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Amoeboid protist systematics: A report on the "Systematics of amoeboid protists" symposium at the VIIIth ECOP/ISOP meeting in Rome, 2019
No full textAmoeboid protists are extremely abundant and diverse in natural systems where they often play outstanding ecological roles. They can be found in almost all major eukaryotic divisions, and genomic approaches are bringing major changes in our perception of their deep evolutionary relationships. At fine taxonomic levels, the generalization of barcoding is revealing a considerable and unsuspected specific diversity that can be appreciated with careful morphometric analyses based on light and electron microscopic observations. We provide examples on the difficulties and advances in amoeboid protists systematics in a selection of groups that were presented at the VIIIth ECOP/ISOP meeting in Rome, 2019. We conclude that, in all studied groups, important taxonomical rearrangements will certainly take place in the next few years, and systematics must be adapted to incorporate these changes. Notably, nomenclature should be flexible enough to integrate many new high level taxa, and a unified policy must be adopted to species description and to the establishment of types. (C) 2020 Elsevier GmbH. All rights reserved
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Novel Lineages in Cercozoa and Their Feeding Strategies
No full textThe term protist describes an informal grouping of unicellular eukaryotic organisms that do not form tissues. With a tremendous diversity in morphology and ecology, they represent the vast majority of eukaryotic heterogeneity of which only a small fraction is yet known. Ubiquitously dispersed in marine, freshwater and terrestrial habitats they occupy various ecological niches as e.g. primary producers, osmotrophs, bacterivores, fungivores, algivores, omnivores, predators or parasites of e.g. animals and plants. However, methodological drawbacks in culturing impeded research of protists. Research focused on the easily culturable taxa, especially bacterivores and algae, leading to a skewed image of protist diversity and many ‘unculturable’ protist taxa are still unknown to science.
Therefore we focused on protists with unusual feeding types (in particular bacterivorous sit-and-wait predators and eukaryvorous predators) in the phylum Cercozoa. The Cercozoa CAVALIER-SMITH 1998, were discovered to be closely related based on molecular analyses although being highly divergent in morphology and ecology. Molecular surveys revealed a high genetic diversity in the Cercozoa of which only a small fraction can yet be linked to morphological data. Based on culture material, cell morphology, feeding processes and life history stages of several cercozoan amoebae have been studied by us. This was achieved by using mainly light microscopy and time-lapse photography but also ultra structure data was obtained. Genetic markers, e.g. SSU rDNA and LSU rDNA were subjected to phylogenetic analyses to draw conclusions on cercozoan evolution.
Based on six isolates from German and Spanish soils a novel lineage of bacterivorous amoebae was described. Kraken carinae gen. nov. sp. nov. is an amoeba distinguished by a scale bearing cell body (usually <10 µm in diameter) and a network of filopodia (up to 0.5 mm in diameter). K. carinae is one of the few known sit-and-wait predators in the Cercozoa, preying on bacteria that get in contact with its large filopodia network. Unlike other cercozoan amoebae that usually use the filopodia to drag prey to their cell bodies for ingestion, K. carinae ingests bacteria directly at the point of contact and transports them through the filopodia to the cell body for digestion. SSU rDNA phylogeny showed an affinity to the order Cercomonadida in the class Sarcomonadea with only weak support, but a concatenated approach, by combining SSU rDNA and LSU rDNA sequences, confirmed the results with higher (though still moderate) support, in particular with the family Paracercomonadidae. However, Kraken carinae still remains incertae sedis as ultrastructure revealed the presence of scales, a morphological character predominantly known from the class Imbricatea, contradicting the phylogenetic results.
By combining literature research with phylogenetic examination focusing on Lecythium (HERTWIG et LESSER, 1874) and its family the Chlamydophryidae (DE SAEDELEER 1934) we were able to clarify the confusing taxonomy of genera like Plagiophrys, Lecythium, Rhizaspis and others. All of these amoebae bear a flexible organic theca, branching and anastomosing filopodia. However, they differ in cell shape and show species (or strain) specific feeding preferences. SSU rDNA phylogenies reflected the phenotypic differences between those genera but also revealed surprising results: The genera Lecythium (Novel Clade 4) and Rhizaspis (Tectofilosida) were polyphyletic and had to be separated, resulting in a secession of Fisculla gen. nov. (Tectofilosida) from Lecythium and Sacciforma gen. nov. (Cryomonadida) from Rhizaspis.
As these thecofilosean amoebae, similar to the predominantly known eukaryvores in the Cercozoa, the Vampyrellida, have been shown to be eukaryvorous, we further focused on eukaryvorous protists in terrestrial habitats, by investigating (a) their feeding preferences (b) their physiological requirements to consume eukaryotic prey and (c) their dispersal in terrestrial and freshwater systems. This was achieved by conducting thorough sampling, observing individuals in their unaltered sample (if possible) and performing experiments on feeding preference, chemical sensing, and enzyme production with several omnivorous or eukaryvorous Cercozoa. In laboratory experiments, we could show that the eukaryvorous protist Fisculla terrestris is able to sense and select its preferred prey and produce a battery of enzymes needed to digest cell wall compounds of eukaryotes, such as chitin. F. terrestris preferred fungal prey (in particular Saccharomyces cerevisiae) and only fed to a small extend on algae. To get more insight into the dispersal of eukaryvorous protists in terrestrial systems, we screened metatranscriptomes of different terrestrial habitats for the eukaryvorous Vampyrellida and Grossglockneriidae, showing high dispersal, since they were present in all screened habitats, with up to 3% of total reads.
The phenotypic, phylogenetic and ecologic data on the investigated cercozoan amoebae resulted in a comprehensive characterization of the Thecofilosea and the novel lineage Krakenidae. Based on intensive literature research and a critical evaluation of it, first steps for a phylogeny-based taxonomy of these cercozoan lineages were made. Finally, this thesis provides an evaluation of the hidden diversity of eukaryvorous Cercozoa in terrestrial and freshwater habitats
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Cell rupture in Arcellinida through the lens of evolution
No full textThe majority of predatory protists are size-limited. Arcellinida (Amoebozoa) exhibit the remarkable ability to prey upon larger organisms. Here, we examine the co-evolution of their robust shells and predatory behavior. Tracing back to the emergence of eukaryotes, we explore how early amoebozoan predators adapted their cytoskeletons to master phagocytosis. We speculate that the diversity of shell morphology as we see it in extant Arcellinida might be a direct result to their adaptation to prey on large organisms
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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