Challenging the term symbiosis in plant-microbe associations to create an understanding across sciences.

Scientific progress relies on clear and consistent definitions for effective communication and collaboration. The term "symbiosis" in the context of plant-microbe associations suffers from diverse interpretations, leading to ambiguity in classification of these associations. This review elaborates on the issue, proposing an inclusive definition as well as a keyword.

Identification of the novel FOXP3-dependent Treg cell transcription factor MEOX1 by high-dimensional analysis of human CD4+ T cells.

CD4+ T cells play a central role in the adaptive immune response through their capacity to activate, support and control other immune cells. Although these cells have become the focus of intense research, a comprehensive understanding of the underlying regulatory networks that orchestrate CD4+ T cell function and activation is still incomplete. Here, we analyzed a large transcriptomic dataset consisting of 48 different human CD4+ T cell conditions. By performing reverse network engineering, we identified six common denominators of CD4+ T cell functionality (CREB1, E2F3, AHR, STAT1, NFAT5 and NFATC3). Moreover, we also analyzed condition-specific genes which led us to the identification of the transcription factor MEOX1 in Treg cells. Expression of MEOX1 was comparable to FOXP3 in Treg cells and can be upregulated by IL-2. Epigenetic analyses revealed a permissive epigenetic landscape for MEOX1 solely in Treg cells. Knockdown of MEOX1 in Treg cells revealed a profound impact on downstream gene expression programs and Treg cell suppressive capacity. These findings in the context of CD4+ T cells contribute to a better understanding of the transcriptional networks and biological mechanisms controlling CD4+ T cell functionality, which opens new avenues for future therapeutic strategies.

What can hornworts teach us?

The hornworts are a small group of land plants, consisting of only 11 families and approximately 220 species. Despite their small size as a group, their phylogenetic position and unique biology are of great importance. Hornworts, together with mosses and liverworts, form the monophyletic group of bryophytes that is sister to all other land plants (Tracheophytes). It is only recently that hornworts became amenable to experimental investigation with the establishment of Anthoceros agrestis as a model system. In this perspective, we summarize the recent advances in the development of A. agrestis as an experimental system and compare it with other plant model systems. We also discuss how A. agrestis can help to further research in comparative developmental studies across land plants and to solve key questions of plant biology associated with the colonization of the terrestrial environment. Finally, we explore the significance of A. agrestis in crop improvement and synthetic biology applications in general.

Step-by-step protocol for the isolation and transient transformation of hornwort protoplasts.

Premise: A detailed protocol for the protoplast transformation of hornwort tissue is not yet available, limiting molecular biological investigations of these plants and comparative analyses with other bryophytes, which display a gametophyte-dominant life cycle and are critical to understanding the evolution of key land plant traits. Methods and Results: We describe a detailed protocol to isolate and transiently transform protoplasts of the model hornwort Anthoceros agrestis. The digestion of liquid cultures with Driselase yields a high number of viable protoplasts suitable for polyethylene glycol (PEG)-mediated transformation. We also report early signs of protoplast regeneration, such as chloroplast division and cell wall reconstitution. Conclusions: This protocol represents a straightforward method for isolating and transforming A. agrestis protoplasts that is less laborious than previously described approaches. In combination with the recently developed stable genome transformation technique, this work further expands the prospects of functional studies in this model hornwort.

Transcriptional Landscapes of Divergent Sporophyte Development in Two Mosses, Physcomitrium (Physcomitrella) patens and Funaria hygrometrica.

Understanding the molecular basis of morphological shifts is a fundamental question of evolutionary biology. New morphologies may arise through the birth/death of genes (gene gain/loss) or by reutilizing existing gene sets. Yet, the relative contribution of these two processes to radical morphological shifts is still poorly understood. Here, we use the model system of two mosses, Funaria hygrometrica and Physcomitrium (Physcomitrella) patens, to investigate the molecular mechanisms underlying contrasting sporophyte architectures. We used comparative analysis of time-series expression data for four stages of sporophyte development in both species to address this question in detail. We found that large-scale differences in sporophytic architecture are mainly governed by orthologous (i.e., shared) genes frequently experiencing temporal gene expression shifts between the two species. While the absolute number of species-specific genes expressed during sporophyte development is somewhat smaller, we observed a significant increase of their proportion in preferentially sporophyte expressed genes, suggesting a fundamental role in the sporophyte phase. However, further functional studies are necessary to determine their contribution to diverging sporophyte morphologies. Our results add to the growing set of studies suggesting that radical changes in morphology may rely on the heterochronic expression of conserved regulators.

Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts.

Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.

A pseudomolecule-scale genome assembly of the liverwort Marchantia polymorpha.

Marchantia polymorpha has recently become a prime model for cellular, evo-devo, synthetic biological, and evolutionary investigations. We present a pseudomolecule-scale assembly of the M. polymorpha genome, making comparative genome structure analysis and classical genetic mapping approaches feasible. We anchored 88% of the M. polymorpha draft genome to a high-density linkage map resulting in eight pseudomolecules. We found that the overall genome structure of M. polymorpha is in some respects different from that of the model moss Physcomitrella patens. Specifically, genome collinearity between the two bryophyte genomes and vascular plants is limited, suggesting extensive rearrangements since divergence. Furthermore, recombination rates are greatest in the middle of the chromosome arms in M. polymorpha like in most vascular plant genomes, which is in contrast with P. patens where recombination rates are evenly distributed along the chromosomes. Nevertheless, some other properties of the genome are shared with P. patens. As in P. patens, DNA methylation in M. polymorpha is spread evenly along the chromosomes, which is in stark contrast with the angiosperm model Arabidopsis thaliana, where DNA methylation is strongly enriched at the centromeres. Nevertheless, DNA methylation and recombination rate are anticorrelated in all three species. Finally, M. polymorpha and P. patens centromeres are of similar structure and marked by high abundance of retroelements unlike in vascular plants. Taken together, the highly contiguous genome assembly we present opens unexplored avenues for M. polymorpha research by linking the physical and genetic maps, making novel genomic and genetic analyses, including map-based cloning, feasible.

Towards a plant model for enigmatic U-to-C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis.

Hornworts are crucial to understand the phylogeny of early land plants. The emergence of 'reverse' U-to-C RNA editing accompanying the widespread C-to-U RNA editing in plant chloroplasts and mitochondria may be a molecular synapomorphy of a hornwort-tracheophyte clade. C-to-U RNA editing is well understood after identification of many editing factors in models like Arabidopsis thaliana and Physcomitrella patens, but there is no plant model yet to investigate U-to-C RNA editing. The hornwort Anthoceros agrestis is now emerging as such a model system. We report on the assembly and analyses of the A. agrestis chloroplast and mitochondrial genomes, their transcriptomes and editomes, and a large nuclear gene family encoding pentatricopeptide repeat (PPR) proteins likely acting as RNA editing factors. Both organelles in A. agrestis feature high amounts of RNA editing, with altogether > 1100 sites of C-to-U and 1300 sites of U-to-C editing. The nuclear genome reveals > 1400 genes for PPR proteins with variable carboxyterminal DYW domains. We observe significant variants of the 'classic' DYW domain, in the meantime confirmed as the cytidine deaminase for C-to-U editing, and discuss the first attractive candidates for reverse editing factors given their excellent matches to U-to-C editing targets according to the PPR-RNA binding code.

Augmentation index and pulse wave velocity in normotensive and pre-eclamptic pregnancies.

OBJECTIVE: Hypertensive disorders during pregnancy remain a major health burden. Normal pregnancy is associated with systemic cardiovascular adaptation. The augmentation index and pulse wave velocity measures may serve as surrogate markers of cardiovascular pathology, including pre-eclampsia. We evaluated these parameters during and after normotensive and pre-eclamptic pregnancies. DESIGN: Longitudinal cohort trial involving a case-control analysis of healthy women and women with pre-eclampsia. SETTING: University hospital. POPULATION: Fifty-three healthy pregnant women between 11(+6) and 13(+6) gestational weeks, as well as 21 patients with pre-eclampsia. METHODS: The augmentation index and pulse wave velocity were measured seven times during pregnancy and postpartum. MAIN OUTCOME MEASURES: Changes in augmentation index and pulse wave velocity during and after healthy pregnancies were measured. The influence of early-onset and late-onset pre-eclampsia on these measurements both during and after pregnancy was evaluated. RESULTS: The normotensive pregnancies exhibited a significant decrease in the augmentation index from the first trimester to the end of the second trimester; however, the normotensive pregnancies showed an increase in the augmentation index during the third trimester as term approached. The patients with early-onset and late-onset pre-eclampsia displayed a significantly elevated augmentation index during pregnancy. The postpartum augmentation index and pulse wave velocity were significantly elevated in the early-onset pre-eclampsia group. CONCLUSION: After pregnancy, early-onset and late-onset pre-eclamptic patients exhibit differences in vascular function. This result indicates the presence of a higher cardiovascular risk in patients after early-onset pre-eclampsia.

NT-proBNP is increased in healthy pregnancies compared to non-pregnant controls.

Serum concentrations of the amino-terminal pro-B-type natriuretic peptide (NT-proBNP) may be used to monitor cardiac function during pregnancy but normal values are not established for this purpose. Therefore, we investigated NT-proBNP in normotensive healthy pregnancies compared to a non-pregnant control group. Serum NT-proBNP was measured in 94 normotensive, healthy pregnant women (32+/-6 years) every five weeks beginning from 12th gestational week (GW) in a longitudinal study and compared to a non-pregnant control group of 521 women (32+/-7 years). Pooled median serum NT-proBNP levels (25th; 75th percentile) were significantly higher in pregnant women compared to non-pregnant women (56 (33; 95) pg/ml vs. 38 (22; 62) pg/ml (p<0.001)). NT-proBNP increased during pregnancy to 73 (51; 124) pg/ml in the 11+6 to 15+6 GW (p<0.001). However, NT-proBNP levels from 23+0 GW towards term were comparable to non-pregnant controls. NT-proBNP is significantly elevated in healthy pregnancies until mid-pregnancy. As preeclampsia and gestational hypertension are associated with increased NT-proBNP, our results have to be considered in future diagnostic approaches using NT-proBNP for these pathologic conditions.