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Lopes-Lima M, Geist J, Egg S, Beran L, Bikashvili A, Van Bocxlaer B, Bogan AE, Bolotov IN, Chelpanovskaya OA, Douda K, Fernandes V, Gomes-Dos-Santos A, Gonçalves DV, Gürlek ME, Johnson NA, Karaouzas I, Kebapçı Ü, Kondakov AV, Kuehn R, Lajtner J, Mumladze L, Nagel KO, Neubert E, Österling M, Pfeiffer J, Prié V, Riccardi N, Sell J, Schneider LD, Shumka S, Sîrbu I, Skujienė G, Smith CH, Sousa R, Stöckl K, Taskinen J, Teixeira A, Todorov M, Trichkova T, Urbańska M, Välilä S, Varandas S, Veríssimo J, Vikhrev IV, Woschitz G, Zając K, Zając T, Zanatta D, Zieritz A, Zogaris S, Froufe E. Integrative phylogenetic, phylogeographic and morphological characterisation of the Unio crassus species complex reveals cryptic diversity with important conservation implications. Mol Phylogenet Evol 2024; 195:108046. [PMID: 38447924 DOI: 10.1016/j.ympev.2024.108046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 02/16/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
The global decline of freshwater mussels and their crucial ecological services highlight the need to understand their phylogeny, phylogeography and patterns of genetic diversity to guide conservation efforts. Such knowledge is urgently needed for Unio crassus, a highly imperilled species originally widespread throughout Europe and southwest Asia. Recent studies have resurrected several species from synonymy based on mitochondrial data, revealing U. crassus to be a complex of cryptic species. To address long-standing taxonomic uncertainties hindering effective conservation, we integrate morphometric, phylogenetic, and phylogeographic analyses to examine species diversity within the U. crassus complex across its entire range. Phylogenetic analyses were performed using cytochrome c oxidase subunit I (815 specimens from 182 populations) and, for selected specimens, whole mitogenome sequences and Anchored Hybrid Enrichment (AHE) data on ∼ 600 nuclear loci. Mito-nuclear discordance was detected, consistent with mitochondrial DNA gene flow between some species during the Pliocene and Pleistocene. Fossil-calibrated phylogenies based on AHE data support a Mediterranean origin for the U. crassus complex in the Early Miocene. The results of our integrative approach support 12 species in the group: the previously recognised Unio bruguierianus, Unio carneus, Unio crassus, Unio damascensis, Unio ionicus, Unio sesirmensis, and Unio tumidiformis, and the reinstatement of five nominal taxa: Unio desectusstat. rev., Unio gontieriistat. rev., Unio mardinensisstat. rev., Unio nanusstat. rev., and Unio vicariusstat. rev. Morphometric analyses of shell contours reveal important morphospace overlaps among these species, highlighting cryptic, but geographically structured, diversity. The distribution, taxonomy, phylogeography, and conservation of each species are succinctly described.
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Affiliation(s)
- M Lopes-Lima
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.
| | - J Geist
- Aquatic Systems Biology, Technical University of Munich, TUM School of Life Sciences, Mühlenweg 22, 85354 Freising, Germany
| | - S Egg
- Aquatic Systems Biology, Technical University of Munich, TUM School of Life Sciences, Mühlenweg 22, 85354 Freising, Germany; Molecular Zoology, Technical University of Munich, TUM School of Life Sciences, Hans-Carl-von-Carlowitz-Platz 2, Freising, Germany
| | - L Beran
- Regional Office Kokořínsko - Máchův kraj Protected Landscape Area Administration, Nature Conservation Agency of the Czech Republic, Česká 149, CZ-27601 Mělnik, Czech Republic
| | - A Bikashvili
- Institute of Zoology, Ilia State University, Cholokashvili ave. 3/5, 0162 Tbilisi, Georgia
| | - B Van Bocxlaer
- CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - A E Bogan
- North Carolina Museum of Natural Sciences, 11 West Jones Street, Raleigh, NC 27601 USA
| | - I N Bolotov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - O A Chelpanovskaya
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - K Douda
- Department of Zoology and Fisheries, FAFNR, Czech University of Life Sciences Prague, Kamýcká 129, CZ-16500 Prague, Czech Republic
| | - V Fernandes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - A Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - D V Gonçalves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - M E Gürlek
- Burdur Vocational School of Food Agriculture and Livestock, Mehmet Akif Ersoy University, 15100 Burdur, Türkiye
| | - N A Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - I Karaouzas
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 46.7 km Athens-Sounio Av., Anavyssos 19013, Greece
| | - Ü Kebapçı
- Biology Department, Faculty of Science and Arts, Burdur Mehmet Akif Ersoy University, Burdur, Türkiye
| | - A V Kondakov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - R Kuehn
- Molecular Zoology, Technical University of Munich, TUM School of Life Sciences, Hans-Carl-von-Carlowitz-Platz 2, Freising, Germany
| | - J Lajtner
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - L Mumladze
- Institute of Zoology, Ilia State University, Cholokashvili ave. 3/5, 0162 Tbilisi, Georgia
| | - K-O Nagel
- Malacological Section, Senckenberg Research Institute and Natural History Museum Frankfurt/M., Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - E Neubert
- Natural History Museum, 3005 Bern, Switzerland; Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - M Österling
- Institution of Environmental and Life Sciences, Karlstad University, Biology, 65188 Karlstad, Sweden
| | - J Pfeiffer
- National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue, Washington, DC, USA
| | - V Prié
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005 Paris, France
| | - N Riccardi
- CNR Water Research Institute, Largo Tonolli 50, 28922 Verbania, Italy
| | - J Sell
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - L D Schneider
- The Rural Economy and Agricultural Society, 305 96 Eldsberga, Sweden
| | - S Shumka
- Faculty Of Biotechnology and Food, Agricultural University of Tirana, Koder Kamez, Tirana 2029, Albania
| | - I Sîrbu
- Lucian Blaga University of Sibiu, Faculty of Sciences, 5-7 Dr. I. Rațiu St., 550012 Sibiu, Romania
| | - G Skujienė
- Department of Zoology, Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10223 Vilnius, Lithuania
| | - C H Smith
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - R Sousa
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - K Stöckl
- Bavarian Academy for Nature Conservation and Landscape Management, Seethalerstrasse 6, 83410 Laufen, Germany
| | - J Taskinen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - A Teixeira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - M Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - T Trichkova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - M Urbańska
- Department of Zoology, Poznań University of Life Sciences, ul. Wojska Polskiego 28, 60-637 Poznań, Poland
| | - S Välilä
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - S Varandas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; CITAB-UTAD - Centre for Research and Technology of Agro-Environment and Biological Sciences, University of Trás-os-Montes and Alto Douro, Forestry Department, Vila Real, Portugal
| | - J Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - I V Vikhrev
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - G Woschitz
- IFIS - Ichthyological Research Initiative Styria, 1160 Vienna, Austria
| | - K Zając
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Adama Mickiewicza 33, 31-120 Kraków, Poland
| | - T Zając
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Adama Mickiewicza 33, 31-120 Kraków, Poland
| | - D Zanatta
- Biology Department, Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - A Zieritz
- School of Geography, University of Nottingham, University Park, Sir Clive Granger Building, Nottingham NG7 2RD, United Kingdom
| | - S Zogaris
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 46.7 km Athens-Sounio Av., Anavyssos 19013, Greece
| | - E Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
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González-Miguéns R, Todorov M, Blandenier Q, Duckert C, Porfirio-Sousa AL, Ribeiro GM, Ramos D, Lahr DJG, Buckley D, Lara E. Deconstructing Difflugia: The tangled evolution of lobose testate amoebae shells (Amoebozoa: Arcellinida) illustrates the importance of convergent evolution in protist phylogeny. Mol Phylogenet Evol 2022; 175:107557. [PMID: 35777650 DOI: 10.1016/j.ympev.2022.107557] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 10/17/2022]
Abstract
Protists, the micro-eukaryotes that are neither plants, animals nor fungi build up the greatest part of eukaryotic diversity on Earth. Yet, their evolutionary histories and patterns are still mostly ignored, and their complexity overlooked. Protists are often assumed to keep stable morphologies for long periods of time (morphological stasis). In this work, we test this paradigm taking Arcellinida testate amoebae as a model. We build a taxon-rich phylogeny based on two mitochondrial (COI and NADH) and one nuclear (SSU) gene, and reconstruct morphological evolution among clades. In addition, we prove the existence of mitochondrial mRNA editing for the COI gene. The trees show a lack of conservatism of shell outlines within the main clades, as well as a widespread occurrence of morphological convergences between far-related taxa. Our results refute, therefore, a widespread morphological stasis, which may be an artefact resulting from low taxon coverage. As a corollary, we also revise the groups systematics, notably by emending the large and highly polyphyletic genus Difflugia. These results lead, amongst others, to the erection of a new infraorder Cylindrothecina, as well as two new genera Cylindrifflugia and Golemanskia.
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Affiliation(s)
| | - Milcho Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Science, 1113 Sofia, Bulgaria
| | - Quentin Blandenier
- Laboratory of Soil Biodiversity, University of Neuchâtel, Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Clément Duckert
- Laboratory of Soil Biodiversity, University of Neuchâtel, Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | | | - Giulia M Ribeiro
- Department of Zoology, Institute of Biosciences, University of São Paulo, Brazil
| | - Diana Ramos
- Real Jardín Botánico (RJB-CSIC), Plaza Murillo 2, 28014 Madrid, Spain
| | - Daniel J G Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, Brazil
| | - David Buckley
- Department of Biology (Genetics), Universidad Autónoma de Madrid, Spain; Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Spain
| | - Enrique Lara
- Real Jardín Botánico (RJB-CSIC), Plaza Murillo 2, 28014 Madrid, Spain.
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Gecheva G, Pall K, Todorov M, Traykov I, Gribacheva N, Stankova S, Birk S. Anthropogenic Stressors in Upland Rivers: Aquatic Macrophyte Responses. A Case Study from Bulgaria. Plants (Basel) 2021; 10:plants10122708. [PMID: 34961179 PMCID: PMC8703415 DOI: 10.3390/plants10122708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Upland rivers across Europe still exhibit undisturbed conditions and represent a treasure that we cannot afford to lose. We hypothesize that the combination of pristine and modified conditions could demonstrate biological responses along the stressor gradients. Thus, the response of aquatic macrophyte communities to anthropogenic stressors along upland rivers in Bulgaria was studied. Six stressors were selected out of 36 parameters grouped into hydromorphological, chemical variables and combined drivers (catchment land use). The stressors strongly affected species richness on the basis of biological type (bryophytes vs. vascular plants) and ecomorphological type (hydrophytes vs. helophytes). Hydrological alteration expressed by the change of the river's base flow and altered riparian habitats has led to a suppression of bryophytes and a dominance of riverbank plant communities. Seventy-five percent of mountain sites were lacking bryophytes, and the vegetation at semi-mountainous sites was dominated by vascular plants. It can be concluded that hydropeaking, organic and inorganic pollution, and discontinuous urban structures caused important modifications in the aquatic macrophyte assemblages. Macrophyte abundance and the biological and ecomorphological type of aquatic macrophytes reflect multi-stressor effects in upland rivers.
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Affiliation(s)
- Gana Gecheva
- Faculty of Biology, Plovdiv University, 4000 Plovdiv, Bulgaria; (N.G.); (S.S.)
| | - Karin Pall
- Systema GmbH, 8 Bensasteig, 1140 Vienna, Austria;
| | - Milcho Todorov
- Institute of Biodiversity and Ecosystem Research, BAS, 1113 Sofia, Bulgaria;
| | - Ivan Traykov
- Faculty of Biology, Sofia University, 1164 Sofia, Bulgaria;
| | - Nikolina Gribacheva
- Faculty of Biology, Plovdiv University, 4000 Plovdiv, Bulgaria; (N.G.); (S.S.)
| | - Silviya Stankova
- Faculty of Biology, Plovdiv University, 4000 Plovdiv, Bulgaria; (N.G.); (S.S.)
| | - Sebastian Birk
- Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany;
- Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Germany
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Vidinova Y, Park J, Varadinova E, Tyufekchieva V, Todorov M. Invasion of Corbicula fluminea (Müller, 1774) (Bivalvia: Corbiculidae) in water bodies from the East Aegean River Basin in Bulgaria. Ecol Monten 2021. [DOI: 10.37828/em.2021.47.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two decades after the first record of the invasive mussel Corbicula fluminea (Müller, 1774) in Bulgaria in 2001, it has been found in many surface lotic and standing waters in the Bulgarian Danube River Basin.
The aim of the current study is to report the finding of C. fluminea in lotic environment of the East Aegean water basin in Bulgaria. Six new localities of the mussel, all situated in the lower stretches of the Tundzha (two) and Maritsa (four) River were registered. The distributional patterns of the mussel and the abundance of its populations in relation to the environmental conditions were analyzed. The adaptive character of the Corbicula, the possible path for invasion as well as the probability of rapid spread of the mussel in the largest rivers and their tributary systems in south-eastern part of Balkan Peninsula was discussed.
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González-Miguéns R, Soler-Zamora C, Villar-Depablo M, Todorov M, Lara E. Multiple convergences in the evolutionary history of the testate amoeba family Arcellidae (Amoebozoa: Arcellinida: Sphaerothecina): when the ecology rules the morphology. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Protists are probably the most species-rich eukaryotes, yet their systematics are inaccurate, leading to an underestimation of their actual diversity. Arcellinida (= lobose testate amoebae) are amoebozoans that build a test (a hard shell) whose shape and composition are taxonomically informative. One of the most successful groups is Arcellidae, a family found worldwide in many freshwater and terrestrial environments where they are indicators of environmental quality. However, the systematics of the family is based on works published nearly a century ago. We re-evaluated the systematics based on single-cell barcoding, morphological and ecological data. Overall, test shape appears to be more related to environmental characteristics than to the species’ phylogenetic position. We show several convergences in organisms with similar ecology, some traditionally described species being paraphyletic. Based on conservative traits, we review the synapomorphies of the infraorder Sphaerothecina, compile a list of synonyms and describe a new genus Galeripora, with five new combinations. Seven new species: Arcella guadarramensis sp. nov., Galeripora balari sp. nov., Galeripora bufonipellita sp. nov., Galeripora galeriformis sp. nov., Galeripora naiadis sp. nov., Galeripora sitiens sp. nov. andGaleripora succelli sp. nov. are also described here.
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Affiliation(s)
| | | | - Mar Villar-Depablo
- Real Jardín Botánico (RJB-CSIC), Plaza Murillo 2, Madrid, Spain
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), Serrano 115 bis, Madrid, Spain
| | - Milcho Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Science, Sofia, Bulgaria
| | - Enrique Lara
- Real Jardín Botánico (RJB-CSIC), Plaza Murillo 2, Madrid, Spain
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Macumber AL, Blandenier Q, Todorov M, Duckert C, Lara E, Lahr DJ, Mitchell EA, Roe HM. Phylogenetic divergence within the Arcellinida (Amoebozoa) is congruent with test size and metabolism type. Eur J Protistol 2020; 72:125645. [DOI: 10.1016/j.ejop.2019.125645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/01/2019] [Accepted: 10/14/2019] [Indexed: 12/21/2022]
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Abstract
BACKGROUND Until now, a complete checklist of Sphagnum-dwelling testate amoebae in Bulgaria has never been published. Records for species diversity and distribution in the country were scattered in many faunistic and ecological publications. The aim of the present study is to summarise all data for the species distribution at the level of country by reviewing the existing literature and by additional data obtained in our research over the past two years. NEW INFORMATION The checklist comprises 171 species, classified into 43 genera, 20 families, three orders, three classes and three phyla. We present data for 16 new Sphagnum-dwelling testate amoebae in Bulgaria and new distribution data for 134 species. Of them, 99 species are recorded from Stara Planina Mt., for which there was no available data to date. Additionally are recorded 69 new species for Pirin Mt., 21 for Vitosha Mt. and 18 for Rila Mt. Thirty six species are synonymised according to the latest taxonomic changes. Two misidentified taxa (Euglypha brachiata Penard, 1902 and Difflugia compressa var. africana Gauthier-Lièvre et Thomas, 1958) are transferred into valid species E. acanthophora and Zivkovicia compressa, respectively. Three of the recorded species have not been included in the checklist, because they are currently not refering to testate amoebae (Cochliopodium bilimbosum (Auerbach 1856) and Cochliopodium echinatum Korotneef, 1879 are gymnamoebae (naked amoebae) and Microgromia elegantula (Penard 1904) = Paralieberkuehnia elegantula (Penard 1904) is freshwater foraminifera).
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Affiliation(s)
- Nikola Bankov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Milcho Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Anna Ganeva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
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Compelli A, Ivanov R, Todorov M. Hamiltonian models for the propagation of irrotational surface gravity waves over a variable bottom. Philos Trans A Math Phys Eng Sci 2018; 376:rsta.2017.0091. [PMID: 29229791 PMCID: PMC5740291 DOI: 10.1098/rsta.2017.0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
A single incompressible, inviscid, irrotational fluid medium bounded by a free surface and varying bottom is considered. The Hamiltonian of the system is expressed in terms of the so-called Dirichlet-Neumann operators. The equations for the surface waves are presented in Hamiltonian form. Specific scaling of the variables is selected which leads to approximations of Boussinesq and Korteweg-de Vries (KdV) types, taking into account the effect of the slowly varying bottom. The arising KdV equation with variable coefficients is studied numerically when the initial condition is in the form of the one-soliton solution for the initial depth.This article is part of the theme issue 'Nonlinear water waves'.
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Affiliation(s)
- A Compelli
- School of Mathematical Sciences, Dublin Institute of Technology, Kevin Street, Dublin 8, Ireland
- Erwin Schrödinger International Institute for Mathematics and Physics, University of Vienna, 1090 Vienna, Austria
| | - R Ivanov
- School of Mathematical Sciences, Dublin Institute of Technology, Kevin Street, Dublin 8, Ireland
- Erwin Schrödinger International Institute for Mathematics and Physics, University of Vienna, 1090 Vienna, Austria
| | - M Todorov
- Department of Differential Equations, Faculty of Applied Mathematics and Informatics, Technical University of Sofia, 8 Kliment Ohridski Boulevard, 1000 Sofia, Bulgaria
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Gomaa F, Lahr DJG, Todorov M, Li J, Lara E. A contribution to the phylogeny of agglutinating Arcellinida (Amoebozoa) based on SSU rRNA gene sequences. Eur J Protistol 2017; 59:99-107. [PMID: 28433921 DOI: 10.1016/j.ejop.2017.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 03/17/2017] [Accepted: 03/22/2017] [Indexed: 10/19/2022]
Abstract
Arcellinid testate amoebae include a wide variety of amoeboid organisms whose test (shell) varies in shape, composition and size. A decade ago, we initiated molecular phylogenetic analyses based on SSU rRNA gene sequences and a taxonomic revision of Arcellinida. However, many lineages within Arcellinida still lack molecular data, and the phylogeny of this group is largely incomplete. In this study, we obtained SSU rRNA gene sequences from seven taxa, of which six have agglutinated shell (Difflugia oblonga, D. labiosa, D. gramen, Mediolus corona, Netzelia wailesi, and N. tuberculata), and one has an entirely proteinaceous shell (Arcella intermedia). All species but Difflugia oblonga branched within the recently erected suborder Sphaerothecina, confirming the synapomorphic value of an oviform or discoid shell. Thus, we propose that species with an oviform or discoid shell currently classified within genus Difflugia must be transferred to other genera, thus continuing the process of taxonomic revision of genus Difflugia, the largest Arcellinida genus. We therefore transferred the current and the previously sequenced oviform Difflugia spp. to Netzelia spp., based on the shared globular/oviform shell shape and their monophyly. Another species, D. labiosa, formed an independent lineage that branched as a sister clade to Arcella spp.; based on the shell morphology and their phylogenetic position, we considered D. labiosa as incertae sedis.
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Affiliation(s)
- Fatma Gomaa
- Department of Organismic and Evolutionary Biology, Biological Laboratory, Harvard University, Cambridge, Massachusetts, USA; Ain Shams University, Faculty of Science, Zoology Department, Cairo, Egypt.
| | - Daniel J G Lahr
- Department of Zoology, University of Sao Paulo, Sao Paulo, Brazil
| | - Milcho Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin St., 1113 Sofia, Bulgaria
| | - Jingchun Li
- Department of Organismic and Evolutionary Biology, Biological Laboratory, Harvard University, Cambridge, Massachusetts, USA
| | - Enrique Lara
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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Blandenier Q, Lara E, Mitchell EA, Alcantara DM, Siemensma FJ, Todorov M, Lahr DJ. NAD9/NAD7 (mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene)—A new “Holy Grail” phylogenetic and DNA-barcoding marker for Arcellinida (Amoebozoa)? Eur J Protistol 2017; 58:175-186. [DOI: 10.1016/j.ejop.2016.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 11/22/2016] [Accepted: 12/12/2016] [Indexed: 11/17/2022]
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Todorov M. On the morphology, biometry and biogeography of Lamtopyxiscallistoma (Amoebozoa: Arcellinida). Biodivers Data J 2015:e4297. [PMID: 25632260 PMCID: PMC4304259 DOI: 10.3897/bdj.3.e4297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/07/2015] [Indexed: 11/22/2022] Open
Abstract
The ultra-structure of the shell and the morphometric variability of soil inhabiting testate amoeba Lamtopyxiscallistoma from Madagascar were studied by using light- and scanning electron microscopy. The biometrical characteristic of the species was made on the basis of 75 specimens measured. In addition to the diameter of the shell, six other shell characters were described biometrically for the first time. The analysis of the variation coefficients shows that the studied population of L.callistoma is comparatively homogeneous and almost all measured characters are weakly to moderate variable (CV less than 10%). Scanning electron microscopy (SEM) studies on the shell ultra-morphology show that it has a smooth apertural surface with a thick layer of porous and fibrous organic cement and a rough dorsal surface composed of bigger and angular pieces of quartz. The shell wall has a thickness of about 5-6 µm and is composed of three layers. Unlike the previously accepted opinion that species is characterized by the presence of four teeth, this study shows that population of L.callistoma from Madagascar is comprised of both, specimens with four teeth and specimens with three teeth, in ratio of about 60% to 40%. Taking into account the restricted geographical distribution, large sizes and characteristic apertural morphology of L.callistoma it is assumed that this species, like some bryophilic ‘Nebelas’ with circumaustral distribution (e.g. Apoderavas, Alocoderacockayni, Certesellacertesi, Certesellamartiali, etc.), can be used as an example that in free-living microbial eukaryotes ‘not everything is everywhere’.
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Affiliation(s)
- Milcho Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin Str., 1113 Sofia, Bulgaria
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12
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Todorov M, Gerdjikov VS, Kyuldjiev AV. Multisoliton interactions for the Manakov system under composite external potentials. Proc Estonian Acad Sci 2015. [DOI: 10.3176/proc.2015.3s.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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Gomaa F, Yang J, Mitchell EAD, Zhang WJ, Yu Z, Todorov M, Lara E. Morphological and molecular diversification of Asian endemic Difflugia tuberspinifera (Amoebozoa, Arcellinida): a case of fast morphological evolution in protists? Protist 2014; 166:122-30. [PMID: 25594492 DOI: 10.1016/j.protis.2014.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 11/11/2014] [Accepted: 11/29/2014] [Indexed: 10/24/2022]
Abstract
Planktonic arcellinid testate amoebae exhibit a broad-range of morphological variability but it is currently unclear to what extent this variability represents phenotypic plasticity or if it is genetically determined. We investigated the morphology and phylogenetic relationships of three endemic east-asian Difflugia taxa 1) the vase-shaped D. mulanensis, 2) and a spinose and a spineless morphotypes of D. tuberspinifera using scanning electron microscopy and two ribosomal genetic markers (SSU rDNA and ITS sequences). Our phylogenetic analyses shows that all three taxa are genetically distinct and closely related to D. achlora and Netzelia oviformis. The genetic variations between the spineless and spinose morphotypes of D. tuberspinifera were low at the SSU rRNA level (0.4%), but ten times higher at the ITS level (4.5-6%). Our data suggest that the two forms of D. tuberspinifera are sufficiently differentiated in terms of morphology and genetic characteristics to constitute two separate entities and that the presence of spines does not result from phenotypic plasticity due to environmental selective pressure. However further observational and experimental data are needed to determine if these two forms constitute different biological species.
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Affiliation(s)
- Fatma Gomaa
- Laboratory of Soil Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland; Zoology Department, Faculty of Science, Ain Shams University, Cairo, Egypt.
| | - Jun Yang
- Aquatic Ecohealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Edward A D Mitchell
- Laboratory of Soil Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland; Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, CH-2000 Neuchâtel, Switzerland
| | - Wen-Jing Zhang
- Marine Biodiversity and Global Change Center, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Zheng Yu
- Aquatic Ecohealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Milcho Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin St., 1113 Sofia, Bulgaria
| | - Enrique Lara
- Laboratory of Soil Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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Mekenyan O, Dimitrov S, Pavlov T, Dimitrova G, Todorov M, Petkov P, Kotov S. Simulation of chemical metabolism for fate and hazard assessment. V. Mammalian hazard assessment. SAR QSAR Environ Res 2012; 23:553-606. [PMID: 22536822 DOI: 10.1080/1062936x.2012.679689] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Animals and humans are exposed to a wide array of xenobiotics and have developed complex enzymatic mechanisms to detoxify these chemicals. Detoxification pathways involve a number of biotransformations, such as oxidation, reduction, hydrolysis and conjugation reactions. The intermediate substances created during the detoxification process can be extremely toxic compared with the original toxins, hence metabolism should be accounted for when hazard effects of chemicals are assessed. Alternatively, metabolic transformations could detoxify chemicals that are toxic as parents. The aim of the present paper is to describe specificity of eukaryotic metabolism and its simulation and incorporation in models for predicting skin sensitization, mutagenicity, chromosomal aberration, micronuclei formation and estrogen receptor binding affinity implemented in the TIMES software platform. The current progress in model refinement, data used to parameterize models, logic of simulating metabolism, applicability domain and interpretation of predictions are discussed. Examples illustrating the model predictions are also provided.
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Affiliation(s)
- O Mekenyan
- Laboratory of Mathematical Chemistry, University "Prof. As. Zlatarov", Bourgas, Bulgaria.
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Kosakyan A, Heger TJ, Leander BS, Todorov M, Mitchell EA, Lara E. COI Barcoding of Nebelid Testate Amoebae (Amoebozoa: Arcellinida): Extensive Cryptic Diversity and Redefinition of the Hyalospheniidae Schultze. Protist 2012; 163:415-34. [DOI: 10.1016/j.protis.2011.10.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 09/17/2011] [Indexed: 11/30/2022]
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16
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Abstract
The multiparameter formulation of the COmmon REactivity PAttern (COREPA) approach has been used to describe the structural requirements for eliciting rat androgen receptor (AR) binding affinity, accounting for molecular flexibility. Chemical affinity for AR binding was related to the distances between nucleophilic sites and structural features describing electronic and hydrophobic interactions between the receptor and ligands. Categorical models were derived for each binding affinity range in terms of specific distances, local (maximal donor delocalizability associated with the oxygen atom of the A ring), global nucleophilicity (partial positive surface areas and energy of the highest occupied molecular orbital) and hydrophobicity (log Kow) of the molecules. An integral screening tool for predicting binding affinity to AR was constructed as a battery of models, each associated with different activity bins. The quality of the screening battery of models was assessed using a high value (0.9) of the Pearson contingency coefficient. The predictability of the model was assessed by testing the model performance on external validation sets. A recently developed technique for selection of potential androgenically active chemicals was used to test the performance of the model in its applicability domain. Some of the selected chemicals were tested for AR transcriptional activation. The experimental results confirmed the theoretical predictions.
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Affiliation(s)
- M Todorov
- Laboratory of Mathematical Chemistry, Bourgas As. Zlatarov University, Bourgas, Bulgaria
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Patlewicz G, Mekenyan O, Dimitrova G, Kuseva C, Todorov M, Kotov S, Stoeva S, Donner EM. Can mutagenicity information be useful in an Integrated Testing Strategy (ITS) for skin sensitization? SAR QSAR Environ Res 2010; 21:619-656. [PMID: 21120753 DOI: 10.1080/1062936x.2010.528447] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Our previous work has investigated the utility of mutagenicity data in the development and application of Integrated Testing Strategies (ITS) for skin sensitization by focusing on the chemical mechanisms at play and substantiating these with experimental data where available. The hybrid expert system TIMES (Tissue Metabolism Simulator) was applied in the identification of the chemical mechanisms since it encodes a comprehensive set of established structure-activity relationships for both skin sensitization and mutagenicity. Based on the evaluation, the experimental determination of mutagenicity was thought to be potentially helpful in the evaluation of skin sensitization potential. This study has evaluated the dataset reported by Wolfreys and Basketter (Cutan. Ocul. Toxicol. 23 (2004), pp. 197-205). Upon an update of the experimental data, the original reported concordance of 68% was found to increase to 88%. There were several compounds that were 'outliers' in the two experimental evaluations which are discussed from a mechanistic basis. The discrepancies were found to be mainly associated with the differences between skin and liver metabolism. Mutagenicity information can play a significant role in evaluating sensitization potential as part of an ITS though careful attention needs to be made to ensure that any information is interpreted in the appropriate context.
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Affiliation(s)
- G Patlewicz
- DuPont Haskell Global Centers for Health and Environmental Sciences, Newark, Delaware, USA.
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Heger TJ, Pawlowski J, Lara E, Leander BS, Todorov M, Golemansky V, Mitchell EAD. Comparing potential COI and SSU rDNA barcodes for assessing the diversity and phylogenetic relationships of cyphoderiid testate amoebae (Rhizaria: Euglyphida). Protist 2010; 162:131-41. [PMID: 20702136 DOI: 10.1016/j.protis.2010.05.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 05/01/2010] [Indexed: 11/19/2022]
Abstract
The mitochondrial Cytochrome Oxidase Subunit 1 gene (COI) has been promoted as an ideal "DNA barcode" for animal species and other groups of eukaryotes. However, the utility of the COI marker for species level discrimination and for phylogenetic analyses has yet to be tested within the Rhizaria. Accordingly, we analysed mitochondrial COI gene sequences and nuclear small subunit rDNA (SSU) sequences from several morphospecies of euglyphid testate amoebae (Cercozoa, Rhizaria) in order to evaluate the utility of these DNA markers for species discrimination and phylogenetic reconstructions. Sequences were obtained from eleven populations belonging to sixCyphoderiamorphospecies that were isolated from field samples in North America and Europe. Mean inter-population COI sequence dissimilarities were on average 2.9 times greater than in the SSU, while the intra-population sequence dissimilarities were higher in the SSU (0-0.95%) than in the COI (0%); this suggests that the COI fragment is valuable for discriminating Cyphoderiidae isolates. Our study also demonstrated that COI sequences are useful for inferring phylogenetic relationships among Cyphoderiidae isolates. COI and SSU tree topologies were very similar even though the COI fragment used in these analyses (500bp) was much shorter than the SSU sequences (1600bp). Altogether, these results demonstrate the utility of the COI as a potential taxonomic DNA barcode for assessing cyphoderiid species diversity and for inferring phylogenetic relationships within the group.
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Affiliation(s)
- Thierry J Heger
- WSL, Swiss Federal Institute for Forest, Snow and Landscape Research, Ecosystem Boundaries Research Unit, Wetlands Research Group, Station 2, CH-1015 Lausanne, Switzerland.
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Ringeissen S, Marrot L, Note R, Labarussiat A, Imbert S, Todorov M, Mekenyan O, Meunier J. Development of a mechanistic QSAR model for the detection of phototoxic chemicals and use in an integrated testing strategy. Toxicol Lett 2010. [DOI: 10.1016/j.toxlet.2010.03.802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Heger TJ, Mitchell EA, Todorov M, Golemansky V, Lara E, Leander BS, Pawlowski J. Molecular phylogeny of euglyphid testate amoebae (Cercozoa: Euglyphida) suggests transitions between marine supralittoral and freshwater/terrestrial environments are infrequent. Mol Phylogenet Evol 2010; 55:113-122. [DOI: 10.1016/j.ympev.2009.11.023] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Revised: 11/22/2009] [Accepted: 11/25/2009] [Indexed: 11/17/2022]
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21
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Aladjov H, Todorov M, Schmieder P, Serafimova R, Mekenyan O, Veith G. Strategic selection of chemicals for testing. Part I. Functionalities and performance of basic selection methods. SAR QSAR Environ Res 2009; 20:159-183. [PMID: 19343590 DOI: 10.1080/10629360902723996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To develop quantitative structure-activity relationships (QSAR) models capable of predicting adverse effects for large chemical inventories and diverse structures, an interactive approach is presented that includes testing of strategically selected chemicals to expand the scope of a preliminary model to cover a target inventory. The goal of chemical selection in this context is to make the testing more effective in terms of adding maximal new structural information to the predictive model with minimal testing. The aim of this paper is to describe a set of algorithmic solutions and modelling techniques that can be used to efficiently select chemicals for testing to achieve a variety of goals. One purpose of chemical selection is to refine the model thus extending our knowledge about the modelled subject. Alternatively, the selection of chemicals for testing could be targeted at achieving a more adequate structural representation of a specific universe of untested chemicals to extend the model applicability domain on each subsequent step of model development. The chemical selection tools are collectively provided in a software package referred to as ChemPick. The system also allows the visualisation of chemical inventories and training sets in multidimensional (two and three dimensions) descriptor space. The software environment allows one or more datasets to be simultaneously loaded in a three-dimensional (or N-dimensional) chart where each point represents a combination of values for the descriptors for a given conformation of a chemical. The application of the chemical selection tools to select chemicals to expand a preliminary model of human oestrogen receptor (hER) ligand binding to more adequately cover a diverse chemical inventory is presented to demonstrate the application of these tools.
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Affiliation(s)
- H Aladjov
- US EPA, Mid-Continent Ecology Division, Duluth, MN 55804, USA
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Serafimova R, Todorov M, Pavlov T, Kotov S, Jacob E, Aptula A, Mekenyan O. Correction to Identification of the Structural Requirements for Mutagencity, by Incorporating Molecular Flexibility and Metabolic Activation of Chemicals. II. General Ames Mutagenicity Model. Chem Res Toxicol 2007. [DOI: 10.1021/tx7002596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Serafimova R, Todorov M, Nedelcheva D, Pavlov T, Akahori Y, Nakai M, Mekenyan O. QSAR and mechanistic interpretation of estrogen receptor binding. SAR QSAR Environ Res 2007; 18:389-421. [PMID: 17514577 DOI: 10.1080/10629360601053992] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A multi-dimensional formulation of the COmmon REactivity PAttern (COREPA) modeling approach has been used to investigate chemical binding to the human estrogen receptor (hER). A training set of 645 chemicals included 497 steroid and environmental chemicals (database of the Chemical Evaluation and Research Institute, Japan - CERI) and 148 chemicals to further explore hER-structure interactions (selected J. Katzenellenbogen references). Upgrades of modeling approaches were introduced for multivariate COREPA analysis, optimal conformational generation and description of the local hydrophobicity of chemicals. Analysis of reactivity patterns based on the distance between nucleophilic sites resulted in identification of distinct interaction types: a steroid-like A-B type described by frontier orbital energies and distance between nucleophilic sites with specific charge requirements; an A-C type where local hydrophobic effects are combined with electronic interactions to modulate binding; and mixed A-B-C (AD) type. Chemicals were grouped by type, then COREPA models were developed for within specific relative binding affinity ranges of >10%, 10 > RBA > or = 0.1%, and 0.1 > RBA > 0.0%. The derived models for each interaction type and affinity range combined specific prefiltering requirements (interatomic distances) and a COREPA classification node using no more than 2 discriminating parameters. The interaction types are becoming less distinct in the lowest activity range for each chemicals of each type; here, the modeling was performed within chemical classes (phenols, phthalates, etc.). The ultimate model was organized as a battery of local models associated to interaction type and mechanism.
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Affiliation(s)
- R Serafimova
- Laboratory of Mathematical Chemistry, Bourgas As. Zlatarov University, Bourgas, Bulgaria
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Serafimova R, Todorov M, Pavlov T, Kotov S, Jacob E, Aptula A, Mekenyan O. Identification of the structural requirements for mutagencitiy, by incorporating molecular flexibility and metabolic activation of chemicals. II. General Ames mutagenicity model. Chem Res Toxicol 2007; 20:662-76. [PMID: 17381132 DOI: 10.1021/tx6003369] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tissue metabolic simulator (TIMES) modeling approach is a hybrid expert system that couples a metabolic simulator together with structure toxicity rules, underpinned by structural alerts, to predict interaction of chemicals or their metabolites with target macromolecules. Some of the structural alerts representing the reactivity pattern-causing effect could interact directly with the target whereas others necessitated a combination with two- or three-dimensional quantitative structure-activity relationship models describing the firing of the alerts from the rest of the molecules. Recently, TIMES has been used to model bacterial mutagenicity [Mekenyan, O., Dimitrov, S., Serafimova, R., Thompson, E., Kotov, S., Dimitrova, N., and Walker, J. (2004) Identification of the structural requirements for mutagenicity by incorporating molecular flexibility and metabolic activation of chemicals I: TA100 model. Chem. Res. Toxicol. 17 (6), 753-766]. The original model was derived for a single tester strain, Salmonella typhimurium (TA100), using the Ames test by the National Toxicology Program (NTP). The model correctly identified 82% of the primary acting mutagens, 94% of the nonmutagens, and 77% of the metabolically activated chemicals in a training set. The identified high correlation between activities across different strains changed the initial strategic direction to look at the other strains in the next modeling developments. In this respect, the focus of the present work was to build a general mutagenicity model predicting mutagenicity with respect to any of the Ames tester strains. The use of all reactivity alerts in the model was justified by their interaction mechanisms with DNA, found in the literature. The alerts identified for the current model were analyzed by comparison with other established alerts derived from human experts. In the new model, the original NTP training set with 1341 structures was expanded by 1626 proprietary chemicals provided by BASF AG. Eventually, the training set consisted of 435 chemicals, which are mutagenic as parents, 397 chemicals that are mutagenic after S9 metabolic activation, and 2012 nonmutagenic chemicals. The general mutagenicity model was found to have 82% sensitivity, 89% specificity, and 88% concordance for training set chemicals. The model applicability domain was introduced accounting for similarity (structural, mechanistic, etc.) between predicted chemicals and training set chemicals for which the model performs correctly.
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Affiliation(s)
- R Serafimova
- Laboratory of Mathematical Chemistry, University Prof. As. Zlatarov, 8000 Bourgas, Bulgaria
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