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12. Convergent somatic evolution commences in utero in a germline ribosomopathy

Author

Machado, Heather E., Øbro, Nina F., Williams, Nicholas, Tan, Shengjiang, Boukerrou, Ahmed Z., Davies, Megan, Belmonte, Miriam, Mitchell, Emily, Baxter, E. Joanna, Mende, Nicole, Clay, Anna, Ancliff, Philip, Köglmeier, Jutta, Killick, Sally B., Kulasekararaj, Austin, Meyer, Stefan, Laurenti, Elisa, Campbell, Peter J., Kent, David G., Nangalia, Jyoti, and Warren, Alan J.

Published
2023
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23. Morphology and molecular phylogeny of four epibiotic ciliates (Ciliophora, Peritrichia) from farmed red swamp crayfish Procambarus clarkii Girard, 1852, with notes on the geographic distributions of related taxa.

Author

Tong Wu, Yuan Li, Borong Lu, Danxu Tang, Shijing Zhang, Yan Liu, Ya Wang, Xiao Cao, Al-Farraj, Saleh A., Warren, Alan, Weibo Song, and Zhe Wang

Subjects
PROCAMBARUS clarkii, AQUATIC animals, MOLECULAR phylogeny, SWAMPS, EMERGING industries, CRAYFISH, CILIATA
Abstract

Aquaculture of red swamp crayfish Procambarus clarkii is an emerging farming industry in China. As shown recently, one of the most significant diseases affecting the red swamp crayfish is caused by overabundance of epibiotic peritrichs, a group of ciliated protists that are commonly found living as epibionts on aquatic animals. Nevertheless, few studies focusing on this issue have been performed. As part of a faunal study carried out in the Lake Weishan Wetland, China, four colonial sessilid peritrichs, namely Epicarchesium granulatum, Epistylis bimarginata, Epistylis semiciculus, and Zoothamnium procerius, attached to P. clarkii are documented. For each species, redescriptions and improved diagnoses are supplied. As a further aid to identification, 14 new rDNA sequences of these four and a closely related species were obtained. In addition, as an aid for future studies on epibiotic ciliates, we supply a list and information about recent integrative studies that document the geographic distributions of related taxa. [ABSTRACT FROM AUTHOR]

Published
2024
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28. Publisher Correction: Somatic genetic rescue of a germline ribosome assembly defect

Author

Tan, Shengjiang, Kermasson, Laëtitia, Hilcenko, Christine, Kargas, Vasileios, Traynor, David, Boukerrou, Ahmed Z., Escudero-Urquijo, Norberto, Faille, Alexandre, Bertrand, Alexis, Rossmann, Maxim, Goyenechea, Beatriz, Jin, Li, Moreil, Jonathan, Alibeu, Olivier, Beaupain, Blandine, Bôle-Feysot, Christine, Fumagalli, Stefano, Kaltenbach, Sophie, Martignoles, Jean-Alain, Masson, Cécile, Nitschké, Patrick, Parisot, Mélanie, Pouliet, Aurore, Radford-Weiss, Isabelle, Tores, Frédéric, de Villartay, Jean-Pierre, Zarhrate, Mohammed, Koh, Ai Ling, Phua, Kong Boo, Reversade, Bruno, Bond, Peter J., Bellanné-Chantelot, Christine, Callebaut, Isabelle, Delhommeau, François, Donadieu, Jean, Warren, Alan J., and Revy, Patrick

Published
2022
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32. A Machine Learning Algorithm for the Detection of Paroxysmal Nocturnal Haemoglobinuria (PNH) in UK Primary Care Electronic Health Records

Author

Worker, Amanda, primary, Mahon, Hadley, additional, Sams, Jack, additional, Boardman-Pretty, Freya, additional, Marchini, Elena, additional, Dubis, Rand, additional, Warren, Alan, additional, Varones, Liz, additional, Ollerenshaw, Daniel, additional, Grant, Calum, additional, Fish, Peter, additional, and Kelly, Richard J, additional

Published
2024
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37. Endemicity and climatic niche differentiation in three marine ciliated protists

Author

Williams, Richard Alexander John, Owens, Hannah L, Clamp, John, Peterson, A Townsend, Warren, Alan, Martín Cereceda, María Mercedes, Williams, Richard Alexander John, Owens, Hannah L, Clamp, John, Peterson, A Townsend, Warren, Alan, and Martín Cereceda, María Mercedes

Abstract

Primary occurrence data are fully and openly accessible via the Global Biodiversity Information Facility (GBIF; http://www.gbif.org/) and Ocean Biogeographic Information System (OBIS; http://www.iobis.org/). Environmental coverages were drawn from National Oceanic and Atmospheric Administration’s (NOAA) World Ocean Atlas (NOAA 1999), The biogeographic pattern of single-celled eukaryotes (protists), including ciliates, is poorly understood. Most marine species are believed to have a relatively high dispersal potential, such that both globally distributed and geographically isolated taxa exist. Primary occurrence data for three large, easily identified ciliate species, Parafavella gigantea, Schmidingerella serrata, and Zoothamnium pelagicum, and environmental data drawn from the National Oceanic and Atmospheric Administration’s World Ocean Atlas were used to estimate each species’ spatial and environmental distributions using Maxent v3.3.3k. The predictive power of the models was tested with a series of spatial stratification studies, which were evaluated using partial receiver operating characteristic (ROC) statistics. Differences between niches occupied by each taxon were evaluated using background similarity tests. All predictions showed significant ability to anticipate test points. The null hypotheses of niche similarity were rejected in all background similarity tests comparing the niches among the three species. This article provides the first quantitative assessment of environmental conditions associated with three species of ciliates and a first estimate of their spatial distributions in the North Atlantic, which can serve as a benchmark against which to document distributional shifts. These species follow consistent, predictable patterns related to climate and environmental biochemistry; the importance of climatic conditions as regards protist distributions is noteworthy considering the effects of global climate change., Depto. de Genética, Fisiología y Microbiología, Fac. de Ciencias Biológicas, TRUE, pub

Published
2024

39. Soil water content drives the spatiotemporal the distribution and community assembly of soil ciliates in the Nianchu River Basin, Qinghai-Tibet Plateau, China.

Author

Zhu, Shiying, Huang, Qian, Li, Tianshun, Li, Mingyan, Yang, Qing, Li, Xiaodong, Warren, Alan, and Pu, Bu

Subjects
SOIL moisture, WATERSHEDS, PLATEAUS, CILIATA, SOILS, STAINS & staining (Microscopy)
Abstract

Ciliated protozoa (ciliates) are an ecologically important group of microeukaryotes that play roles in the flow of energy and nutrients in aquatic and terrestrial ecosystems. The community distribution and diversity of soil ciliates in the Nianchu River Basin were investigated by sampling four major habitats, i.e., grassland, farmland, wetland and sea buckthorn forest during May, August and October 2020. Cultivation identification and enumeration of soil ciliates were performed by the non-submerged culture method, in vivo observations and protargol silver staining, and direct counting methods, respectively. A total of 199 species were identified representing, 89 genera, 67 families, 31 orders and 11 classes. Haptorida was the dominant group with 35 species, accounting for 17.59% of the total. The results showed that the α and β diversity indices of soil ciliate communities in the Nianchu River Basin varied significantly in spatial distribution, but not in temporal distribution. Mantel test showed that soil water content, total nitrogen and organic matter were significantly correlated with soil ciliates. Soil water content was the main environmental factor driving the spatial distribution of soil ciliates. Co-occurrence network analysis showed that soil ciliate species in the Nianchu River Basin depend on each other in the relationship of solidarity and cooperation or ecological complementarity. Thus maintaining or enhancing the diversity and stability of the community. Community assembly shows that randomness process was an important ecological process driving soil ciliate community construction in the Nianchu River Basin. [ABSTRACT FROM AUTHOR]

Published
2024
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40. Comparative genomics reveals the evolutionary history of the unicellular eukaryote class Litostomatea and its adaptive evolution based on biochemical metabolic capacity.

Author

Zhang, Ying, Fu, Yu, Vďačný, Peter, Liang, Fasheng, Dou, Huan, Warren, Alan, and Li, Lifang

Subjects
BIOLOGICAL evolution, STOP codons, MOLECULAR evolution, GENE families, UNICELLULAR organisms, CILIATA
Abstract

Ciliated protists are unicellular eukaryotic organisms characterized by their morphological diversity, ubiquitous distribution, and the important roles they play in a wide range of biological studies. The class Litostomatea is a morphologically diverse ciliate group that comprises hundreds of free-living and endosymbiotic species. Here, we sequenced 14 predatory litostomateans, i.e. 12 haptorians and two rhynchostomatians. A comparative analysis was performed with other published omics' data on litostomateans. Our first phylogenomic analysis of litostomateans showed the monophyly of the subclasses Trichostomatia and Rhynchostomatia, the non-monophyly of the subclass Haptoria, and the monophyly of all orders and families that were analysed. Evolutionary history analysis suggested that Litostomatea diverged during the Late Neoproterozoic, the family Chaeneidae was the earliest diverging haptorian lineage, and the Rhynchostomatia probably separated from the order Lacrymariida (subclass Haptoria) during the Early Palaeozoic. Stop codon usage analysis of 28 litostomateans showed that they use TAA as the biased stop codon and reassign the other two stop codons (TAG and TGA) to code for amino acids. In addition, the preferred codons in the 14 newly sequenced litostomateans are strongly biased towards A/U bases in the third position, very probably due to the comparatively low GC content. Genes encoding carbohydrate-active enzymes (CAZymes) are more diversified in the endosymbiotic Trichostomatia than in the free-living predatory Rhynchostomatia and Haptoria, suggesting that trichostomes have the strongest capability of carbohydrate utilization. Notably, we found that three free-living litostomateans (Didinium sp.1, Myriokaryon sp. and Apodileptus visscheri) exhibit substantial differences from other free-living ciliates in terms of their number of CAZymes. Considering the potency and versatility of CAZymes in the degradation and biotransformation of carbohydates, we propose that the multifarious CAZymes in these three ciliates could be a survival strategy for nutrient acquisition and niche adaptation. Finally, the functional annotation of significantly expanded gene families in these three ciliates revealed their vigorous potency in biochemical metabolism. These findings will facilitate wider omic-scale phylogenetic analyses of Litostomatea and deepen our understanding of this group from an evolutionary standpoint. [ABSTRACT FROM AUTHOR]

Published
2024
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