Genetic differentiation between Arctic and Antarctic monothalamous foraminiferans

Monothalamous (single-chambered) foraminifers are a major component of the benthic meiofauna in high latitude regions. Several morphologically similar species are common in the Arctic and Antarctic. However, it is uncertain whether these morphospecies are genetically identical, or whether their accurate identification is compromised by a lack of distinctive morphological features. To determine the relationship between Arctic and Antarctic species, we have compared SSU rDNA sequences of specimens belonging to four morphotaxa: Micrometula, Psammophaga, Gloiogullmia, and one morphospecies Hippocrepinella hirudinea from western Svalbard (Arctic) and McMurdo Sound (Antarctic). Wherever possible, we include in our analyses representatives of these taxa from the deep Arctic and Southern Oceans, as well as from Northern European fjords. We found that in all cases, the bipolar populations were clearly distinct genetically. As expected, Arctic specimens were usually more closely related to those from Northern Europe than to their Antarctic representatives. The deep-sea specimens from Weddell Sea branched as a sister to the McMurdo Sound population, while those from the Arctic Ocean clustered with ones from Norwegian fjords. Our study has revealed a high number of cryptic species within each of the examined genera, and demonstrates the unexplored potential of monothalamous foraminifers for use as a tool to evaluate the origin and biogeography of polar meiofaun

Immunogenicity of COVID ‐19 vaccines in patients with follicular lymphoma receiving frontline chemoimmunotherapy

Summary: Immune responses to primary COVID‐19 vaccination were investigated in 58 patients with follicular lymphoma (FL) as part of the PETReA trial of frontline therapy (EudraCT 2016–004010‐10). COVID‐19 vaccines (BNT162b2 or ChAdOx1) were administered before, during or after cytoreductive treatment comprising rituximab (depletes B cells) and either bendamustine (depletes CD4+ T cells) or cyclophosphamide‐based chemotherapy. Blood samples obtained after vaccine doses 1 and 2 (V1, V2) were analysed for antibodies and T cells reactive to the SARS‐CoV‐2 spike protein using the Abbott Architect and interferon‐gamma ELISpot assays respectively. Compared to 149 healthy controls, patients with FL exhibited lower antibody but preserved T‐cell responses. Within the FL cohort, multivariable analysis identified low pre‐treatment serum IgA levels and V2 administration during induction or maintenance treatment as independent determinants of lower antibody and higher T‐cell responses, and bendamustine and high/intermediate FLIPI‐2 score as additional determinants of a lower antibody response. Several clinical scenarios were identified where dichotomous immune responses were estimated with >95% confidence based on combinations of predictive variables. In conclusion, the immunogenicity of COVID‐19 vaccines in FL patients is influenced by multiple disease‐ and treatment‐related factors, among which B‐cell depletion showed differential effects on antibody and T‐cell responses

Serum HCoV-spike specific antibodies do not protect against subsequent SARS-CoV-2 infection in children and adolescents

SARS-CoV-2 infections in children are generally asymptomatic or mild and rarely progress to severe disease and hospitalization. Why this is so remains unclear. Here we explore the potential for protection due to pre-existing cross-reactive seasonal coronavirus antibodies and compare the rate of antibody decline for nucleocapsid and spike protein in serum and oral fluid against SARS-CoV-2 within the pediatric population. No differences in seasonal coronaviruses antibody concentrations were found at baseline between cases and controls, suggesting no protective effect from pre-existing immunity against seasonal coronaviruses. Antibodies against seasonal betacoronaviruses were boosted in response to SARS-CoV-2 infection. In serum, anti-nucleocapsid antibodies fell below the threshold of positivity more quickly than anti-spike protein antibodies. These findings add to our understanding of protection against infection with SARS-CoV-2 within the pediatric population, which is important when considering pediatric SARS-CoV-2 immunization policies

SARS-CoV-2-specific immune responses and clinical outcomes after COVID-19 vaccination in patients with immune-suppressive disease

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune responses and infection outcomes were evaluated in 2,686 patients with varying immune-suppressive disease states after administration of two Coronavirus Disease 2019 (COVID-19) vaccines. Overall, 255 of 2,204 (12%) patients failed to develop anti-spike antibodies, with an additional 600 of 2,204 (27%) patients generating low levels (<380 AU ml−1). Vaccine failure rates were highest in ANCA-associated vasculitis on rituximab (21/29, 72%), hemodialysis on immunosuppressive therapy (6/30, 20%) and solid organ transplant recipients (20/81, 25% and 141/458, 31%). SARS-CoV-2-specific T cell responses were detected in 513 of 580 (88%) patients, with lower T cell magnitude or proportion in hemodialysis, allogeneic hematopoietic stem cell transplantation and liver transplant recipients (versus healthy controls). Humoral responses against Omicron (BA.1) were reduced, although cross-reactive T cell responses were sustained in all participants for whom these data were available. BNT162b2 was associated with higher antibody but lower cellular responses compared to ChAdOx1 nCoV-19 vaccination. We report 474 SARS-CoV-2 infection episodes, including 48 individuals with hospitalization or death from COVID-19. Decreased magnitude of both the serological and the T cell response was associated with severe COVID-19. Overall, we identified clinical phenotypes that may benefit from targeted COVID-19 therapeutic strategies

The class III peroxidase multigenic family in rice and its evolution in land plants☆☆☆

Plant peroxidases (class III peroxidases, E.C. 1.11.1.7) are secreted glycoproteins known to be involved in the mechanism of cell elongation, in cell wall construction and differentiation, and in the defense against pathogens. They usually form large multigenic families in angiosperms. The recent completion of rice (Oryza sativa japonica c.v. Nipponbare) genome sequencing allowed drawing up the full inventory of the genes encoding class III peroxidases in this plant. We found 138 peroxidase genes distributed among the 12 rice chromosomes. In contrast to several other gene families studied so far, peroxidase genes are twice as numerous in rice as in Arabidopsis. This large number of genes results from various duplication events that were tentatively traced back using a phylogenetic tree based on the alignment of conserved amino acid sequences. We also searched for peroxidase encoding genes in the major phyla of plant kingdom. In addition to gymnosperms and angiosperms, sequences were found in liverworts, mosses and ferns, but not in unicellular green algae. Two rice and one Arabidopsis peroxidase genes appeared to be rather close to the only known sequence from the liverwort Marchantia polymorpha. The possible relationship of these peroxidases with the putative ancestor of peroxidase genes is discussed, as well as the connection between the development of the class III peroxidase multigenic family and the emergence of the first land plants. An extensive search was performed in rice genome in order to draw up the complete list of class III peroxidases present in this organism. Phylogenetic studies performed in rice and other plants identified a putative primitive peroxidase, which probably played a crucial role in apparition of land plants

Effects of 12 years operation of a sewage treatment plant on trace metal occurrence within a Mediterranean commercial sponge (Spongia officinalis, Demospongiae)

The present field study uses Spongia officinalis for assessing trace metals occurrence in time and space within Mediterranean rocky communities. Nine sites were selected in the Marseille area for studying spatial trends in 12 metal concentrations. Long term changes in 8 metal concentrations were assessed at sites that had been sampled before and 12 years after the opening of a treatment plant. Spongia officinalis highly concentrated all the trace metal surveyed excepted Hg and Cd. The overall contamination level registered provided a classification of the study sites which is congruent with that given by other studies on pollutant accumulation in neighbouring sandy-bottoms or benthic assemblages. Among the metals studied, Fe, Pb, Cr are those that best highlighted a pollution gradient. In the present study, only Cd concentration did not vary in space. Except for Ni, all pollutant concentrations clearly decreased between 1984 and 1999. This very impressive decrease in heavy metal concentrations within the Marseille area represents an indisputable evidence of the improvement of the seawater quality resulting from 12 years' operation of the Marseille sewage plant. Moreover, the significant decrease also recorded in the reference population at Port-Cros might reflect an overall improvement in the seawater quality of the NW Mediterranean

A Novel Polyubiquitin Structure in Cercozoa and Foraminifera: Evidence for a New Eukaryotic Supergroup

Ubiquitin is a 76 amino acid protein with a remarkable degree of evolutionary conservation. Ubiquitin plays an essential role in a large number of eukaryotic cellular processes by targeting proteins for proteasome-mediated degradation. Most ubiquitin genes are found as head-to-tail polymers whose products are posttranslationally processed to ubiquitin monomers. We have characterized polyubuiquitin genes from the photosynthetic amoeboflagellate Chlorarachnion sp. CCMP 621 (also known as Bigelowiella natans) and found that they deviate from the canonical polyubiquitin structure in having an amino acid insertion at the junction between each monomer, suggesting that polyubiquitin processing in this organism is unique among eukaryotes. The gene structure indicates that processing likely cleaves monomers at the amino terminus of the insertion. We examined the phylogenetic distribution of the insertion by sequencing polyubiquitin genes from several other eukaryotic groups and found it to be confined to Cercozoa (including Chlorarachnion, Lotharella, Cercomonas, and Euglypha) and Foraminifera (including Reticulomyxa and Haynesina). This character strongly suggests that Cercozoa and Foraminifera are close relatives and form a new “supergroup” of eukaryotes

Multigene evidence for close evolutionary relations between Gromia and Foraminifera

Gromia oviformis is a common marine rhizopod, possessing a large ovoid membraneous theca that resembles the tests of certain monothalamous (single-chambered) foraminifers. In fact, the genus Gromia was initially classified among the Foraminifera, but because of its non-granular, filose pseudopodia it was later included among filopodia-bearing protists (the Filosea). Recent molecular phylogenies suggested that Gromia branches among Cercozoa, a heterogeneous assemblage of mainly amoeboid protists, which show some affinities to Foraminifera. To test how closely related are Gromia and Foraminifera, we have analysed the sequences of actin, large subunit of the RNA polymerase II (RPB1) and small subunit (SSU) rRNA genes. We also analysed the structure of the polyubiquitin gene of G. oviformis. Our analyses show that Gromia’s actin is specifically related to one of the two actin genes families known in Foraminifera. In RPB1-based phylogenies, Gromia appears as the closest relative of Foraminifera, while in the SSU rRNA trees it branches as sister to Foraminifera and Haplosporidia. We identified also a single serine insertion in the polyubiquitin of Gromia, similar to that found in Foraminifera, Plasmodiophorida and some Cercozoa. Altogether, these findings support the hypothesis that the morphological resemblance between Gromia and Foraminifera may be due to a shared common ancestor. If further analyses of protein-coding genes including a more representative sampling of Cercozoa confirm this relationship, then the molecular study of G. oviformis will be of key importance for understanding the origin of Foraminifera

A Three-Dimensional Engineered Cardiac In Vitro Model: Controlled Alignment of Cardiomyocytes in 3D Microphysiological Systems

Cardiomyocyte alignment in myocardium tissue plays a significant role in the physiological, electrical, and mechanical functions of the myocardium. It remains, however, difficult to align cardiac cells in a 3D in vitro heart model. This paper proposes a simple method to align cells using microfabricated Polydimethylsiloxane (PDMS) grooves with large dimensions (of up to 350 µm in width), similar to the dimensions of trabeculae carneae, the smallest functional unit of the myocardium. Two cell groups were used in this work; first, H9c2 cells in combination with Nor10 cells for proof of concept, and second, neonatal cardiac cells to investigate the functionality of the 3D model. This model compared the patterned and nonpatterned 3D constructs, as well as the 2D cell cultures, with and without patterns. In addition to alignment, we assessed the functionality of our proposed 3D model by comparing beating rates between aligned and non-aligned structures. In order to assess the practicality of the model, the 3D aligned structures should be demonstrated to be detachable and alignable. This evaluation is crucial to the use of this 3D functional model in future studies related to drug screening, building blocks for tissue engineering, and as a heart-on-chip by integrating microfluidics

Genetic differentiation between Arctic and Antarctic monothalamous foraminiferans

Monothalamous (single-chambered) foraminifers are a major component of the benthic meiofauna in high latitude regions. Several morphologically similar species are common in the Arctic and Antarctic. However, it is uncertain whether these morphospecies are genetically identical, or whether their accurate identification is compromised by a lack of distinctive morphological features. To determine the relationship between Arctic and Antarctic species, we have compared SSU rDNA sequences of specimens belonging to four morphotaxa: Micrometula, Psammophaga, Gloiogullmia, and one morphospecies Hippocrepinella hirudinea from western Svalbard (Arctic) and McMurdo Sound (Antarctic). Wherever possible, we include in our analyses representatives of these taxa from the deep Arctic and Southern Oceans, as well as from Northern European fjords. We found that in all cases, the bipolar populations were clearly distinct genetically. As expected, Arctic specimens were usually more closely related to those from Northern Europe than to their Antarctic representatives. The deep-sea specimens from Weddell Sea branched as a sister to the McMurdo Sound population, while those from the Arctic Ocean clustered with ones from Norwegian fjords. Our study has revealed a high number of cryptic species within each of the examined genera, and demonstrates the unexplored potential of monothalamous foraminifers for use as a tool to evaluate the origin and biogeography of polar meiofauna