El empleo del vocablo phantasma en las fuentes literarias latinas: de los primeros registros a los autores cristianos tardorromanos

Ghosts are the cultural product of a series of beliefs that stem from the existence of a dissociated numen that inhabits the human body. It is this separation that makes possible to conceive the autonomous presence of the spiritual entity. This ancestral type of story has been reproduced since the dawn of humanity, although this work seeks to elucidate what the connotations of use of a Greek term are, that passes into Latin and that undergoes an evolution through the filter of Christianity. Through a study of a historical-philological nature with a comparative perspective, this article aims to show the differences in use, paying special attention to the patristic texts of Tertullian and the allegorical and Christian poetry of Prudentius. Los fantasmas son el producto cultural de una serie de creencias que parten de la existencia de un numen disociado que habita dentro del cuerpo humano. Es esta separación la que permite concebir la presencia autónoma de la entidad espiritual. Este tipo ancestral de relato viene reproduciéndose desde los albores de la humanidad, si bien en este trabajo se persigue dilucidar cuáles son las connotaciones de empleo de un término griego que pasa al latín y que experimenta una evolución a través del filtro del cristianismo. Mediante un estudio de carácter histórico-filológico y con una perspectiva comparativa, el presente artículo se propone manifestar las diferencias de uso, prestando especial atención a los textos patrísticos de Tertuliano y a la poesía alegórica y cristiana de Prudencio.

Carbon dioxide levels and ventilation in Acromyrmex nests: significance and evolution of architectural innovations in leaf-cutting ants

Leaf-cutting ant colonies largely differ in size, yet all consume O 2 and produce CO 2 in large amounts because of their underground fungus gardens. We have shown that in the Acromyrmex genus, three basic nest morphologies occur, and investigated the effects of architectural innovations on nest ventilation. We recognized (i) serial nests, similar to the ancestral type of the sister genus Trachymyrmex , with chambers excavated along a vertical tunnel connecting to the outside via a single opening, (ii) shallow nests, with one/few chambers extending shallowly with multiple connections to the outside, and (iii) thatched nests, with an above-ground fungus garden covered with plant material. Ventilation in shallow and thatched nests, but not in serial nests, occurred via wind-induced flows and thermal convection. CO 2 concentrations were below the values known to affect the respiration of the symbiotic fungus, indicating that shallow and thatched nests are not constrained by harmful CO 2 levels. Serial nests may be constrained depending on the soil CO 2 levels. We suggest that in Acromyrmex , selective pressures acting on temperature and humidity control led to nesting habits closer to or above the soil surface and to the evolution of architectural innovations that improved gas exchanges.

Distribution of bacteriocin genes in the lineages of Lactiplantibacillus plantarum

Lactiplantibacillus plantarum, previously named “Lactobacillus plantarum,” is found in a wide variety of environments exhibiting a high level of intraspecies genetic diversity. To investigate the strain diversity, we performed comparative genomic analyses of the 54 complete genome sequences. The results revealed that L. plantarum subsp. plantarum was split into three lineages, A, B and C. Of the genes beneficial for probiotic activity, only those associated with the biosynthesis of plantaricin (Pln), an L. plantarum-specific bacteriocin, were found to be significantly different among the lineages. The genes related to the biosynthesis of plnE/F were conserved throughout the three lineages, whereas the outgroups did not possess any Pln-producing genes. In lineage C, the deepest and ancestral type branch, plnE/F genes, were well conserved. In lineage B, loss of gene function was observed due to mobile elements in the pln loci. In lineage A, most strains were predicted to produce more than one type of Pln by possessing diverse Pln-encoding genes. These results showed the presence of functional diversity arising from the trifurcating evolution in L. plantarum subsp. plantarum and demonstrated that Pln is an indicator for differentiating the three lineages.

First person – Shigetaka Nishiguchi

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. Shigetaka Nishiguchi is first author on ‘ Structural variability and dynamics in the ectodomain of an ancestral-type classical cadherin revealed by AFM imaging’, published in JCS. Shigetaka conducted the research described in this article while an assistant manager at Olympus Corporation and a graduate student in Hiroki Oda's lab at the JT Biohistory Research Hall and Osaka University, Osaka, Japan. He is now a postdoc in the lab of Takayuki Uchihashi at the Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan, investigating cadherin using atomic force microscopy.

The diversity of the Polytrichopsida—a review

The class Polytrichopsida are a phylogenetically isolated moss lineage of around 200 species. The nematodontous peristome found in most species has a fundamentally different structure from the arthrodontous peristome of the Bryopsida and may be independently evolved from an ancestral type of spore dehiscence apparatus. Within the class generic circumscriptions and relationships are now fairly confidently resolved and more or less congruent with the most developed pre-molecular taxonomy. Drawing on previously published datasets, we conducted a phylogenetic analysis of a novel matrix of terminals representing diversity across the Polytrichopsida. The class comprises 17 extant genera and two known only from fossils. Most of these are numerically small, the most notable exception being Pogonatum with over 50 species. Considering current phylogenetic hypotheses in the light of morphology and global distributions, Alophosia, Bartramiopsis and Lyellia, the earliest diverging lineages according to recent phylogenetic analyses, appear to be relicts, with scattered and disjunct distributions. All of these genera lack peristomes, while all later originating lineages have nematodontous peristomes developed from bundles of “u-shaped” whole cells. The genus Dawsonia, sister to all other peristomate taxa, differs in its unique peristome composed of long, bristle-like teeth arranged in concentric layers. Many members of some traditional genera found to be polyphyletic in recent studies are part of a southern hemisphere grade and only distantly related to the superficially similar northern hemisphere species with which they were historically classified. A large apical clade including eight genera accounts for the majority of the diversity, these being most speciose in northern temperate regions or the Asian tropics. Many of the Polytrichopsida are relatively large plants with well-developed vasculature and a “pseudo-mesophyll” capable of supporting relatively high rates of photosynthesis in moist, well-illuminated environments. With ten described species, Cenozoic fossils of Polytrichopsida are fairly numerous compared with other mosses. Records of fossils from older sediments have been rare, but recently several well-preserved fossils of Polytrichopsida have been found, most of which still await detailed description.

Structural variability and dynamics in the ectodomain of an ancestral-type classical cadherin revealed by AFM imaging

Type III cadherin represents the ancestral form of classical cadherin in bilaterian metazoans. Drosophila possesses type III and type IVa cadherins, known as DN- and DE-cadherins, respectively. Mature DN- and DE-cadherins have 15 and 7 extracellular cadherin domain (EC) repeats, respectively, with DN-cadherin EC6–11 homologous to DE-cadherin EC1–6. These EC repeats contain predicted complete or partial Ca2+-free inter-EC linkers that potentially contribute to adhesion. Comparative structure-function studies of DN- and DE-cadherins may help us understand the ancestral and derived states of classical cadherin-mediated adhesion mechanisms. Here, using bead aggregation assays, we found that DN-cadherin EC1–11 and DE-cadherin EC1–6 exhibit Ca2+-dependent adhesive properties. Using high-speed atomic force microscopy (HS-AFM) imaging in solution, we showed that both DN- and DE-cadherin ectodomains share a common morphological framework consisting of a strand-like and a globule-like portion. Furthermore, the DN-cadherin EC repeats were highly variable, flexible in morphology, and with at least three bendable sites, one of which is located in EC6–11 and can act as a flexible hinge. Our findings provide insights into diversification of classical cadherin-mediated adhesion mechanisms. (180 words or less)

Respiratory Heme A-Containing Oxidases Originated in the Ancestors of Iron-Oxidizing Bacteria

Respiration is a major trait shaping the biology of many environments. Cytochrome oxidase containing heme A (COX) is a common terminal oxidase in aerobic bacteria and is the only one in mammalian mitochondria. The synthesis of heme A is catalyzed by heme A synthase (CtaA/Cox15), an enzyme that most likely coevolved with COX. The evolutionary origin of COX in bacteria has remained unknown. Using extensive sequence and phylogenetic analysis, we show that the ancestral type of heme A synthases is present in iron-oxidizing Proteobacteria such as Acidithiobacillus spp. These bacteria also contain a deep branching form of the major COX subunit (COX1) and an ancestral variant of CtaG, a protein that is specifically required for COX biogenesis. Our work thus suggests that the ancestors of extant iron-oxidizers were the first to evolve COX. Consistent with this conclusion, acidophilic iron-oxidizing prokaryotes lived on emerged land around the time for which there is the earliest geochemical evidence of aerobic respiration on earth. Hence, ecological niches of iron oxidation have apparently promoted the evolution of aerobic respiration.

Distinct mutations and lineages of SARS-CoV-2 virus in the early phase of COVID-19 pandemic and subsequent global expansion

A novel coronavirus, SARS-CoV-2, has caused over 85 million cases and over 1.8 million deaths worldwide since it occurred twelve months ago in Wuhan, China. Here we first analyzed 4,013 full-length SARS-CoV-2 genomes from different continents over a 14-week timespan since the outbreak in Wuhan. 2,954 unique nucleotide substitutions were identified with 31 of the 4,013 genomes remaining as ancestral type, and 952 (32.2%) mutations recurred in more than one genome. A viral genotype from the Seafood Market in Wuhan featured with two concurrent mutations was the dominant genotype (80.9%) of the pandemic. We also identified unique genotypic compositions from different geographic locations, and time-series viral genotypic dynamics in the early phase that reveal transmission routes and subsequent expansion. In the end, as the pandemic has been unfolding for more than one year, we also used the same approach to analyze 261,350 full-length SARS-CoV-2 genomes from the world since the outbreak in Wuhan (i.e. all the available viral genomes in the GISAID database as of 25 December 2020) in order to recapitulate our findings in a real-time fashion. Our study indicates the viral genotypes can be utilized as molecular barcodes in combination with epidemiologic data to monitor the spreading routes of the pandemic and evaluate the effectiveness of control measures.

Phylogenetic network analysis of SARS-CoV-2 genomes

In a phylogenetic network analysis of 160 complete human severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) genomes, we find three central variants distinguished by amino acid changes, which we have named A, B, and C, with A being the ancestral type according to the bat outgroup coronavirus. The A and C types are found in significant proportions outside East Asia, that is, in Europeans and Americans. In contrast, the B type is the most common type in East Asia, and its ancestral genome appears not to have spread outside East Asia without first mutating into derived B types, pointing to founder effects or immunological or environmental resistance against this type outside Asia. The network faithfully traces routes of infections for documented coronavirus disease 2019 (COVID-19) cases, indicating that phylogenetic networks can likewise be successfully used to help trace undocumented COVID-19 infection sources, which can then be quarantined to prevent recurrent spread of the disease worldwide.