Publications

Single-chambered (monothalamous) foraminifera are poorly known compared to their multichambered relatives. In this first study of monothalamids from Greenland, we describe one new genus and two new species belonging to different clades from the Nuuk fjord system. Nujappikia idaliae Gooday & Holzmann gen. nov. sp. nov. (Clade Y) has a bottle-shaped test terminating in a single aperture located on a short neck. The flexible wall is basically organic but with a very fine agglutinated veneer. Bathyallogromia kalaallita Gooday & Holzmann sp. nov. (Clade C) has a broadly ovate test with an organic wall and a mound-like apertural structure. It is larger and genetically distinct from the two other Bathyallogromia species, both from the Southern Ocean. A survey of the morphological diversity of monothalamids in our samples revealed 49 morphospecies, of which 19, including the two new species, yielded DNA sequences. Five were assigned to the genera Bathysiphon, (Clade BM), Micrometula. (Clade BM), Psammophaga. (Clade E), Hippocrepinella (Clade D) and Crithionina (Clade J). The remaining twelve represented unknown taxa branching in clades A, C, F, and Y and one new clade. Our results add to growing evidence that monothalamids are common and diverse in fjords and other high-latitude settings.

In this paper we propose a new mathematical model for describing the complex interplay between skin cell populations with fibroblast growth factor and bone morphogenetic protein, occurring within deformable porous media describing feather primordia patterning. Tissue growth, in turn, modifies the transport of morphogens (described by reaction-diffusion equations) through diverse mechanisms such as advection from the solid velocity generated by mechanical stress, and mass supply. By performing an asymptotic linear stability analysis on the coupled poromechanical-chemotaxis system (assuming rheological properties of the skin cell aggregates that reside in the regime of infinitesimal strains and where the porous structure is fully saturated with interstitial fluid and encoding the coupling mechanisms through active stress) we obtain the conditions on the parameters—especially those encoding coupling mechanisms—under which the system will give rise to spatially heterogeneous solutions. We also extend the mechanical model to the case of incompressible poro-hyperelasticity and include the mechanisms of anisotropic solid growth and feedback by means of standard Lee decompositions of the tensor gradient of deformation. Because the model in question involves the coupling of several nonlinear PDEs, we cannot straightforwardly obtain closed-form solutions. We therefore design a suitable numerical method that employs backward Euler time discretisation, linearisation of the semidiscrete problem through Newton–Raphson’s method, a seven-field finite element formulation for the spatial discretisation, and we also advocate the construction and efficient implementation of tailored robust solvers. We present a few illustrative computational examples in 2D and 3D, briefly discussing different spatio-temporal patterns of growth factors as well as the associated solid response scenario depending on the specific poromechanical regime. Our findings confirm the theoretically predicted behaviour of spatio-temporal patterns, and the produced results reveal a qualitative agreement with respect to the expected experimental behaviour. We stress that the present study provides insight on several biomechanical properties of primordia patterning.

In biomedical research, population differences are of central interest. Variations in the frequency and severity of diseases and in treatment effects among human subpopulation groups are common in many medical conditions. Unfortunately, the practices in terms of subpopulation labeling do not exhibit the level of rigor one would expect in biomedical research, especially when studying multifactorial diseases such as cancer or atherosclerosis. The reporting of population differences in clinical research is characterized by large disparities in practices, and fraught with methodological issues and inconsistencies. The actual designations such as "Black" or "Asian" refer to broad and heterogeneous groups, with a great discrepancy among countries. Moreover, the use of obsolete concepts such as "Caucasian" is unfortunate and imprecise. The use of adequate labeling to reflect the scientific hypothesis needs to be promoted. Furthermore, the use of "race/ethnicity" as a unique cause of human heterogeneity may distract from investigating other factors related to a medical condition, particularly if this label is employed as a proxy for cultural habits, diet, or environmental exposure. In addition, the wide range of opinions among researchers does not facilitate the attempts made for resolving this heterogeneity in labeling. "Race", "ethnicity", "ancestry", "geographical origin", and other similar concepts are saturated with meanings. Even if the feasibility of a global consensus on labeling seems difficult, geneticists, sociologists, anthropologists, and ethicists should help develop policies and practices for the biomedical field. This article is protected by copyright. All rights reserved.

The genus Operculina, a large symbiont-bearing benthic foraminifer, is characterized by high morphological variability showing thick involute to intermediate semi-involute to flat evolute tests. Different morphotypes are either considered as ecophenotypes or distinct species. In order to test the hypothesis of ecophenotypes versus different species, a single cell high throughput sequencing approach was applied to assess the interspecific diversity of Operculina. This results in two groups of ribotypes, one corresponding to Operculina ammonoides/Operculina discoidalis, the other containing Operculina complanata/Operculina elegans. These groups can also be separated morphologically. Therefore, O. complanata and O. elegans represent a single species and the latter can be regarded as a junior synonym of O. complanata. Operculina ammonoides and O. discoidalis also form a single species, which makes the latter a junior synonym of O. ammonoides. Because generic differences in Operculina species are manifested in morphology and molecular genetics, the genus Neoassilina with the designated species Neoassilina ammonoides is installed. Additional analysis of ribosomal SSU rDNA data of eight recent nummulitid genera confirms the obtained high troughput sequencing results and further shows that Palaeonummulites venosus builds a clade with O. complanata that branches at the base of other Nummulitidae containing Planostegina, Planoperculina, Cycloclypeus, Heterostegina, Operculinella and Neoassilina.

Collective motions of epithelial cells are essential for morphogenesis. Tissues elongate, contract, flow, and oscillate, thus sculpting embryos. These tissue level dynamics are known, but the physical mechanisms at the cellular level are unclear. Here, we demonstrate that a single epithelial monolayer of MDCK cells can exhibit two types of local tissue kinematics, pulsations and long range coherent flows, characterized by using quantitative live imaging. We report that these motions can be controlled with internal and external cues such as specific inhibitors and substrate friction modulation. We demonstrate the associated mechanisms with a unified vertex model. When cell velocity alignment and random diffusion of cell polarization are comparable, a pulsatile flow emerges whereas tissue undergoes long-range flows when velocity alignment dominates which is consistent with cytoskeletal dynamics measurements. We propose that environmental friction, acto-myosin distributions, and cell polarization kinetics are important in regulating dynamics of tissue morphogenesis.

Coelacanths form a clade of sarcopterygian fish represented today by a single genus, Latimeria. The fossil record of the group, which dates back to the Early Devonian, is sparse. In Switzerland, only Triassic sites in the east and southeast of the country have yielded fossils of coelacanths. Here, we describe and study the very first coelacanth of the Jurassic period (Toarcian stage) from Switzerland. The unique specimen, represented by a sub-complete individual, possesses morphological characteristics allowing assignment to the genus Libys (e.g., sensory canals opening through a large groove crossed by pillars), a marine coelacanth previously known only in the Late Jurassic of Germany. Morphological characters are different enough from the type species, Libys polypterus, to erect a new species of Libys named Libys callolepis sp. nov. The presence of Libys callolepis sp. nov. in Lower Jurassic beds extends the stratigraphic range of the genus Libys by about 34 million years, but without increasing considerably its geographic distribution. Belonging to the modern family Latimeriidae, the occurrence of Libys callolepis sp. nov. heralds a long period, up to the present day, of coelacanth genera with very long stratigraphic range and reduced morphological disparity, which have earned them the nickname of 'living fossils'.

El nombre de la especie de paseriforme Aphrastura subantarctica, propuesto por Rozzi et al. (2022), no está disponible, dado que la publicación donde el mismo fue propuesto no cumplió con todos los requisitos del Código Internacional de Nomenclatura Zoológica. En esta nota establecemos la disponibilidad del nombre de la especie Aphrastura subantarctica, cumpliendo esos requisitos.

Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in most marine environments. Molecular methods such as metabarcoding have revealed a high, yet undescribed diversity of Foraminifera. However, so far only one molecular marker, the 18S ribosomal RNA, was available for metabarcoding studies on Foraminifera. Primers that allow amplification of foraminiferal mitochondrial cytochrome oxidase I (COI) and identification of Foraminifera species were recently published. Here we test the performance of these primers for the amplification of whole foraminiferal communities, and compare their performance to that of the highly degenerate LerayXT primers, which amplify the same COI region in a wide range of eukaryotes. We applied metabarcoding to 48 samples taken along three transects spanning a North Sea beach in the Netherlands from dunes to the low tide level, and analysed both sediment samples and meiofauna samples, which contained taxa between 42 µm and 1 mm in body size obtained by decantation from sand samples. We used single-cell metabarcoding (Girard et al., 2022) to generate a COI reference library containing 32 species of Foraminifera, and used this to taxonomically annotate our community metabarcoding data. Our analyses show that the highly degenerate LerayXT primers do not amplify Foraminifera, while the Foraminifera primers are highly Foraminifera- specific, with about 90% of reads assigned to Foraminifera and amplifying taxa from all major groups, i.e., monothalamids, Globothalamea, and Tubothalamea. We identified 176 Foraminifera ASVs and found a change in Foraminifera community composition along the beach transects from high tide to low tide level, and a dominance of single-chambered monothalamid Foraminifera. Our results highlight that COI metabarcoding can be a powerful tool for assessing Foraminiferal communities.

Foraminifera, classified in the supergroup Rhizaria, are a common and highly diverse group of mainly marine protists. Despite their evolutionary and ecological importance, only limited genomic data (one partial genome and nine transcriptomic datasets) have been published for this group. Foraminiferal molecular phylogeny is largely based on 18S rRNA gene sequence analysis. However, due to highly variable evolutionary rates of substitution in ribosomal genes plus the existence of intragenomic variation at this locus, the relationships between and within foraminiferal classes remain uncertain. We analyze transcriptomic data from 28 species, adding 19 new species to the previously published dataset, including members of the strongly under-represented class Monothalamea. A phylogenomic reconstruction of Rhizaria, rooted with alveolates and stramenopiles, based on 199 genes and 68 species supports the monophyly of Foraminifera and their sister relationship to Polycystinea. The phylogenomic tree of Foraminifera is very similar to the 18S rRNA tree, with the paraphyletic single-chambered monothalamids giving rise to the multi-chambered Tubothalamea and Globothalamea. Within the Monothalamea, our analyses confirm the monophyly of the giant, deep-sea xenophyophores that branch within clade C and indicate the basal position of monothalamous clades D and E. The multi-chambered Globothalamea are monophyletic and comprise the paraphyletic Textulariida and monophyletic Rotaliida. Our phylogenomic analyses support major evolutionary trends of Foraminifera revealed by ribosomal phylogenies and reinforce their current higher-level classification.

We derive a fully covariant theory of the hydrodynamics of nematic and polar active surfaces, subjected to internal and external forces and torques. We study the symmetries of polar and nematic surfaces and find that in addition to five different types of in-plane isotropic surfaces, polar and nematic surfaces can be classified into five polar, two pseudopolar, five nematic and two pseudonematic types of surfaces. We give examples of physical realisations of the different types of surfaces we have identified. We obtain expressions for the equilibrium tensions, moments, and external forces and torques acting on a passive polar or nematic surface. We calculate the entropy production rate using the framework of thermodynamics close to equilibrium and find constitutive equations for polar and nematic active surfaces with different symmetries. We study the instabilities of a confined flat planar-chiral polar active layer and of a confined deformable polar active surface with broken up-down symmetry.