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Whole genome duplication (WGD) generates new genetic material that can contribute to the evolution of gene regulatory networks and phenotypes. After WGD, retained ohnologues can undergo subfunctionalisation to partition ancestral functions and/or neofunctionalisation, where one copy assumes a new function. We previously found that there had been a WGD in an ancestor of arachnopulmonates, the lineage including spiders and scorpions but excluding other arachnids like mites, ticks, and harvestmen. This WGD was evidenced by many duplicated homeobox genes, including two Hox clusters, in spiders. However, it was unclear which homeobox paralogues were produced by WGD versus tandem duplications. Understanding this is key to determining the relative contributions of tandem duplications and WGD to arachnopulmonate genome evolution. Here we characterised the distribution of duplicated homeobox genes across eight chromosome-level spider genomes. We found that the majority of retained duplicate homeobox genes in spiders likely originated from WGD. We also found two copies of conserved homeobox gene clusters, including the Hox, NK, HRO, Irx, and SINE, in all eight species. Consistently, we noticed one degenerated copy of each cluster in terms of gene content and organisation while the other remained more intact. Focussing on the NK cluster, we found evidence for regulatory subfunctionalisation between the duplicated NK genes in the spider Parasteatoda tepidariorum to their single-copy orthologues in the harvestman Phalangium opilio. Our study provides new insights into the contributions of multiple modes of duplication to the homeobox gene repertoire during the evolution of spiders and the function of NK genes.

In the arthropod model species Drosophila melanogaster, a dipteran fly, segmentation of the anterior–posterior body axis is under control of a hierarchic gene cascade. Segmental boundaries that form morphological grooves are established posteriorly within the segmental expression domain of the segment-polarity gene (SPG) engrailed (en). More important for the development of the fly, however, are the parasegmental boundaries that are established at the interface of en expressing cells and anteriorly adjacent wingless (wg) expressing cells. In Drosophila, both segmental and transient parasegmental grooves form. The latter are positioned anterior to the expression of en. Although the function of the SPGs in establishing and maintaining segmental and parasegmental boundaries is highly conserved among arthropods, parasegmental grooves have only been reported for Drosophila, and a spider (Cupiennius salei). Here, we present new data on en expression, and re-evaluate published data, from four distantly related spiders, including Cupiennius, and a distantly related chelicerate, the harvestman Phalangium opilio. Gene expression analysis of en genes in these animals does not corroborate the presence of parasegmental grooves. Consequently, our data question the general presence of parasegmental grooves in arthropods.

Hox genes are known for their role in the specification of typical body plan features in animals. Evolutionary changes in Hox gene function are believed to be involved in the emergence of the diverse body plans we observe in animals today. Spiders share many body plan features with other arthropods, but also have numerous unique traits of their own. Studies of spider Hox genes have already provided insights into evolutionarily conserved and derived features of the spider body plan and their genetic basis. However, many aspects of Hox gene biology have been insufficiently studied in spiders so far. In this review, we highlight previous comparative studies of Hox genes in spiders and their significance for our understanding of the evolution of the spider body plan. We also identify aspects of Hox gene biology that need to be studied in greater detail. Many spider Hox genes have not been investigated beyond their mRNA expression patterns, and the role of Hox genes with apparently plesiomorphic or dual functions, like ftz and Hox3 is still unclear. Spiders have a duplicated Hox gene cluster, but possible sub- or neofunctionalisation of duplicates have not yet been studied systematically. Future research should therefore focus on these issues, in addition to the role of Polycomb and trithorax-mediated regulation, the identification of regulatory regions, cofactors or spider-specific target genes, and the significance of non-coding RNAs transcribed from within the Hox cluster and even from the antisense strand of particular Hox genes.

The aim of this study is to report on the liver transplantation (LT) activity and posttransplant outcome, over time, of patients with grade 3 acute-on-chronic liver failure (ACLF-3) in a single transplant center performing a large number of LTs for patients with ACLF-3. It aims at showing how pre-LT intensive care unit (ICU) management impacts post-LT outcomes, in particular through monitoring the transplantation for ACLF-3 model (TAM) score. A total of 100 patients who had ACLF-3 at the time of LT between 2007 and 2019 were included retrospectively. The cohort was divided in 2 periods, with 50 patients in each period. There was an increase in the number of patients with ACLF-3 who received an LT during the course of the study period and significantly higher 1-year post-LT survival rates in the second period compared with the first period (86% versus 66%, respectively; P = 0.02). Interestingly, patients during both periods had similar severity profiles and scores apart from a significantly lower number of patients with TAM scores >2 at the time of LT in the second period compared with the first period (1 [2%] versus 11 [22%], respectively; P ≤ 0.01). In addition, patients whose clinical condition improved in the ICU (with a TAM score downstaged between admission and LT) had significantly higher post-LT survival rates than those whose TAM score stayed the same or increased: 88% versus 70%, respectively (P = 0.04). This study shows a learning curve in LT for patients with ACLF-3, with optimized ICU management and patient selection leading to increased numbers of LTs for patients with ACLF-3 and improved post-LT outcomes. It also delineates how the TAM score can be used to identify the optimal transplantability window for patients with ACLF-3.

The so-called extra-embryonic tissues are important for embryonic development in many animals, although they are not considered to be part of the germ band or the embryo proper. They can serve a variety of functions, such as nutrient uptake and waste removal, protection of the embryo against mechanical stress, immune response and morphogenesis. In insects, a subgroup of arthropods, extra-embryonic tissues have been studied extensively and there is increasing evidence that they might contribute more to embryonic development than previously thought. In this review, we provide an assessment of the occurrence and possible functions of extra-embryonic tissues in the closest arthropod relatives, onychophorans (velvet worms) and tardigrades (water bears). While there is no evidence for their existence in tardigrades, these tissues show a remarkable diversity across the onychophoran subgroups. A comparison of extra-embryonic tissues of onychophorans to those of arthropods suggests shared functions in embryonic nutrition and morphogenesis. Apparent contribution to the final form of the embryo in onychophorans and at least some arthropods supports the hypothesis that extra-embryonic tissues are involved in organogenesis. In order to account for this role, the commonly used definition of these tissues as ‘extra-embryonic’ should be reconsidered.This article is part of the theme issue ‘Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom’.

The Sp-family genes encode important transcription factors in animal development. Here we investigate the embryonic expression patterns of the complete set of Sp-genes in the velvet worm Euperipatoides kanangrensis (Onychophora), with a special focus on the Sp6–9 ortholog. In arthropods, Sp6–9, the ortholog of the Drosophila melanogaster D-Sp1 gene plays a conserved role in appendage development. Our data show that the expression of Sp6–9 during the development of the velvet worm is conserved, suggesting that the key function of the Sp6–9 gene dates back to at least the last common ancestor of arthropods and onychophorans and thus likely the last common ancestor of Panarthropoda.

In the spider, determination of the dorsal-ventral body (DV) axis depends on the interplay of the dorsal morphogen encoding genedecapentaplegic(Dpp) and its antagonist,short gastrulation(sog), a gene that is involved in the correct establishment of ventral tissues. Recent work demonstrated that the forkhead domain encoding geneFoxBis involved in dorsal-ventral axis formation in spider limbs. Here, Dpp likely acts as a dorsal morphogen, and FoxB is likely in control of ventral tissues as RNAi-mediated knockdown ofFoxBcauses dorsalization of the limbs. In this study, we present phenotypes ofFoxBknockdown that demonstrate a function in the establishment of the DV body axis. Knockdown of FoxB function leads to embryos with partially duplicated median germ bands (Duplicitas media) that are possibly the result of ectopic activation of Dpp signalling. Another class of phenotypes is characterized by unnaturally slim (dorsal-ventrally compressed) germ bands in which ventral tissue is either not formed, or is specified incorrectly, likely a result of Dpp over-activity. These results suggest that FoxB functions as an antagonist of Dpp signalling during body axis patterning, similarly as it is the case in limb development. FoxB thus represents a general player in the establishment of dorsal-ventral structures during spider ontogeny.

Fox genes encode transcription factors that contain a DNA binding domain, the forkhead domain, and are known from diverse animal species. The exact homology of the Fox genes of different species is debated and this makes inferences about the evolution of the Fox genes, and their duplications and losses difficult. We have performed phylogenetic analyses of the Fox gene complements of 32 panarthropod species. Our results confirm an ancestral complement of FoxA, FoxB, FoxC, FoxD, FoxF, FoxG, FoxJ1, FoxJ2/3, FoxK, FoxL1, FoxL2, FoxN1/4, FoxN2/3, FoxO, FoxP, and FoxQ2 in the Arthropoda, and additionally FoxH and FoxQ1 in the Panarthropoda (including tardigrades and onychophorans). We identify a novel Fox gene sub-family, that we designate as FoxT that includes two genes in Drosophila melanogaster, Circadianly Regulated Gene (Crg-1) and forkhead domain 3F (fd3F). In a very recent paper, the same new Fox gene sub-family was identified in insects (Lin et al. 2021). Our analysis confirms the presence of FoxT and shows that its members are present throughout Panarthropoda. We show that the hitherto unclassified gene CG32006 from the fly Drosophila melanogaster belongs to FoxJ1. We also detect gene losses: FoxE and FoxM were lost already in the panarthropod ancestor, whereas the loss of FoxH occurred in the arthropod ancestor. Finally, we find an ortholog of FoxQ1 in the bark scorpion Centruroides sculpturatus, confirmed not only by phylogenetic analysis, but also by forming an evolutionarily conserved gene cluster with FoxF, FoxC, and FoxL1. This suggests that FoxQ1 belongs to the ancestral Fox gene complement in panarthropods and also in chelicerates, but has been lost at the base of the mandibulate arthropods.

Spiders represent widely used model organisms for chelicerate and even arthropod development and evolution. Wnt genes are important and evolutionary conserved factors that control and regulate numerous developmental processes. Recent studies comprehensively investigated the complement and expression of spider Wnt genes revealing conserved as well as diverged aspects of their expression and thus (likely) function among different groups of spiders representing Mygalomorphae (tarantulas), and both main groups of Araneae (true spiders) (Haplogynae/Synspermiata and Entelegynae). The allegedly most modern/derived group of entelegyne spiders is represented by the RTA-clade of which no comprehensive data on Wnt expression were available prior to this study. Here, we investigated the embryonic expression of all Wnt genes of the RTA-clade spider Cupiennius salei. We found that most of the Wnt expression patterns are conserved between Cupiennius and other spiders, especially more basally branching species. Surprisingly, most differences in Wnt gene expression are seen in the common model spider Parasteatoda tepidariorum (a non-RTA clade entelegyne species). These results show that data and conclusions drawn from research on one member of a group of animals (or any other organism) cannot necessarily be extrapolated to the group as a whole, and instead highlight the need for comprehensive taxon sampling.

Objectives To describe the coinfections in invasive aspergillosis (IA), to identify factors associated with coinfections, and to evaluate the impact of coinfection on mortality. Patients and methods We conducted a monocentric retrospective study of consecutive putative, probable, or proven IA that occurred between 1997 and 2017. All coinfections, with an onset within 7 days before or after the first sign of aspergillosis, were identified. Factors associated with coinfections and mortality were analysed by multivariable analysis. Results Among the 690 patients with IA included in the study, the median age was 57 years (range 7 days to 90 years). A coinfection was diagnosed in 272/690 patients (39.4%, 95%CI 35.8–43.2). The location of this coinfection was pulmonary only in 131/272 patients (48%), bloodstream only in 66/272 patients (24%) and other/multiple sites in 75/272 patients (28%). Coinfections were bacterial (110/272 patients, 40%), viral (58/272, 21%), fungal (57/272, 21%), parasitic (5/272, 2%) or due to multiple types of pathogens (42/272, 15%). Factors associated with a coinfection in adjusted analysis were: allogeneic haematopoietic stem-cell transplantation (OR 2.3 (1.2–4.4)), other haematological malignancies (OR 2.1 (1.2–3.8)), other underlying diseases (OR 4.3 (1.4–13.6)), lymphopenia (OR 1.7 (1.1-2.5)), C-reactive protein >180 mg/L (OR 1.9 (1.2–3.0)), fever (OR 2.4 (1.5–4.1)), tracheal intubation (OR 2.6 (1.5–4.7)), isolation of two or more different Aspergillus species (OR 2.7 (1.1–6.3)), and the presence of non-nodular lesions on chest computed tomography (OR 2.2 (1.3–3.7) and OR 2.2 (1.2–4.0)). Coinfections were independently associated with a higher mortality at week 12 (adjusted HR 1.5 (1.1–1.9), p Conclusions Coinfections are frequent in IA patients and are associated with higher mortality.

Background In the vinegar fly Drosophila melanogaster, the homeodomain containing transcription factor Teashirt (Tsh) appears to specify trunk identity in concert with the function of the Hox genes. While in Drosophila there is a second gene closely related to tsh, called tiptop (tio), in other arthropods species only one copy exists (called tio/tsh). The expression of tsh and tio/tsh, respectively, is surprisingly similar among arthropods suggesting that its function as trunk selector gene may be conserved. Other research, for example on the beetle Tribolium castaneum, questions even conservation of Tsh function among insects. The zinc-finger transcription factor Spalt (Sal) is involved in the regulation of Drosophila tsh, but this regulatory interaction does not appear to be conserved in Tribolium either. Whether the function and interaction of tsh and sal as potential trunk-specifiers, however, is conserved is still unclear because comparative studies on sal expression (except for Tribolium) are lacking, and functional data are (if at all existing) restricted to Insecta. Results Here, we provide additional data on arthropod tsh expression, show the first data on onychophoran tio/tsh expression, and provide a comprehensive investigation on sal expression patterns in arthropods and an onychophoran. Conclusions Our data support the idea that tio/tsh genes are involved in the development of “trunk” segments by regulating limb development. Our data suggest further that the function of Sal is indeed unlikely to be conserved in trunk vs head development like in Drosophila, but early expression of sal is in line with a potential homeotic function, at least in Arthropoda.

Posterior elongation of the developing embryo is a common feature of animal development. One group of genes that is involved in posterior elongation is represented by the Wnt genes, secreted glycoprotein ligands that signal to specific receptors on neighbouring cells and thereby establish cell-to-cell communication. In segmented animals such as annelids and arthropods, Wnt signalling is also likely involved in segment border formation and regionalisation of the segments. Priapulids represent unsegmented worms that are distantly related to arthropods. Despite their interesting phylogenetic position and their importance for the understanding of ecdysozoan evolution, priapulids still represent a highly underinvestigated group of animals. Here, we study the embryonic expression patterns of the complete sets of Wnt genes in the priapulids Priapulus caudatus and Halicryptus spinulosus. We find that both priapulids possess a complete set of 12 Wnt genes. At least in Priapulus, most of these genes are expressed in and around the posterior-located blastopore and thus likely play a role in posterior elongation. Together with previous work on the expression of other genetic factors such as caudal and even-skipped, this suggests that posterior elongation in priapulids is under control of the same (or very similar) conserved gene regulatory network as in arthropods. Electronic supplementary material The online version of this article (10.1007/s00427-019-00636-6) contains supplementary material, which is available to authorized users.

The Ecdysozoa is a major animal clade whose main uniting feature is a distinctive growth strategy that requires the periodical moulting of the external cuticle. The staggering diversity within Ecdysozoa has prompted substantial efforts to reconstruct their origin and early evolution. Based on palaentological and developmental data, we proposed a scenario for the early evolution of the ecdysozoan clade Panarthropoda (Onychophora, Tardigrada, Euarthropoda), and postulated that a terminal mouth is ancestral for this lineage. In light of the accompanying comment by Claus Nielsen, we take this opportunity to clarify the significance of our argumentation for Panarthropoda in the phylogenetic context of Ecdysozoa, and Bilateria more broadly. We conclude that the ancestral ecdysozoan most likely had an adult terminal mouth, and that the last common ancestors of all the phyla that constitute Ecdysozoa almost certainly also had an adult terminal mouth. The occurrence of a ventral-facing mouth in various adult ecdysozoans - particularly panarthropods - is the result of convergence. Despite the paucity of embryological data on fossil taxa, we contemplate the likelihood that a developmentally early ventral mouth opening could be ancestral for Ecdysozoa, and if so, then this would represent a symplesiomorphy of Bilateria as a whole.

Introduction: Cancer patients are at high risk of developing septic shock (SSh) and are increasingly admitted to ICU given their improved long-term prognosis. We, therefore, compared the prognosis of cancer and non-cancer patients with SSh. Methods: We conducted a monocentric, retrospective cohort study (2013-2019) on patients admitted to ICU for SSh. We compared the clinical characteristics and management and studied short- and long-term mortality with ICU and in-hospital mortality and 1-year survival according to cancer status. Results: We analyzed 239 ICU stays in 210 patients, 59.5% of whom were men (n = 125), with a median age of 66.5 (IQR 56.3-77.0). Of the 121 cancer patients (57.6% of all patients), 70 had solid tumors (33.3%), and 51 had hematological malignancies (24.3%). When comparing ICU stays of patients with versus without cancer (n = 148 vs. n = 91 stays, respectively), mortality reached 30.4% (n = 45) vs. 30.0% (n = 27) in the ICU (p = 0.95), and 41.6% (n = 59) vs. 35.6% (n = 32) in hospital (p = 0.36), respectively. ICU length of stay (LOS) was 5.0 (2.0-11.3) vs. 6.0 (3.0-15.0) days (p = 0.27), whereas in-hospital LOS was 25.5 (13.8-42.0) vs. 19.5 (10.8-41.0) days (p = 0.33). Upon multivariate analysis, renal replacement therapy (OR = 2.29, CI95%: 1.06-4.93, p = 0.03), disseminated intravascular coagulation (OR = 5.89, CI95%: 2.49-13.92, p < 0.01), and mechanical ventilation (OR = 7.85, CI95%: 2.90-21.20, p < 0.01) were associated with ICU mortality, whereas malignancy, hematological, or solid tumors were not (OR = 1.41, CI95%: 0.65-3.04; p = 0.38). Similarly, overall cancer status was not associated with in-hospital mortality (OR = 1.99, CI95%: 0.98-4.03, p = 0.06); however, solid cancers were associated with increased in-hospital mortality (OR = 2.52, CI95%: 1.12-5.67, p = 0.03). Lastly, mortality was not significantly different at 365-day follow-up between patients with and without cancer. Conclusions: In-hospital and ICU mortality, as well as LOS, were not different in SSh patients with and without cancer, suggesting that malignancies should no longer be considered a barrier to ICU admission. Keywords: critical care; immunocompromised host; neoplasms; septic shock; treatment outcome.

The Wnt genes represent a large family of secreted glycoprotein ligands that date back to early animal evolution. Multiple duplication events generated a set of 13 Wnt families of which 12 are preserved in protostomes. Embryonic Wnt expression patterns (Wnt-patterning) are complex, representing the plentitude of functions these genes play during development. Here, we comprehensively investigated the embryonic expression patterns of Wnt genes from three species of spiders covering both main groups of true spiders, Haplogynae and Entelegynae, a mygalomorph species (tarantula), as well as a distantly related chelicerate outgroup species, the harvestman Phalangium opilio. All spiders possess the same ten classes of Wnt genes, but retained partially different sets of duplicated Wnt genes after whole genome duplication, some of which representing impressive examples of sub- and neo-functionalization. The harvestman, however, possesses a more complete set of 11 Wnt genes but with no duplicates. Our comprehensive data-analysis suggests a high degree of complexity and evolutionary flexibility of Wnt-patterning likely providing a firm network of mutational protection. We discuss the new data on Wnt gene expression in terms of their potential function in segmentation, posterior elongation, and appendage development and critically review previous research on these topics. We conclude that earlier research may have suffered from the absence of comprehensive gene expression data leading to partial misconceptions about the roles of Wnt genes in development and evolution. Supplementary Information The online version contains supplementary material available at 10.1186/s13227-021-00182-1.

COVID-19 acute respiratory distress syndrome (ARDS) shares the common histological hallmarks with other forms of ARDS. However, the chronology of the histological lesions has not been well established.To describe the chronological histopathological alterations in the lungs of patients with COVID-19 related ARDS.A prospective cohort study was carried out.Intensive Care Unit of a tertiary hospital.The first 22 consecutive COVID-19 deaths.Lung biopsies and histopathological analyses were performed in deceased patients with COVID-19 related ARDS. Clinical data and patient course were evaluated.The median patient age was 66 [63-74] years; 73% were males. The median duration of mechanical ventilation was 17 [8-24] days. COVID-19 induced pulmonary injury was characterized by an exudative phase in the first week of the disease, followed by a proliferative/organizing phase in the second and third weeks, and finally an end-stage fibrosis phase after the third week. Viral RNA and proteins were detected in pneumocytes and macrophages in a very early stage of the disease, and were no longer detected after the second week.Limited sample size.The chronological evolution of COVID-19 lung histopathological lesions seems to be similar to that seen in other forms of ARDS. In particular, lung lesions consistent with potentially corticosteroid-sensitive lesions are seen.El síndrome de dificultad respiratoria aguda (SDRA) asociado a la COVID-19 comparte características histológicas con otros tipos de SDRA. Sin embargo, no se ha establecido adecuadamente la cronología de las lesiones histológicas.Describir las alteraciones histopatológicas cronológicas en los pulmones de los pacientes con síndrome de dificultad respiratoria aguda asociado a COVID-19.Estudio prospectivo de cohortes.Unidad de cuidados intensivos de un hospital terciario.Las primeras 22 muertes consecutivas por COVID-19.Se llevaron a cabo biopsias pulmonares y análisis histopatológicos en pacientes fallecidos por SDRA asociado a COVID-19. Se evaluaron los datos clínicos y la evolución médica.La mediana de edad de los pacientes fue de 66 (63-74) años y el 73% eran varones. La mediana de la duración de la ventilación mecánica fue de 17 (8-24) días. La lesión pulmonar inducida por COVID-19 se caracterizó por una fase exudativa durante la primera semana de la enfermedad, seguida de una fase proliferativa/organizativa en la segunda y tercera semana y, por último, una fase de fibrosis en fase terminal tras la tercera semana de evolución. Se detectaron proteínas y ARN vírico en neumocitos y macrófagos en una fase muy temprana de la enfermedad, pero estos ya no se volvieron a detectar a partir de la segunda semana.Tamaño limitado de la muestra.La evolución cronológica de las lesiones histopatológicas pulmonares asociadas a la COVID-19 parece ser similar a la de otras formas de SDRA. En particular, se observan daños pulmonares coherentes con las lesiones potencialmente sensibles a los corticosteroides.

Whole-genome duplications (WGDs) have occurred multiple times during animal evolution, including in lineages leading to vertebrates, teleosts, horseshoe crabs, and arachnopulmonates. These dramatic events initially produce a wealth of new genetic material, generally followed by extensive gene loss. It appears, however, that developmental genes such as homeobox genes, signaling pathway components and microRNAs are frequently retained as duplicates (so-called ohnologs) following WGD. These not only provide the best evidence for WGD, but an opportunity to study its evolutionary consequences. Although these genes are well studied in the context of vertebrate WGD, similar comparisons across the extant arachnopulmonate orders are patchy. We sequenced embryonic transcriptomes from two spider species and two amblypygid species and surveyed three important gene families, Hox, Wnt, and frizzled, across these and 12 existing transcriptomic and genomic resources for chelicerates. We report extensive retention of putative ohnologs, further supporting the ancestral arachnopulmonate WGD. We also found evidence of consistent evolutionary trajectories in Hox and Wnt gene repertoires across three of the six arachnopulmonate orders, with interorder variation in the retention of specific paralogs. We identified variation between major clades in spiders and are better able to reconstruct the chronology of gene duplications and losses in spiders, amblypygids, and scorpions. These insights shed light on the evolution of the developmental toolkit in arachnopulmonates, highlight the importance of the comparative approach within lineages, and provide substantial new transcriptomic data for future study.

Excretion is an essential physiological process, carried out by all living organisms, regardless of their size or complexity.1, 2, 3 Both protostomes (e.g., flies and flatworms) and deuterostomes (e.g., humans and sea urchins) possess specialized excretory organs serving that purpose. Those organs exhibit an astonishing diversity, ranging from units composed of just few distinct cells (e.g., protonephridia) to complex structures, built by millions of cells of multiple types with divergent morphology and function (e.g., vertebrate kidneys).4,5 Although some molecular similarities between the development of kidneys of vertebrates and the regeneration of the protonephridia of flatworms have been reported,6,7 the molecular underpinnings of the development of excretory organs have never been systematically studied in a comparative context.4 Here, we show that a set of transcription factors (eya, six1/2, pou3, sall, lhx1/5, and osr) and structural proteins (nephrin, kirre, and zo1) is expressed in the excretory organs of a phoronid, brachiopod, annelid, onychophoran, priapulid, and hemichordate that represent major protostome lineages and non-vertebrate deuterostomes. We demonstrate that the molecular similarity observed in the vertebrate kidney and flatworm protonephridia6,7 is also seen in the developing excretory organs of those animals. Our results show that all types of ultrafiltration-based excretory organs are patterned by a conserved set of developmental genes, an observation that supports their homology. We propose that the last common ancestor of protostomes and deuterostomes already possessed an ultrafiltration-based organ that later gave rise to the vast diversity of extant excretory organs, including both proto- and metanephridia. acceptedVersion

Excretion is an essential physiological process, carried out by all living organisms regardless of their size or complexity(1–3). Most animals, which include both protostomes (e.g. flies, flatworms) and deuterostomes (e.g. humans, sea urchins) (together Nephrozoa(4, 5)), possess specialized excretory organs. Those organs exhibit an astonishing diversity, ranging from units composed of just three distinct cells (e.g. protonephridia) to complex structures, built by millions of cells of multiple types with divergent morphology and function (e.g. vertebrate kidneys)(6, 7). Although some molecular similarities between the development of kidneys of vertebrates and the regeneration of the protonephridia of flatworms have been reported(8, 9), the molecular development of nephrozoan excretory organs has never been systematically studied in a comparative context(6). Here we show that a set of highly conserved transcription factors and structural proteins is expressed during the development of excretory organs of six species that represent major protostome lineages and non-vertebrate deuterostomes. We demonstrate that the molecular similarity witnessed in the vertebrate kidney and flatworm protonephridia(8) is also seen in the developing excretory organs of other Nephrozoa. In addition, orthologous structural proteins forming the ultrafiltration apparatus are expressed in all these organs in the filter-forming cells. Our results strongly suggest that excretory organs are homologous and are patterned by the conserved set of developmental genes. We propose that the last common nephrozoan ancestor possessed an ultrafiltration-based, ciliated excretory organ, a structure that later gave rise to the vast diversity of extant excretory organs, including the human kidney.Significance statementMost of the bilaterally symmetrical animals excrete through specialized excretory organs, such as kidneys and nephridia. However, due to the morphological diversity of these organs, it remains unknown whether those structures evolved from a common ancestral organ or appeared several times independently during evolution. In order to answer the question about the origin of excretory organs we investigated the molecular pathways and structural genes involved in the development of nephridia in 6 animal species representing major evolutionary lineages. We show that diverse excretory organs share an ancient molecular patterning and structural molecules. Our results provide strong evidence that all excretory organs originated from a single, simple organ that performed urine production by ultrafiltration in deep geological past.

Whole genome duplications (WGD) have occurred multiple times in the evolution of animals, including in the lineages leading to vertebrates, teleosts, horseshoe crabs and arachnopulmonates. These dramatic genomic events initially produce a wealth of new genetic material, which is generally followed by extensive gene loss. It appears that developmental genes such as homeobox genes, signalling pathway components and microRNAs, however, tend to be more frequently retained in duplicate following WGD (ohnologs). These not only provide the best evidence for the occurrence of WGD, but an opportunity to study its evolutionary implications. Although these genes are relatively well studied in the context of vertebrate WGD, genomic and transcriptomic data for independent comparison in other groups are scarce, with patchy sampling of only two of the five extant arachnopulmonate orders. To improve our knowledge of developmental gene repertoires, and their evolution since the arachnopulmonate WGD, we sequenced embryonic transcriptomes from two additional spider species and two whip spider species and surveyed them for three important gene families: Hox, Wnt and frizzled. We report extensive retention of ohnologs in all four species, further supporting the arachnopulmonate WGD. Thanks to improved sampling we were able to identify patterns of likely ohnolog retention and loss within spiders, including apparent differences between major clades. The two amblypygid species have larger ohnolog repertoires of these genes than both spiders and scorpions; including the first reported duplicated Wnt1/wg, the first Wnt10 recovered in an arachnid, and broad retention of frizzled genes. These insights shed light on the evolution of the enigmatic whip spiders, highlight the importance of the comparative approach within lineages, and provide substantial new transcriptomic data for future study.

In the fly Drosophila melanogaster, a hierarchic segmentation gene cascade patterns the anterior-posterior body axis of the developing embryo. Within this cascade, the pair-rule genes (PRGs) transform the more uniform patterning of the higher-level genes into a metameric pattern that first represents double-segmental units, and then, in a second step, represents a true segmental pattern. Within the PRG network, primary PRGs regulate secondary PRGs that are directly involved in the regulation of the next lower level, the segment-polarity genes (SPGs). While the complement of primary PRGs is different in Drosophila and the beetle Tribolium, another arthropod model organism, both paired (prd) and sloppy-paired (slp), acts as secondary PRGs. In earlier studies, the interaction of PRGs and the role of the single slp ortholog in Tribolium have been investigated in some detail revealing conserved and diverged aspects of PRG function. In this study, I present the identification and the analysis of embryonic expression patterns of a second slp gene (called slp2) in Tribolium. While the previously identified gene, slp, is expressed in a typical PRG pattern, expression of slp2 is more similar to that of the downstream-acting SPGs, and shows expression similarities to slp2 in Drosophila. The previously reported differences between the function of slp in Drosophila and Tribolium may partially account for the function of the newly identified second slp paralog in Tribolium, and it may therefore be advised to conduct further studies on PRG function in the beetle.

Recent research has shown that Toll genes, and in particular a newly defined class of Toll genes, the so-called Long Toll Genes (Loto genes), are crucial factors in embryogenesis. In arthropods, they are involved in axis formation via a process called convergent extension (CE). A hallmark of Loto genes is their relatively (compared to other Toll genes) high number of leucine-rich repeat elements (LRRs) coupled with the fact that they are expressed in transverse stripes in all segments, or a subset of segments, patterns that are reminiscent of classical segmentation genes such as the pair-rule genes. Onychophorans represent a close outgroup to the arthropods; however, their embryonic development differs substantially. It is unclear if convergent extension contributes to onychophoran germ band formation and, if so, whether Loto genes are involved in governing this process. This study identifies a single onychophoran Toll gene from a sequenced embryonic transcriptome in two onychophoran species. The identified gene shows sequence and expression pattern characteristics of Loto genes. However, its expression pattern also comprises some general differences to arthropod Loto genes that are involved in CE. Electronic supplementary material The online version of this article (10.1007/s00427-018-0609-8) contains supplementary material, which is available to authorized users.

This paper summarizes our current knowledge on the expression and assumed function of Drosophila and (other) arthropod segmentation gene orthologs in Onychophora, a closely related outgroup to Arthropoda. This includes orthologs of the so-called Drosophila segmentation gene cascade including the Hox genes, as well as other genetic factors and pathways involved in non-drosophilid arthropods. Open questions about and around the topic are addressed, such as the definition of segments in onychophorans, the unclear regulation of conserved expression patterns downstream of non-conserved factors, and the potential role of mesodermal patterning in onychophoran segmentation.

Forkhead box (Fox) transcription factors evolved early in animal evolution and represent important components of conserved gene regulatory networks (GRNs) during animal development. Most of the researches concerning Fox genes, however, are on vertebrates and only a relatively low number of studies investigate Fox gene function in invertebrates. In addition to this shortcoming, the focus of attention is often restricted to a few well-characterized Fox genes such asFoxA(forkhead),FoxC(crocodile) andFoxQ2. Although arthropods represent the largest and most diverse animal group, most other Fox genes have not been investigated in detail, not even in the arthropod model speciesDrosophila melanogaster. In a general gene expression pattern screen for panarthropod Fox genes including the red flour beetleTribolium castaneum, the pill millipedeGlomeris marginata, the common house spiderParasteatoda tepidariorum, and the velvet wormEuperipatoides kanangrensis, we identified a Fox gene with a highly conserved expression pattern along the ventral ectoderm of arthropod and onychophoran limbs. Functional investigation ofFoxBinParasteatodareveals a hitherto unrecognized important function of FoxB upstream ofwingless(wg) anddecapentaplegic(dpp) in the GRN orchestrating dorsal–ventral limb patterning.

To assess the benefit-to-risk balance of bronchoalveolar lavage (BAL) in intensive care unit (ICU) patients. In 16 ICUs, we prospectively collected adverse events during or within 24 h after BAL and assessed the BAL input for decision making in consecutive adult patients. The occurrence of a clinical adverse event at least of grade 3, i.e., sufficiently severe to need therapeutic action(s), including modification(s) in respiratory support, defined poor BAL tolerance. The BAL input for decision making was declared satisfactory if it allowed to interrupt or initiate one or several treatments. We included 483 BAL in 483 patients [age 63 years (interquartile range (IQR) 53–72); female gender: 162 (33.5%); simplified acute physiology score II: 48 (IQR 37-61); immunosuppression 244 (50.5%)]. BAL was begun in non-intubated patients in 105 (21.7%) cases. Sixty-seven (13.9%) patients reached the grade 3 of adverse event or higher. Logistic regression showed that a BAL performed by a non-experienced physician (non-pulmonologist, or intensivist with less than 10 years in the specialty or less than 50 BAL performed) was the main predictor of poor BAL tolerance in non-intubated patients [OR: 3.57 (95% confidence interval 1.04–12.35); P = 0.04]. A satisfactory BAL input for decision making was observed in 227 (47.0%) cases and was not predictable using logistic regression. Adverse events related to BAL in ICU patients are not infrequent nor necessarily benign. Our findings call for an extreme caution, when envisaging a BAL in ICU patients and for a mandatory accompaniment of the less experienced physicians.

Forkhead box (Fox) genes code for a class of transcription factors with many different fundamental functions in animal development including cell cycle control. Other important factors of cell cycle control are Cyclins and Cyclin-dependent kinases (CDKs). Here we report on the oscillating expression of three Fox genes, FoxM, FoxN14 (jumeaux) and FoxN23 (Checkpoint suppressor like-1), Cyclins and CDKs in an onychophoran, a representative of a relatively small group of animals that are closely related to the arthropods. Expression of these genes is in the form of several waves that start as dot-like domains in the center of each segment and then transform into concentric rings that run towards the periphery of the segments. This oscillating gene expression, however, occurs exclusively along the anterior-posterior body axis in the tissue ventral to the base of the appendages, a region where the central nervous system and the enigmatic ventral and preventral organs of the onychophoran develop. We suggest that the oscillating gene expression and the resulting waves of expression we report are likely correlated with cell cycle control during the development of the onychophoran nervous system. This intriguing patterning appears to be unique for onychophorans as it is not found in any of the arthropods we also investigated in this study, and is likely correlated with the slow embryonic development of onychophorans compared to arthropods.

Delta/Notch (Dl/N) signalling is involved in the gene regulatory network underlying the segmentation process in vertebrates and possibly also in annelids and arthropods, leading to the hypothesis that segmentation may have evolved in the last common ancestor of bilaterian animals. Because of seemingly contradicting results within the well-studied arthropods, however, the role and origin of Dl/N signalling in segmentation generally is still unclear. In this study, we investigate core components of Dl/N signalling by means of gene expression analysis in the onychophoran Euperipatoides kanangrensis, a close relative to the arthropods. We find that neither Delta or Notch nor any other investigated components of its signalling pathway are likely to be involved in segment addition in onychophorans. We instead suggest that Dl/N signalling may be involved in posterior elongation, another conserved function of these genes. We suggest further that the posterior elongation network, rather than classic Dl/N signalling, may be in the control of the highly conserved segment polarity gene network and the lower-level pair-rule gene network in onychophorans. Consequently, we believe that the pair-rule gene network and its interaction with Dl/N signalling may have evolved within the arthropod lineage and that Dl/N signalling has thus likely been recruited independently for segment addition in different phyla. Electronic supplementary material The online version of this article (doi:10.1007/s00427-016-0529-4) contains supplementary material, which is available to authorized users.

Background Inflammatory myopathies (IM) are life-threatening but treatable diseases. The risk factors for admission in Intensive care unit (ICU), the management and the outcome of patients with IM admitted to ICU has not yet been assessed. Objectives To assess the clinical features, risk factors and outcome of patients with IM admitted in ICU. Methods A single centre cohort of 509 patients with IM was screened for admission in ICU from 1992 to 2017. Patients admitted for trauma or for complications from elective surgery were excluded. Control patients with IM who had not been hospitalised in ICU were randomly selected from the cohort. Results Thirty-two ICU admissions were recorded in 27 IM patients during the study period ( Characteristics and prognosis of patients in ICU Patients hospitalised in ICU had a mean age of 63 y.±15 with SAPS II score of 58±24 and LODS score of 9±5 corresponding to an intermediate severity at admission in ICU. The delay between IM diagnosis and first ICU admission was 27±43 months. It is noteworthy that 12 patients (44%) were admitted in the ICU within the first month of IM diagnosis, among whom 4 (15%) were diagnosed with IM during ICU stay. Sixteen patients (60%) were not treated at the time of their first ICU admission. In 56% of the ICU stays, patients had active disease at admission. Patients were most frequently admitted for respiratory failure (88%) but cardiac (47%), renal (47%), neurologic (47%), haematological (22%) and hepatic (15%) failures were also recorded. Infections were present in 72% of the ICU stays, with septic shock in 44%. Nine patients (33%) died in ICU and 3 others (11%) within 90 days of the last ICU discharge (vs. 15% during a 7.5±5 years period of follow-up in the control group, p Risk factors of ICU admission The case control analysis identified 6 risk factors significantly associated with hospitalisation in the ICU, 3 of which were independently associated with hospitalisation in multivariate analysis. ICU patients had a higher age at first clinical signs of illness (62±13 years old vs. 53±13 years old, p The type of myositis was not significantly associated with admission in ICU, although no patient admitted in ICU had sIBM. It is noteworthy that cumulative number of immunomodulatory treatments in patients at the time of hospitalisation in ICU was lower than in the control group (0.5±0.7 vs. 1.9±0.8 p Conclusions IM patients admitted in ICU frequently have recent onset and untreated active IM with respiratory failure. Admission to ICU is associated with older age and a higher number of comorbidities. Mortality of IM patients in ICU is high. Disclosure of Interest None declared

Background Morphogen signalling represents a key mechanism of developmental processes during animal development. Previously, several evolutionary conserved morphogen signalling pathways have been identified, and their players such as the morphogen receptors, morphogen modulating factors (MMFs) and the morphogens themselves have been studied. MMFs are factors that regulate morphogen distribution and activity. The interactions of MMFs with different morphogen signalling pathways such as Wnt signalling, Hedgehog (Hh) signalling and Decapentaplegic (Dpp) signalling are complex because some of the MMFs have been shown to interact with more than one signalling pathway, and depending on genetic context, to have different, biphasic or even opposing function. This complicates the interpretation of expression data and functional data of MMFs and may be one reason why data on MMFs in other arthropods than Drosophila are scarce or totally lacking. Results As a first step to a better understanding of the potential roles of MMFs in arthropod development, we investigate here the embryonic expression patterns of division abnormally delayed (dally), dally-like protein (dlp), shifted (shf) and secreted frizzled-related protein 125 (sFRP125) and sFRP34 in the beetle Tribolium castaneum, the spider Parasteatoda tepidariorum, the millipede Glomeris marginata and the onychophoran Euperipatoides kanangrensis. This pioneer study represents the first comprehensive comparative data set of these genes in panarthropods. Conclusions Expression profiles reveal a high degree of diversity, suggesting that MMFs may represent highly evolvable nodes in otherwise conserved gene regulatory networks. Conserved aspects of MMF expression, however, appear to concern function in segmentation and limb development, two of the key topics of evolutionary developmental research. Electronic supplementary material The online version of this article (10.1186/s13227-018-0109-y) contains supplementary material, which is available to authorized users.

Onychophorans (velvet worms) are closely related to the arthropods, but their limb morphology represents a stage before arthropodization (i.e., the segmentation of the limbs). We investigated the expression of onychophoran homologs of genes that are involved in dorso-ventral (DV) and proximo-distal (PD) limb patterning in arthropods. We find that the two onychophoran optomotor-blind (omb) genes, omb-1 and omb-2, are both expressed in conserved patterns in the dorsal ectoderm of the limbs, including the onychophoran antennae (the frontal appendages). Surprisingly, the expression of decapentaplegic (dpp), which acts upstream of omb in Drosophila, is partially reversed in onychophoran limbs compared to its expression in arthropods. A conserved feature of dpp expression in arthropods and onychophorans, however, is the prominent expression of dpp in the tips of developing limbs, which, therefore, may represent the ancestral pattern. The expression patterns of wingless (wg) and H15 are very diverged in onychophorans. The wg gene is only expressed in the limb tips and the single H15 gene is expressed in a few dorsal limb cells, but not on the ventral side. The expression of wg and dpp at the limb tips is one of the three possible alternatives predicted by the topology model of arthropod limb patterning and is, thus, compatible with a conserved function of wg and dpp in the patterning of the PD axis. On the other hand, DV limb gene expression is less conserved, and the specification of ventral fate appears to involve neither wg nor H15 expression.

La Presse Medicale - In Press.Proof corrected by the author Available online since vendredi 12 fevrier 2016

et al., [Background]: The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. [Results]: We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. [Conclusions]: Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes., This work was supported by NIH grant NHGRI U54 HG003273 to RAG, the National Science Foundation (IOS-0951886 to NAA and DEB-1257053 to JHW), a Leverhulme visiting fellowship for EES (VF-2012-016), funding and PhD studentships (DJL, LG and AS) from Oxford Brookes University, and a Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) scholarship to CLBP. N-MP was funded by the Deutsche Forschungsgemeinschaft (grant numbers PR 1109/ 4-1, PR 1109/7-1 and PR 1109/6-1 to N-MP). Additional financial backing has been received from the Göttingen Graduate School for Neurosciences, Biophysics and Molecular Biosciences (GGNB), the Göttingen Center for Molecular Biosciences (GZMB), and the University of Göttingen (GAU). NT is supported by a Christiane Nüsslein-Volhard-Foundation fellowship and a “Women in Science” Award by L'Oréal Deutschland and the Deutsche UNESCO-Kommission. NP has been funded by the Volkswagen Foundation (project number: 85 983) and the Emmy Noether Programme of the Deutsche Forschungsgemeinschaft (grant number: PO 1648/3-1). Funding to RJ was provided by the Swedish Research Council VR grant 621-2011-4703.