Discrimination, Crypticity, and Incipient Taxa in Entamoeba

Persistent difficulties in resolving clear lineages in diverging populations of prokaryotes or unicellular eukaryotes (protistan polyphyletic groups) are challenging the classical species concept. Although multiple integrated approaches would render holistic taxonomies, most phylogenetic studies are still based on single-gene or morphological traits. Such methodologies conceal natural lineages, which are considered “cryptic.” The concept of species is considered artificial and inadequate to define natural populations. Social organisms display differential behaviors toward kin than to nonrelated individuals. In “social” microbes, kin discrimination has been used to help resolve crypticity. Aggregative behavior could be explored in a nonsocial protist to define phylogenetic varieties that are considered “cryptic.” Two Entamoeba invadens strains, IP-1 and VK-1:NS are considered close populations of the same “species.” This study demonstrates that IP-1 and VK-1:NS trophozoites aggregate only with alike members and discriminate members of different strains based on behavioral and chemical signals. Combined morphological, behavioral/chemical, and ecological studies could improve Archamoebae phylogenies and define cryptic varieties. Evolutionary processes in which selection acted continuously and cumulatively on ancestors of Entamoeba populations gave rise to chemical and behavioral signals that allowed individuals to discriminate nonpopulation members and, gradually, to the emergence of new lineages; alternative views that claim a “Designer” or “Creator” as responsible for protistan diversity are unfounded

The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata)

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ The file attached is the published version of the article

Surgical treatment of displaced intra-articular calcaneal fracture using a single small lateral approach

The objective of this study was to evaluate the outcome of semi-open reduction and minimal internal fixation through a single small lateral approach as a minimally invasive technique for treatment of displaced intra-articular calcaneal fractures. This prospective study was conducted on eighteen patients (16 men and 2 women). The average age was 37.7 (22–55). The most common cause of injury was a fall from height in fourteen patients. Patients were operated on within a mean time of 4.8 days of admission (1–11 days) and were followed up for an average period of 24.1 months (6–39 months). Patients were evaluated clinically using the Creighton-Nebraska Heath Foundation Assessment score of Crosby and Fitzgibbons (J Bone Joint Surg (Am) 72-A:852–859, 1990). The scoring system proposed by Knirk and Jupiter was used for radiological assessment of the posterior subtalar joint (Knirk and Jupiter in J Bone Joint Surg (Am) 68-A: 647–659, 1986). The skin incision healed in all cases without necrosis, infection, or sural nerve injury. All fractures healed after an average of 8 weeks (7–10 weeks), and patients returned to the routine daily activities after an average time of 4.3 months (3–7 months). In conclusion, semi-open reduction and minimal internal fixation through a small lateral approach is an effective treatment for carefully selected cases of displaced intra-articular calcaneal fractures

Phylogenomics of non-model ciliates based on transcriptomic analyses

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Leguminous green manure can drive the stabilisation of the increased soil organic carbon on dryland

Non-Peer ReviewedQuantifying field management on stabilised soil organic carbon (SOC) can be utilised to elucidate the management efficacy on mitigating climate change over the long-term. To achieve this goal, we measured the physico-chemically protected C in aggregates and their contribution to the SOC of the bulk soil to determine whether growing leguminous green manure (LGM) instead of summer fallow can drive the formation of the stable SOC. The field study was a split-plot design with 4 main treatments: growing Huai bean, soybean and mung bean as LGM while fallow as control. The sub-treatments included 4 synthetic N rates (0, 108, 135 and 162 kg ha-1) for the winter wheat. Huai bean significantly increased the mass ratio of the large macroaggregates and the mean weight diameter and geometric mean diameter in the 0-10 cm soil layer compared with the fallow. Huai bean and soybean significantly increased the content of the mineral-associ ated OC (MOC), while all the LGM treatments increased the content of the intra-microaggregate particulate OC (iPOC) by 12-24% in the 0-10 and 10-20 cm soil layers. The increased SOC content in the bulk soil for the LGM treatments compared to the fallow was mainly attributed to the increase in the protected C (iPOC+MOC), which accounted for 69-89% of the total increase, with the exception of 37% for mung bean in the 10-20 cm soil layer. The correlation analysis further suggests that only the increase in the protected C was positively linearly correlated with the SOC change. In conclusion, LGM instead of summer fallow can increase the SOC in the bulk soil mainly by increasing the protected C, which supports the concept that introducing the LGM can be an efficient alternative to mitigate climate change by sequestering the C in the soil for a prolonged period

An interactome-centered protein discovery approach reveals novel components involved in mitosome function and homeostasis in giardia lamblia

Protozoan parasites of the genus Giardia are highly prevalent globally, and infect a wide range of vertebrate hosts including humans, with proliferation and pathology restricted to the small intestine. This narrow ecological specialization entailed extensive structural and functional adaptations during host-parasite co-evolution. An example is the streamlined mitosomal proteome with iron-sulphur protein maturation as the only biochemical pathway clearly associated with this organelle. Here, we applied techniques in microscopy and protein biochemistry to investigate the mitosomal membrane proteome in association to mitosome homeostasis. Live cell imaging revealed a highly immobilized array of 30–40 physically distinct mitosome organelles in trophozoites. We provide direct evidence for the single giardial dynamin-related protein as a contributor to mitosomal morphogenesis and homeostasis. To overcome inherent limitations that have hitherto severely hampered the characterization of these unique organelles we applied a novel interaction-based proteome discovery strategy using forward and reverse protein co-immunoprecipitation. This allowed generation of organelle proteome data strictly in a protein-protein interaction context. We built an initial Tom40-centered outer membrane interactome by co-immunoprecipitation experiments, identifying small GTPases, factors with dual mitosome and endoplasmic reticulum (ER) distribution, as well as novel matrix proteins. Through iterative expansion of this protein-protein interaction network, we were able to i) significantly extend this interaction-based mitosomal proteome to include other membrane-associated proteins with possible roles in mitosome morphogenesis and connection to other subcellular compartments, and ii) identify novel matrix proteins which may shed light on mitosome-associated metabolic functions other than Fe-S cluster biogenesis. Functional analysis also revealed conceptual conservation of protein translocation despite the massive divergence and reduction of protein import machinery in Giardia mitosomes

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se

Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations