Angela, Spurgeon, David J., Orozco-terWengel, Pablo, Kille, Peter, Perry, Iain, Hernadi, Szabolcs Balazs, Cunha, Luis, Short, Stephen, Marchbank, Angela, Spurgeon, David J., Orozco-terWengel, Pablo, and Kille, Peter

Abstract

Here, we explore the high-altitude adaptions and acclimatisation of Aporrectodea caliginosa. Population diversity is assessed through mitochondrial barcoding, identifying closely related populations across the island of Pico (Azores). We present the first megabase N50 assembly size (1.2 Mbp) genome for A. caliginosa. High- and low-altitude populations were exposed experimentally to a range of oxygen and temperature conditions, simulating altitudinal conditions, and the transcriptomic responses explored. SNP densities are assessed to identify signatures of selective pressure and their link to differentially expressed genes. The high-altitude A. caliginosa population had lower differential expression and fewer co-expressed genes between conditions, indicating a more condition-refined epigenetic response. Genes identified as under adaptive pressure through Fst and nucleotide diversity in the high-altitude population clustered around the differentially expressed an upstream environmental response control gene, HMGB1. The high-altitude population of A. caliginosa indicated adaption and acclimatisation to high-altitude conditions and suggested resilience to extreme weather events. This mechanistic understanding could help offer a strategy in further identifying other species capable of maintaining soil fertility in extreme environments.

Published
2022

50. Impacts of life-time exposure of arsenic, cadmium and fluoranthene on the earthworms’ L. rubellus global DNA methylation as detected by msAFLP

Author

Rasnaca, Ilze, Kille, Peter, Newbold, Lindsay K., Spurgeon, David J., Rasnaca, Ilze, Kille, Peter, Newbold, Lindsay K., and Spurgeon, David J.

Abstract

This study reports on the effects of long-term exposure to the metals arsenic (As), cadmium (Cd) and the polycyclic aromatic hydrocarbon fluoranthene on the survival, growth, development and DNA methylation status of the earthworm Lumbricus rubellus. Exposures to the three chemicals were conducted over their whole juvenile developmental period from egg to adult. Significant effects on one or more measured endpoints were found for all three chemicals. Arsenic had no effect on survival, but had a significant effect on growth rates at concentrations of 36 mg/kg or higher and also slowed the rate of maturation. Cadmium significantly reduced juvenile survival at 500 mg/kg, juvenile growth at 148 mg/kg and maturation rates at all tested concentrations. Fluoranthene had no effect on survival or the developmental period, but did significantly reduce growth rates at 800 mg/kg. Effects at these concentrations are consistent with the known effects of these three chemicals on earthworms from previous studies conducted mainly with Eisenia fetida. Both As and Cd had no effect on DNA methylation patterning in earthworms measured at the end of the exposure. Fluoranthene was shown, for the first time. to have an effect on a species’ DNA methylation levels. These results suggest that apical phenotypic changes for As and Cd are not necessarily associated with changes in DNA methylation profiles. However, exposure to the organic chemical fluoranthene influenced DNA methylation patterns, suggesting wider remodelling of the epigenome for this chemical.

Published
2022

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