Ploidy-specific transcriptomes shed light on the heterogeneous identity and metabolism of developing tomato pericarp cells

Endoreduplication, during which cells increase their DNA content through successive rounds of full genome replication without cell division, is the major source of endopolyploidy in higher plants. Endoreduplication plays pivotal roles in plant growth and development and is associated with the activation of specific transcriptional programmes that are characteristic of each cell type, thereby defining their identity. In plants, endoreduplication is found in numerous organs and cell types, especially in agronomically valuable ones, such as the fleshy fruit (pericarp) of tomato presenting high ploidy levels. We used the tomato pericarp tissue as a model system to explore the transcriptomes associated with endoreduplication progression during fruit growth. We confirmed that expression globally scales with ploidy level and identified sets of differentially expressed genes presenting only developmental-specific, only ploidy-specific expression patterns or profiles resulting from an additive effect of ploidy and development. When comparing ploidy levels at a specific developmental stage, we found that non-endoreduplicated cells are defined by cell division state and cuticle synthesis while endoreduplicated cells are mainly defined by their metabolic activity changing rapidly over time. By combining this dataset with publicly available spatiotemporal pericarp expression data, we proposed a map describing the distribution of ploidy levels within the pericarp. These transcriptome-based predictions were validated by quantifying ploidy levels within the pericarp tissue. This in situ ploidy quantification revealed the dynamic progression of endoreduplication and its cell layer specificity during early fruit development. In summary, the study sheds light on the complex relationship between endoreduplication, cell differentiation and gene expression patterns in the tomato pericarp.

Light-Activatable Photocaged UNC2025 for Triggering TAM Kinase Inhibition in Bladder Cancer

Photopharmacology is an emerging field that utilizes photo-responsive molecules to enable control over the activity of a drug using light. The aim is to limit the therapeutic action of a drug at the level of diseased tissues and organs. Considering the well-known implications of protein kinases in cancer and the therapeutic issues associated with protein kinase inhibitors, the photopharmacology is seen as an innovative and alternative solution with great potential in oncology. In this context, we developed the first photocaged TAM kinase inhibitors based on UNC2025, a first-in-class small molecule kinase inhibitor. These prodrugs showed good stability in biologically relevant buffer and rapid photorelease of the photoremovable protecting group upon UV-light irradiation (<10 min.). These light-activatable prodrugs led to a 16-fold decrease to a complete loss of kinase inhibition, depending on the protein and the position at which the coumarin-type phototrigger was introduced. The most promising candidate was the N,O-dicaged compound, showing the superiority of having two photolabile protecting groups on UNC2025 for being entirely inactive on TAM kinases. Under UV-light irradiation, the N,O-dicaged compound recovered its inhibitory potency in enzymatic assays and displayed excellent antiproliferative activity in RT112 cell lines.

How children generalize novel nouns: An eye-tracking analysis of their generalization strategies

Recent research has shown that comparisons of multiple learning stimuli which are associated with the same novel noun favor taxonomic generalization of this noun. These findings contrast with single-stimulus learning in which children follow so-called lexical biases. However, little is known about the underlying search strategies. The present experiment provides an eye-tracking analysis of search strategies during novel word learning in a comparison design. We manipulated both the conceptual distance between the two learning items, i.e., children saw examples which were associated with a noun (e.g., the two learning items were either two bracelets in a "close" comparison condition or a bracelet and a watch in a "far" comparison condition), and the conceptual distance between the learning items and the taxonomically related items in the generalization options (e.g., the taxonomic generalization answer; a pendant, a near generalization item; versus a bow tie, a distant generalization item). We tested 5-, 6- and 8-year-old children's taxonomic (versus perceptual and thematic) generalization of novel names for objects. The search patterns showed that participants first focused on the learning items and then compared them with each of the possible choices. They also spent less time comparing the various options with one another; this search profile remained stable across age groups. Data also revealed that early comparisons, (i.e., reflecting alignment strategies) predicted generalization performance. We discuss four search strategies as well as the effect of age and conceptual distance on these strategies.

HadBD dehydratase from Mycobacterium tuberculosis fatty acid synthase type II: A singular structure for a unique function

Worldwide, tuberculosis is the second leading infectious killer and multidrug resistance severely hampers disease control. Mycolic acids are a unique category of lipids that are essential for viability, virulence, and persistence of the causative agent, Mycobacterium tuberculosis (Mtb). Therefore, enzymes involved in mycolic acid biosynthesis represent an important class of drug targets. We previously showed that the (3R)-hydroxyacyl-ACP dehydratase (HAD) protein HadD is dedicated mainly to the production of ketomycolic acids and plays a determinant role in Mtb biofilm formation and virulence. Here, we discovered that HAD activity requires the formation of a tight heterotetramer between HadD and HadB, a HAD unit encoded by a distinct chromosomal region. Using biochemical, structural, and cell-based analyses, we showed that HadB is the catalytic subunit, whereas HadD is involved in substrate binding. Based on HadBDMtb crystal structure and substrate-bound models, we identified determinants of the ultra-long-chain lipid substrate specificity and revealed details of structure-function relationship. HadBDMtb unique function is partly due to a wider opening and a higher flexibility of the substrate-binding crevice in HadD, as well as the drastically truncated central α-helix of HadD hotdog fold, a feature described for the first time in a HAD enzyme. Taken together, our study shows that HadBDMtb , and not HadD alone, is the biologically relevant functional unit. These results have important implications for designing innovative antivirulence molecules to fight tuberculosis, as they suggest that the target to consider is not an isolated subunit, but the whole HadBD complex.

Renal replacement therapy initiation strategies in comatose patients with severe acute kidney injury: a secondary analysis of a multicenter randomized controlled trial

PURPOSE

The effect of renal replacement therapy (RRT) in comatose patients with acute kidney injury (AKI) remains unclear. We compared two RRT initiation strategies on the probability of awakening in comatose patients with severe AKI.

METHODS

We conducted a post hoc analysis of a trial comparing two delayed RRT initiation strategies in patients with severe AKI. Patients were monitored until they had oliguria for more than 72 h and/or blood urea nitrogen higher than 112 mg/dL and then randomized to a delayed strategy (RRT initiated after randomization) or a more-delayed one (RRT initiated if complication occurred or when blood urea nitrogen exceeded 140 mg/dL). We included only comatose patients (Richmond Agitation-Sedation scale [RASS] < - 3), irrespective of sedation, at randomization. A multi-state model was built, defining five mutually exclusive states: death, coma (RASS < - 3), incomplete awakening (RASS [- 3; - 2]), awakening (RASS [- 1; + 1] two consecutive days), and agitation (RASS >  + 1). Primary outcome was the transition from coma to awakening during 28 days after randomization.

RESULTS

A total of 168 comatose patients (90 delayed and 78 more-delayed) underwent randomization. The transition intensity from coma to awakening was lower in the more-delayed group (hazard ratio [HR] = 0.36 [0.17-0.78]; p = 0.010). Time spent awake was 10.11 days [8.11-12.15] and 7.63 days [5.57-9.64] in the delayed and the more-delayed groups, respectively. Two sensitivity analyses were performed based on sedation status and sedation practices across centers, yielding comparable results.

CONCLUSION

In comatose patients with severe AKI, a more-delayed RRT initiation strategy resulted in a lower chance of transitioning from coma to awakening.

Microclimate modulation: An overlooked mechanism influencing the impact of plant diversity on ecosystem functioning

Changes in climate and biodiversity are widely recognized as primary global change drivers of ecosystem structure and functioning, also affecting ecosystem services provided to human populations. Increasing plant diversity not only enhances ecosystem functioning and stability but also mitigates climate change effects and buffers extreme weather conditions, yet the underlying mechanisms remain largely unclear. Recent studies have shown that plant diversity can mitigate climate change (e.g. reduce temperature fluctuations or drought through microclimatic effects) in different compartments of the focal ecosystem, which as such may contribute to the effect of plant diversity on ecosystem properties and functioning. However, these potential plant diversity-induced microclimate effects are not sufficiently understood. Here, we explored the consequences of climate modulation through microclimate modification by plant diversity for ecosystem functioning as a potential mechanism contributing to the widely documented biodiversity-ecosystem functioning (BEF) relationships, using a combination of theoretical and simulation approaches. We focused on a diverse set of response variables at various levels of integration ranging from ecosystem-level carbon exchange to soil enzyme activity, including population dynamics and the activity of specific organisms. Here, we demonstrated that a vegetation layer composed of many plant species has the potential to influence ecosystem functioning and stability through the modification of microclimatic conditions, thus mitigating the negative impacts of climate extremes on ecosystem functioning. Integrating microclimatic processes (e.g. temperature, humidity and light modulation) as a mechanism contributing to the BEF relationships is a promising avenue to improve our understanding of the effects of climate change on ecosystem functioning and to better predict future ecosystem structure, functioning and services. In addition, microclimate management and monitoring should be seen as a potential tool by practitioners to adapt ecosystems to climate change.

Inhibition of choline metabolism in an angioimmunoblastic T-cell lymphoma preclinical model reveals a new metabolic vulnerability as possible target for treatment

BACKGROUND

Angioimmunoblastic T-cell lymphoma (AITL) is a malignancy with very poor survival outcome, in urgent need of more specific therapeutic strategies. The drivers of malignancy in this disease are CD4+ follicular helper T cells (Tfh). The metabolism of these malignant Tfh cells was not yet elucidated. Therefore, we decided to identify their metabolic requirements with the objective to propose a novel therapeutic option.

METHODS

To reveal the prominent metabolic pathways used by the AITL lymphoma cells, we relied on metabolomic and proteomic analysis of murine AITL (mAITL) T cells isolated from our established mAITL model. We confirmed these results using AITL patient and healthy T cell expression data.

RESULTS

Strikingly, the mAITL Tfh cells were highly dependent on the second branch of the Kennedy pathway, the choline lipid pathway, responsible for the production of the major membrane constituent phosphatidylcholine. Moreover, gene expression data from Tfh cells isolated from AITL patient tumors, confirmed the upregulation of the choline lipid pathway. Several enzymes involved in this pathway such as choline kinase, catalyzing the first step in the phosphatidylcholine pathway, are upregulated in multiple tumors other than AITL. Here we showed that treatment of our mAITL preclinical mouse model with a fatty acid oxydation inhibitor, significantly increased their survival and even reverted the exhausted CD8 T cells in the tumor into potent cytotoxic anti-tumor cells. Specific inhibition of Chokα confirmed the importance of the phosphatidylcholine production pathway in neoplastic CD4 + T cells, nearly eradicating mAITL Tfh cells from the tumors. Finally, the same inhibitor induced in human AITL lymphoma biopsies cell death of the majority of the hAITL PD-1high neoplastic cells.

CONCLUSION

Our results suggest that interfering with choline metabolism in AITL reveals a specific metabolic vulnerability and might represent a new therapeutic strategy for these patients.

Use of double-stranded RNA targeting β2 divergent nicotinic acetylcholine receptor subunit to control pea aphid Acyrthosiphon pisum at larval and adult stages

BACKGROUND

In recent years, the use of the RNA interference technology (RNAi) has emerged as one of the new strategies for species-specific control of insect pests. Its specificity depends on the distinctiveness of the target gene sequence for a given species. In this work, we assessed in the pea aphid Acyrthosiphon pisum (A. pisum) the use of a double-stranded RNA (dsRNA) that targets the β2 divergent nicotinic acetylcholine receptor (nAChR) subunit (dsRNA-β2), which shares low sequence identity with other subunits, to control populations of this pest at different developmental stages. Because nAChRs are targeted by neonicotinoid insecticides such as imidacloprid, we also assessed the effect of dsRNA-β2 coupled to this insecticide on aphid survival. Finally, because the effect of a control agent on beneficial insect must be considered before any use of new pest management strategies, the acute toxicity of dsRNA-β2 combined with imidacloprid was evaluated on honeybee Apis mellifera.

RESULTS

In this work, we demonstrated that dsRNA-β2 alone has an insecticidal effect on aphid larvae and adults. Moreover, dsRNA-β2 and imidacloprid effects on aphid larvae and adults were additive, meaning that dsRNA-β2 did not alter the efficacy of imidacloprid on these two developmental stages. Also, no obvious acute toxicity on Apis mellifera was reported.

CONCLUSION

Using RNAi that targets β2 divergent nAChR subunit is effective alone or combined with imidacloprid to control A. pisum at larval and adult stages. Because no obvious Apis mellifera mortality has been reported, this RNAi-based pest management strategy should be considered to control insect pest. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Stability of the protactinium(V) mono-oxo cation probed by first-principle calculations

This study explores the distinctive behavior of protactinium (Z=91) within the actinide series. In contrast to neighboring elements like uranium or plutonium, protactinium in the pentavalent state diverges by not forming the typical dioxo protactinyl moiety PaO2 + in aqueous phase. Instead, it manifests as a monooxo PaO3+ cation or a Pa5+ . Employing first-principle calculations with implicit and explicit solvation, we investigate two stoichiometrically equivalent neutral complexes: PaO(OH)2 (X)(H2 O) and Pa(OH)4 (X), where X represents various monodentate and bidentate ligands. Calculating the Gibbs free energy for the reaction PaO(OH)2 (X)(H2 O)→Pa(OH)4 (X), we find that the PaO(OH)2 (X)(H2 O) complex is stabilized with Cl- , Br- , I- , NCS- , NO3 - , and SO4 2- ligands, while it is not favored with OH- , F- , and C2 O4 2- ligands. Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbital (NBO) methods reveal the Pa mono-oxo bond as a triple bond, with significant contributions from the 5f and 6d shells. Covalency of the Pa mono-oxo bond increases with certain ligands, such as Cl- , Br- , I- , NCS- , and NO3 - . These findings elucidate protactinium's unique chemical attributes and provide insights into the conditions supporting the stability of relevant complexes.

A model of hemodialysis after acute kidney injury in rats

BACKGROUND

Acute kidney injury (AKI) is frequent among critically ill patients. Renal replacement therapy (RRT) is often required to deal with severe complications of AKI. This technique is however associated with side effects such as hemodynamic instability and delayed renal recovery. In this study, we aimed to describe a novel model of hemodialysis in rats with AKI and depict a dialysis membrane performance.

METHODS

Eighteen Sprague-Dawley rats received 0.75% adenine-rich diet to induce AKI. After 2 weeks, nine underwent an arterio-venous extracorporeal circulation (ECC) (ECC group) for 2 h without a dialysis membrane on the circuit and nine received a hemodialysis session (HD group) for 2 h with an ECC circuit. All rats were hemodynamically monitored, and glomerular filtration rate (GFR) was measured by transcutaneous fluorescence after the injection of FITC-Sinistrin. Blood samples were collected at different time points to assess serum creatinine and serum urea concentrations and to determine the Kt/V. Sinistrin concentration was also quantified in both plasma and dialysis effluent.

RESULTS

After 2 weeks of adenine-rich diet, rats exhibited a decrease in GFR. Both serum urea and serum creatinine concentrations increased in the ECC group but remained stable in the HD group. We found no significant difference in serum creatinine and serum urea concentrations between groups. At the end of experiments, mean serum urea was 36.7 mmol/l (95%CI 19.7-46.9 mmol/l) and 23.6 mmol/l (95%CI 15.2-33.5 mmol/l) in the ECC and HD groups, respectively (p = 0.15), and mean serum creatinine concentration was 158.0 µmol/l (95%CI 108.1-191.9 µmol/l) and 114.0 µmol/l (95%CI 90.2-140.9 µmol/l) in the ECC and HD groups, respectively (p = 0.11). The Kt/V of the model was estimated at 0.23. Sinistrin quantity in the ultrafiltrate raised steadily during the dialysis session. After 2 h, the median quantity was 149.2 µg (95% CI 99.7-250.3 µg).

CONCLUSIONS

This hemodialysis model is an acceptable compromise between the requirement of hemodynamic tolerance which implies reducing extracorporeal blood volume (using a small dialyzer) and the demonstration that diffusion of molecules through the membrane is achieved.

Processing of the same narrative stimuli elicits common functional connectivity dynamics between individuals

It has been suggested that conscious experience is linked to the richness of brain state repertories, which change in response to environmental and internal stimuli. High-level sensory stimulation has been shown to alter local brain activity and induce neural synchrony across participants. However, the dynamic interplay of cognitive processes underlying moment-to-moment information processing remains poorly understood. Using naturalistic movies as an ecological laboratory model of the real world, here we investigate how the processing of complex naturalistic stimuli alters the dynamics of brain network interactions and how these in turn support information processing. Participants underwent fMRI recordings during movie watching, scrambled movie watching, and resting. By measuring the phase-synchrony between different brain networks, we analyzed whole-brain connectivity patterns. Our finding revealed distinct connectivity patterns associated with each experimental condition. We found higher synchronization of brain patterns across participants during movie watching compared to rest and scrambled movie conditions. Furthermore, synchronization levels increased during the most engaging parts of the movie. The synchronization dynamics among participants were associated with suspense; scenes with higher levels of suspense induced greater synchronization. These results suggest that processing the same high-level information elicits common neural dynamics across individuals, and that whole-brain functional connectivity tracks variations in processed information and subjective experience.

Genomic content of wheat has a higher influence than plant domestication status on the ability to interact with Pseudomonas plant growth-promoting rhizobacteria

Plant evolutionary history has had profound effects on belowground traits, which is likely to have impacted the ability to interact with microorganisms, but consequences on root colonization and gene expression by plant growth-promoting rhizobacteria (PGPR) remain poorly understood. Here, we tested the hypothesis that wheat genomic content and domestication are key factors determining the capacity for PGPR interaction. Thus, 331 wheat representatives from eight Triticum or Aegilops species were inoculated under standardized conditions with the generalist PGPR Pseudomonas ogarae F113, using an autofluorescent reporter system for monitoring F113 colonization and expression of phl genes coding for the auxinic inducing signal 2,4-diacetylphloroglucinol. The interaction with P. ogarae F113 was influenced by ploidy level, presence of genomes AA, BB, DD, and domestication. While root colonization was higher for hexaploid and tetraploid species, and phl expression level higher for hexaploid wheat, the diploid Ae. tauschii displayed higher phl induction rate (i.e., expression:colonisation ratio) on roots. However, a better potential of interaction with F113 (i.e., under non-stress gnotobiotic conditions) did not translate, after seed inoculation, into better performance of wheat landraces in non-sterile soil under drought. Overall, results showed that domestication and especially plant genomic content modulate the PGPR interaction potential of wheats.

Artificial Molecular Ratchets: Tools Enabling Endergonic Processes

Non-equilibrium chemical systems underpin multiple domains of contemporary interest, including supramolecular chemistry, molecular machines, systems chemistry, prebiotic chemistry, and energy transduction. Experimental chemists are now pioneering the realization of artificial systems that can harvest energy away from equilibrium. In this tutorial Review, we provide an overview of artificial molecular ratchets: the chemical mechanisms enabling energy absorption from the environment. By focusing on the mechanism type-rather than the application domain or energy source-we offer a unifying picture of seemingly disparate phenomena, which we hope will foster progress in this fascinating domain of science.

Natural variability in bee brain size and symmetry revealed by micro-CT imaging and deep learning

Analysing large numbers of brain samples can reveal minor, but statistically and biologically relevant variations in brain morphology that provide critical insights into animal behaviour, ecology and evolution. So far, however, such analyses have required extensive manual effort, which considerably limits the scope for comparative research. Here we used micro-CT imaging and deep learning to perform automated analyses of 3D image data from 187 honey bee and bumblebee brains. We revealed strong inter-individual variations in total brain size that are consistent across colonies and species, and may underpin behavioural variability central to complex social organisations. In addition, the bumblebee dataset showed a significant level of lateralization in optic and antennal lobes, providing a potential explanation for reported variations in visual and olfactory learning. Our fast, robust and user-friendly approach holds considerable promises for carrying out large-scale quantitative neuroanatomical comparisons across a wider range of animals. Ultimately, this will help address fundamental unresolved questions related to the evolution of animal brains and cognition.

Efficacy and safety of clonidine for the treatment of impulse control disorder in Parkinson's disease: a multicenter, parallel, randomised, double-blind, Phase 2b Clinical trial

BACKGROUND

Impulse control disorders (ICDs) are frequently encountered in Parkinson's disease (PD).

OBJECTIVES

We aimed to assess whether clonidine, an α2-adrenergic receptor agonist, would improve ICDs.

METHODS

We conducted a multicentre trial in five movement disorder departments. Patients with PD and ICDs (n = 41) were enrolled in an 8-week, randomised (1:1), double-blind, placebo-controlled study of clonidine (75 μg twice a day). Randomisation and allocation to the trial group were carried out by a central computer system. The primary outcome was the change at 8 weeks in symptom severity using the Questionnaire for Impulsive-Compulsive Disorders in Parkinson's Disease-Rating Scale (QUIP-RS) score. A reduction of the most elevated subscore of the QUIP-RS of more than 3 points without any increase in the other QUIP-RS dimension defined success.

RESULTS

Between 15 May 2019 and 10 September 2021, 19 patients in the clonidine group and 20 patients in the placebo group were enrolled. The proportion difference of success in reducing QUIP-RS at 8 weeks, was 7% (one-sided upper 90% CI 27%) with 42.1% of success in the clonidine group and 35.0% in the placebo group. Compared to patients in the placebo group, patients in the clonidine group experienced a greater reduction in the total QUIP-RS score at 8 weeks (11.0 points vs. 3.6).

DISCUSSION

Clonidine was well tolerated but our study was not enough powerful to demonstrate significant superiority compared to placebo in reducing ICDs despite a greater reduction of total QUIP score at 8 weeks. A phase 3 study should be conducted.

TRIAL REGISTRATION

The study was registered (NCT03552068) on clinicaltrials.gov on June 11, 2018.

A systematic approach identifies p53-DREAM pathway target genes associated with blood or brain abnormalities

p53 (encoded by Trp53) is a tumor suppressor, but mouse models have revealed that increased p53 activity may cause bone marrow failure, likely through dimerization partner, RB-like, E2F4/E2F5 and MuvB (DREAM) complex-mediated gene repression. Here, we designed a systematic approach to identify p53-DREAM pathway targets, the repression of which might contribute to abnormal hematopoiesis. We used Gene Ontology analysis to study transcriptomic changes associated with bone marrow cell differentiation, then chromatin immunoprecipitation-sequencing (ChIP-seq) data to identify DREAM-bound promoters. We next created positional frequency matrices to identify evolutionary conserved sequence elements potentially bound by DREAM. The same approach was developed to find p53-DREAM targets associated with brain abnormalities, also observed in mice with increased p53 activity. Putative DREAM-binding sites were found for 151 candidate target genes, of which 106 are mutated in a blood or brain genetic disorder. Twenty-one DREAM-binding sites were tested and found to impact gene expression in luciferase assays, to notably regulate genes mutated in dyskeratosis congenita (Rtel1), Fanconi anemia (Fanca), Diamond-Blackfan anemia (Tsr2), primary microcephaly [Casc5 (or Knl1), Ncaph and Wdr62] and pontocerebellar hypoplasia (Toe1). These results provide clues on the role of the p53-DREAM pathway in regulating hematopoiesis and brain development, with implications for tumorigenesis.

Novel, computational IgE-clustering in a population-based cross-sectional study: Mapping the allergy burden

BACKGROUND

Even though the prevalence of allergies is increasing, population-based data are still scarce. As a read-out for chronic inflammatory information, new methods are needed to integrate individual biological measurements and lifestyle parameters to mitigate the consequences and costs of allergic burden for society.

METHODS

More than 480.000 data points were collected from 1462 Luxembourg adults during the representative, cross-sectional European Health Examination Survey, spanning health and lifestyle reports. Deep IgE-profiles based on unsupervised clustering were correlated with data of the health survey.

FINDINGS

42.6% of the participants reported a physician-diagnosed allergy and 44% were found to be IgE-positive to at least one allergen or extract. The main sensitization sources were tree pollens followed by grass pollens and mites (52.4%, 51.8% and 40.3% of sensitized participants respectively), suggesting seasonal as well as perennial burden. The youngest group of participants (25-34 years old) showed the highest burden of sensitization, with 18.2% of them having IgE to 10 or more allergen groups. Unsupervised clustering revealed that the biggest cluster of 24.4% of participants was also the one with the highest medical need, marked by their multi-sensitization to respiratory sources.

INTERPRETATION

Our novel approach to analyzing large biosample datasets together with health information allows the measurement of the chronic inflammatory disease burden in the general population and led to the identification of the most vulnerable groups in need of better medical care.

Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

BACKGROUND

We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in ~ 80% of cases.

METHODS

We report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded.

RESULTS

No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5-528.7, P = 1.1 × 10-4) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR = 3.70[95%CI 1.3-8.2], P = 2.1 × 10-4). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1-2635.4], P = 3.4 × 10-3), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR = 4.40[9%CI 2.3-8.4], P = 7.7 × 10-8). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD] = 43.3 [20.3] years) than the other patients (56.0 [17.3] years; P = 1.68 × 10-5).

CONCLUSIONS

Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.

The prophage-encoded transcriptional regulator AppY has pleiotropic effects on E. coli physiology

Bacterial genome diversity is influenced by prophages, which are viral genomes integrated into the bacterial chromosome. Most prophage genes are silent but those that are expressed can provide unexpected properties to their host. Using as a model E. coli K-12 that carries 9 defective prophages in its genome, we aimed at highlighting the impact of genes encoded by prophages on host physiology. We focused our work on AppY, a transcriptional regulator encoded on the DLP12 prophage. By performing RNA-Seq experiments, we showed that AppY production modulates the expression of more than 200 genes. Among them, 11 were identified by ChIP-Seq as direct AppY targets. AppY directly and positively regulates several genes involved in the acid stress response including the master regulator gene gadE but also nhaR and gadY, two genes important for biofilm formation. Moreover, AppY indirectly and negatively impacts bacterial motility by favoring the degradation of FlhDC, the master regulator of the flagella biosynthesis. As a consequence of these regulatory effects, AppY increases acid stress resistance and biofilm formation while also causing a strong defect in motility. Our research shed light on the importance to consider the genetic interactions occurring between prophages and bacteria to fully understand bacterial physiology. It also highlights how a prophage-encoded transcriptional regulator integrates in a complex manner into the host regulatory network and how it benefits its host, allowing it to cope with changing environmental conditions.

Sediment reworking of intertidal sediments by the benthic foraminifera Haynesina germanica: the importance of motion behaviour and densities

This study aimed to describe for the first time the vertical motion behaviour of the intertidal foraminifera Haynesina germanica and its contribution to bioturbation. Its infaunal behaviour leads to the creation of a one-end tube within the first centimetre of sediment. In addition, a vertical trail following behaviour was described for the first time in foraminifera, which may be linked to the sustainability of the biogenic sedimentary structures. As a consequence, H. germanica produces a vertical transport of both mud and fine sediment fractions similarly to the sediment reworking mode reported for gallery-diffusor benthic species. This finding allows us to refine the bioturbating mode of H. germanica, previously classified as surficial biodiffusor. Furthermore, sediment reworking intensity appeared to be dependent on the foraminiferal density. H. germanica would adapt its motion behaviour to deal with the intra-specific competition for food and space that may occur when density increases. Consequently, this behavioural modification would affect both the species and the individual contribution to sediment reworking processes. In fine, sediment reworking in H. germanica may further contribute to the bioirrigation of intertidal sediments, which has implications for oxygen availability in sediments and on aerobic microbial processes involved in carbon and nutrient cycling at the sediment-water interface.

An optimized electrotransformation protocol for Lactobacillus jensenii

Engineered bacteria are promising candidates for in situ detection and treatment of diseases. The female uro-genital tract presents several pathologies, such as sexually transmitted diseases or genital cancer, that could benefit from such technology. While bacteria from the gut microbiome are increasingly engineered, the use of chassis isolated from the female uro-genital resident flora has been limited. A major hurdle to implement the experimental throughput required for efficient engineering in these non-model bacteria is their low transformability. Here we report an optimized electrotransformation protocol for Lactobacillus jensenii, one the most widespread species across vaginal microflora. Starting from classical conditions, we optimized buffers, electric field parameters, cuvette type and DNA quantity to achieve an 80-fold improvement in transformation efficiency, with up to 3.5·103 CFUs/μg of DNA in L. jensenii ATCC 25258. We also identify several plasmids that are maintained and support reporter gene expression in L. jensenii. Finally, we demonstrate that our protocol provides increased transformability in three independent clinical isolates of L. jensenii. This work will facilitate the genetic engineering of L. jensenii and enable its use for addressing challenges in gynecological healthcare.

On the function of flower number: disentangling fertility from pollinator-mediated selection

In animal-pollinated angiosperms, the 'male-function' hypothesis claims that male reproductive success (RS) should benefit from large floral displays, through pollinator attraction, while female RS is expected to be mainly limited by resource availability. As appealing as this theory might be, studies comparing selection strength on flower number in both sexes rarely document the expected asymmetry. This discrepancy could arise because flower number impacts both pollinator attraction and overall gamete number. In this study, we artificially manipulate floral displays to disentangle the fertility versus pollinator attraction components of selection, both in terms of mating and RS. In females, flower number was under strong fertility selection, as predicted in the absence of pollen limitation. By contrast, in males, flower number was mainly under sexual selection, which in turn increased male RS. However, these selection patterns were not different in males with artificially increased floral displays. This suggests that sexual selection acting on flower number in males does not occur because flower number increases pollinator attraction, but rather because more pollen is available to disperse on more mates. Our study illustrates the power of disentangling various components of selection with potentially sex-specific effects for understanding the evolution of sexual dimorphism.

Alix is required for activity-dependent bulk endocytosis at brain synapses

In chemical synapses undergoing high frequency stimulation, vesicle components can be retrieved from the plasma membrane via a clathrin-independent process called activity-dependent bulk endocytosis (ADBE). Alix (ALG-2-interacting protein X/PDCD6IP) is an adaptor protein binding to ESCRT and endophilin-A proteins which is required for clathrin-independent endocytosis in fibroblasts. Alix is expressed in neurons and concentrates at synapses during epileptic seizures. Here, we used cultured neurons to show that Alix is recruited to presynapses where it interacts with and concentrates endophilin-A during conditions triggering ADBE. Using Alix knockout (ko) neurons, we showed that this recruitment, which requires interaction with the calcium-binding protein ALG-2, is necessary for ADBE. We also found that presynaptic compartments of Alix ko hippocampi display subtle morphological defects compatible with flawed synaptic activity and plasticity detected electrophysiologically. Furthermore, mice lacking Alix in the forebrain undergo less seizures during kainate-induced status epilepticus and reduced propagation of the epileptiform activity. These results thus show that impairment of ADBE due to the lack of neuronal Alix leads to abnormal synaptic recovery during physiological or pathological repeated stimulations.

The adaptor protein Alix (PDCD6IP) is necessary for membrane shaping underlying various biological processes including endocytosis. This study shows that Alix mediates activity-dependent bulk endocytosis and is required for correct synaptic physiology under normal and pathological conditions.

Social inequalities and dynamics of the early COVID-19 epidemic: a prospective cohort study in France

OBJECTIVE

Although social inequalities in COVID-19 mortality by race, gender and socioeconomic status are well documented, less is known about social disparities in infection rates and their shift over time. We aim to study the evolution of social disparities in infection at the early stage of the epidemic in France with regard to the policies implemented.

DESIGN

Random population-based prospective cohort.

SETTING

From May to June 2020 in France.

PARTICIPANTS

Adults included in the Epidémiologie et Conditions de Vie cohort (n=77 588).

MAIN OUTCOME MEASURES

Self-reported anosmia and/or ageusia in three categories: no symptom, during the first epidemic peak (in March 2020) or thereafter (during lockdown).

RESULTS

In all, 2052 participants (1.53%) reported anosmia/ageusia. The social distribution of exposure factors (density of place of residence, overcrowded housing and working outside the home) was described. Multinomial regressions were used to identify changes in social variables (gender, class and race) associated with symptoms of anosmia/ageusia. Women were more likely to report symptoms during the peak and after. Racialised minorities accumulated more exposure risk factors than the mainstream population and were at higher risk of anosmia/ageusia during the peak and after. By contrast, senior executive professionals were the least exposed to the virus with the lower rate of working outside the home during lockdown. They were more affected than lower social classes at the peak of the epidemic, but this effect disappeared after the peak.

CONCLUSION

The shift in the social profile of the epidemic was related to a shift in exposure factors under the implementation of a stringent stay-at-home order. Our study shows the importance to consider in a dynamic way the gender, socioeconomic and race direct and indirect effects of the COVID-19 pandemic, notably to implement policies that do not widen health inequalities.

Modelling the effects of the repellent scent marks of pollinators on their foraging efficiency and the plant-pollinator community

Pollinator insects forage in complex and unpredictable resource landscapes, often using social information from congeneric individuals to acquire knowledge about their environment. It has long been recognized that this process allows them to exploit floral resources more efficiently and thus increase individual fitness. However, by creating correlations between the behaviors of pollinators within a population, this could also indirectly influence the entire plant-pollinator community. One type of social information used by pollinators is the scent mark left on the corolla of flowers by previous visitors, which can be used as a cue to avoid recently depleted resources. We developed a spatially explicit agent-based model to examine the effects, at both individual and community levels, of pollinators using these scent marks. The model simulates a population of pollinators foraging on flowers in a continuous 2D space in which we can vary the density of pollinators. We showed that the use of scent marks as a source of information significantly increased the foraging efficiency of pollinators except when competition between pollinators was very low. At the community level, this also resulted in a marked homogenization between floral resources within the landscape: in the absence of scent marks, the coefficient of variation of the remaining nectar quantity per flower strongly increased with greater pollinator competition, but it remained low at all levels of competition when scent marks were used by the pollinators. Finally, the use of scent marks markedly decreased the number of pollinator flower visits, especially at high levels of pollinator competition, which can potentially reduce the pollination service.

Emotional behavior and brain anatomy of the mdx52 mouse model of Duchenne muscular dystrophy

The exon-52-deleted mdx52 mouse is a critical model of Duchenne muscular dystrophy (DMD), as it features a deletion in a hotspot region of the DMD gene, frequently mutated in patients. Deletion of exon 52 impedes expression of several brain dystrophins (Dp427, Dp260 and Dp140), thus providing a key model for studying the cognitive impairment associated with DMD and testing rescuing strategies. Here, using in vivo magnetic resonance imaging and neurohistology, we found no gross brain abnormalities in mdx52 mice, suggesting that the neural dysfunctions in this model are likely at the level of brain cellular functionalities. Then, we investigated emotional behavior and fear learning performance of mdx52 mice compared to mdx mice that only lack Dp427 to focus on behavioral phenotypes that could be used in future comparative preclinical studies. mdx52 mice displayed enhanced anxiety and a severe impairment in learning an amygdala-dependent Pavlovian association. These replicable behavioral outcome measures are reminiscent of the internalizing problems reported in a quarter of DMD patients, and will be useful for preclinical estimation of the efficacy of treatments targeting brain dysfunctions in DMD.

Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis

BACKGROUND

The ancestral presence of epithelia in Metazoa is no longer debated. Porifera seem to be one of the best candidates to be the sister group to all other Metazoa. This makes them a key taxon to explore cell-adhesion evolution on animals. For this reason, several transcriptomic, genomic, histological, physiological and biochemical studies focused on sponge epithelia. Nevertheless, the complete and precise protein composition of cell-cell junctions and mechanisms that regulate epithelial morphogenetic processes still remain at the center of attention.

RESULTS

To get insights into the early evolution of epithelial morphogenesis, we focused on morphogenic characteristics of the homoscleromorph sponge Oscarella lobularis. Homoscleromorpha are a sponge class with a typical basement membrane and adhaerens-like junctions unknown in other sponge classes. We took advantage of the dynamic context provided by cell dissociation-reaggregation experiments to explore morphogenetic processes in epithelial cells in a non-bilaterian lineage by combining fluorescent and electron microscopy observations and RNA sequencing approaches at key time-points of the dissociation and reaggregation processes.

CONCLUSIONS

Our results show that part of the molecular toolkit involved in the loss and restoration of epithelial features such as cell-cell and cell-matrix adhesion is conserved between Homoscleromorpha and Bilateria, suggesting their common role in the last common ancestor of animals. In addition, sponge-specific genes are differently expressed during the dissociation and reaggregation processes, calling for future functional characterization of these genes.

Pyridazinone derivatives as potential anti-inflammatory agents: synthesis and biological evaluation as PDE4 inhibitors

Cyclic nucleotide phosphodiesterase type 4 (PDE4), which controls the intracellular level of cyclic adenosine monophosphate (cAMP), has aroused scientific attention as a suitable target for anti-inflammatory therapy of respiratory diseases. This work describes the development and characterization of pyridazinone derivatives bearing an indole moiety as potential PDE4 inhibitors and their evaluation as anti-inflammatory agents. Among these derivatives, 4-(5-methoxy-1H-indol-3-yl)-6-methylpyridazin-3(2H)-one possesses promising activity, and selectivity towards PDE4B isoenzymes and is able to regulate potent pro-inflammatory cytokine and chemokine production by human primary macrophages.

Experimental Type 2 Diabetes Differently Impacts on the Select Functions of Bone Marrow-Derived Multipotent Stromal Cells

Bone marrow-derived multipotent stromal cells (BMMSCs) represent an attractive therapeutic modality for cell therapy in type 2 diabetes mellitus (T2DM)-associated complications. T2DM changes the bone marrow environment; however, its effects on BMMSC properties remain unclear. The present study aimed at investigating select functions and differentiation of BMMSCs harvested from the T2DM microenvironment as potential candidates for regenerative medicine. BMMSCs were obtained from Zucker diabetic fatty (ZDF; an obese-T2DM model) rats and their lean littermates (ZL; controls), and cultured under normoglycemic conditions. The BMMSCs derived from ZDF animals were fewer in number, with limited clonogenicity (by 2-fold), adhesion (by 2.9-fold), proliferation (by 50%), migration capability (by 25%), and increased apoptosis rate (by 2.5-fold) compared to their ZL counterparts. Compared to the cultured ZL-BMMSCs, the ZDF-BMMSCs exhibited (i) enhanced adipogenic differentiation (increased number of lipid droplets by 2-fold; upregulation of the Pparg, AdipoQ, and Fabp genes), possibly due to having been primed to undergo such differentiation in vivo prior to cell isolation, and (ii) different angiogenesis-related gene expression in vitro and decreased proangiogenic potential after transplantation in nude mice. These results provided evidence that the T2DM environment impairs BMMSC expansion and select functions pertinent to their efficacy when used in autologous cell therapies.

The long developmental trajectory of body representation plasticity following tool use

Humans evolution is distinctly characterized by their exquisite mastery of tools, allowing them to shape their environment in more elaborate ways compared to other species. This ability is present ever since infancy and most theories indicate that children become proficient with tool use very early. In adults, tool use has been shown to plastically modify metric aspects of the arm representation, as indexed by changes in movement kinematics. To date, whether and when the plastic capability of updating the body representation develops during childhood remains unknown. This question is particularly important since body representation plasticity could be impacted by the fact that the human body takes years to achieve a stable metric configuration. Here we assessed the kinematics of 90 young participants (8-21 years old) required to reach for an object before and after tool use, as a function of their pubertal development. Results revealed that tool incorporation, as indexed by the adult typical kinematic pattern, develops very slowly and displays a u-shaped developmental trajectory. From early to mid puberty, the changes in kinematics following tool use seem to reflect a shortened arm representation, opposite to what was previously reported in adults. This pattern starts reversing after mid puberty, which is characterized by the lack of any kinematics change following tool use. The typical adult-like pattern emerges only at late puberty, when body size is stable. These findings reveal the complex dynamics of tool incorporation across development, possibly indexing the transition from a vision-based to a proprioception-based body representation plasticity.

How much do we know about the effectiveness of warm-up intervention on work related musculoskeletal disorders, physical and psychosocial functions: protocol for a systematic review

INTRODUCTION

Work-related musculoskeletal disorders (WMSDs) are a growing worldwide burden and effective interventions to prevent them are needed. Physical activity at the workplace is now recognised as a relevant component of WMSDs prevention. Along these lines, warm-up interventions are now offered in a large number of companies to manage WMSDs. Although benefits of warm-up have been previously documented in sports context, to the best of our knowledge, the effectiveness of such intervention in workplaces still remains to be established. Within this context, the aim of the present review is to identify from published literature the available evidence regarding the effects of warm-up on WMSDs and physical and psychosocial functions.

METHODS

The following electronic databases will be searched (from inception onwards to June 2020): Cochrane Central Register of Controlled Trials, PubMed (Medline), Web of Science and Physiotherapy Evidence Database. Randomised and non-randomised controlled studies will be included in this review. Participants should be adult employees without specific comorbidities. Interventions should include a warm-up physical intervention in real-workplaces. The primary outcomes will be pain, discomfort or fatigue. The secondary outcomes will be job control or motivation at work. This review will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and two team members will independently screen all citations, full-text articles and abstract data. A systematic narrative synthesis will be provided with information presented in the text and tables to summarise the characteristics and findings of the included studies.

ETHICS AND DISSEMINATION

The approval of an ethical committee is not required. All the included studies will comply with the current ethical standards. The results of this review will summarise the effects of warm-up intervention on WMSDs, physical or psychosocial functions. This information could help professionals in decision making related to the use of these interventions to prevent WMSDs. Findings will be disseminated to academic audiences through peer-reviewed publications, as well as to policy-makers.

PROSPERO REGISTRATION NUMBER

CRD42019137211.

Fungal Shaker-like channels beyond cellular K+ homeostasis: A role in ectomycorrhizal symbiosis between Hebeloma cylindrosporum and Pinus pinaster

Potassium (K+) acquisition, translocation and cellular homeostasis are mediated by various membrane transport systems in all organisms. We identified and described an ion channel in the ectomycorrhizal fungus Hebeloma cylindrosporum (HcSKC) that harbors features of animal voltage-dependent Shaker-like K+ channels, and investigated its role in both free-living hyphae and symbiotic conditions. RNAi lines affected in the expression of HcSKC were produced and used for in vitro mycorrhizal assays with the maritime pine as host plant, under standard or low K+ conditions. The adaptation of H. cylindrosporum to the downregulation of HcSKC was analyzed by qRT-PCR analyses for other K+-related transport proteins: the transporters HcTrk1, HcTrk2, and HcHAK, and the ion channels HcTOK1, HcTOK2.1, and HcTOK2.2. Downregulated HcSKC transformants displayed greater K+ contents at standard K+ only. In such conditions, plants inoculated with these transgenic lines were impaired in K+ nutrition. Taken together, these results support the hypothesis that the reduced expression of HcSKC modifies the pool of fungal K+ available for the plant and/or affects its symbiotic transfer to the roots. Our study reveals that the maintenance of K+ transport in H. cylindrosporum, through the regulation of HcSKC expression, is required for the K+ nutrition of the host plant.

First trimester screening for pre-eclampsia and intrauterine growth restriction using three-dimensional Doppler angiography (SPIRIT): protocol for a multicentre prospective study in nulliparous pregnant women

INTRODUCTION

Pre-eclampsia (PE) and intrauterine growth restriction (IUGR) are two major pregnancy complications, related to chronic uteroplacental hypoperfusion. Nowadays, there is no screening or diagnostic test for uteroplacental vascularisation deficiency in pregnant women. Since 2004, 3 three-imensional power Doppler (3DPD) angiography has been used for the evaluation of uteroplacental vascularisation and three vascular indices are usually calculated: Vascularisation Index (VI), Flow Index (FI) and vascularisation-FI (VFI). A high intraobserver and interobserver reproducibility and a potential interest for placental function study were reported by our team and others.The main objective of our study is to determine differences in 3DPD indices at first trimester between pregnancies defined at their outcome as uncomplicated pregnancy, PE (mild and severe) and IUGR in nulliparous women.

METHODS AND ANALYSIS

This is a national multicentre prospective cohort study conducted in four French maternity units. We expect to include 2200 women in a period of 36 months. The nulliparous pregnant women will be recruited during their first trimester consultation (11-13+6 gestation week (GW)).The 3DPD and uterine artery Doppler acquisition will be included in the current routine 11-13+6 GW ultrasound. Also, additional blood samples will be taken for biomarker analysis (PAPP-A and P1GF) and biological collection. Uteroplacental VIs (FI and VFI) will be measured. For each subgroup (uncomplicated pregnancy, PE and IUGR), mean values in 3DPD indices will be computed and compared using a pairwise t test with a Bonferroni correction p value adjustment.

ETHICS AND DISSEMINATION

The study was approved by the French Ethics Committee, the Comité de Protection des Personnes SUD MEDITERRANEE IV on 13 February 2018 with reference number 17 12 03. The results of this study will be published in a peer-reviewed journal and will be presented at relevant conferences.

TRIAL REGISTRATION NUMBER

NCT03342014; Pre-results. PHRCN-16-0567.

Pattern regulation in a regenerating jellyfish

Jellyfish, with their tetraradial symmetry, offer a novel paradigm for addressing patterning mechanisms during regeneration. Here we show that an interplay between mechanical forces, cell migration and proliferation allows jellyfish fragments to regain shape and functionality rapidly, notably by efficient restoration of the central feeding organ (manubrium). Fragmentation first triggers actomyosin-powered remodeling that restores body umbrella shape, causing radial smooth muscle fibers to converge around 'hubs' which serve as positional landmarks. Stabilization of these hubs, and associated expression of Wnt6, depends on the configuration of the adjoining muscle fiber 'spokes'. Stabilized hubs presage the site of the manubrium blastema, whose growth is Wnt/β-catenin dependent and fueled by both cell proliferation and long-range cell recruitment. Manubrium morphogenesis is modulated by its connections with the gastrovascular canal system. We conclude that body patterning in regenerating jellyfish emerges mainly from local interactions, triggered and directed by the remodeling process.

Increased temperature has no consequence for behavioral manipulation despite effects on both partners in the interaction between a crustacean host and a manipulative parasite

Parasites alter many traits of their hosts. In particular, parasites known as "manipulative" may increase their probability of transmission by inducing phenotypic alterations in their intermediate hosts. Although parasitic-induced alterations can modify species' ecological roles, the proximate factors modulating this phenomenon remain poorly known. As temperature is known to affect host-parasite associations, understanding its precise impact has become a major challenge in a context of global warming. Gammarids are ecologically important freshwater crustaceans and serve as intermediate hosts for several acanthocephalan species. These parasites induce multiple effects on gammarids, including alterations of their behavior, ultimately leading to modifications in their functional role. Here, experimental infections were used to assess the effect of two temperatures on several traits of the association between Gammarus pulex and its acanthocephalan parasite Pomphorhynchus laevis. Elevated temperature affected hosts and parasites in multiple ways (decreased host survival, increased gammarids activity, faster parasites development and proboscis eversion). However, behavioral manipulation was unaffected by temperature. These results suggest that predicted change in temperature may have little consequences on the trophic transmission of parasites through changes in manipulation, although it may modify it through increased infection success and faster parasites development.

Comparison of single- and multi-trait approaches to identify best wild candidates for aquaculture shows that the simple way fails

In agriculture, diversifying production implies picking up, in the wild biodiversity, species or populations that can be domesticated and fruitfully produced. Two alternative approaches are available to highlight wild candidate(s) with high suitability for aquaculture: the single-trait (i.e. considering a single phenotypic trait and, thus, a single biological function) and multi-trait (i.e. considering multiple phenotypic traits involved in several biological functions) approaches. Although the former is the traditional and the simplest method, the latter could be theoretically more efficient. However, an explicit comparison of advantages and pitfalls between these approaches is lacking to date in aquaculture. Here, we compared the two approaches to identify best candidate(s) between four wild allopatric populations of Perca fluviatilis in standardised aquaculture conditions. Our results showed that the single-trait approach can (1) miss key divergences between populations and (2) highlight different best candidate(s) depending on the trait considered. In contrast, the multi-trait approach allowed identifying the population with the highest domestication potential thanks to several congruent lines of evidence. Nevertheless, such an integrative assessment is achieved with a far more time-consuming and expensive study. Therefore, improvements and rationalisations will be needed to make the multi-trait approach a promising way in the aquaculture development.

Interactions of Calcium with Chlorogenic and Rosmarinic Acids: An Experimental and Theoretical Approach

Chlorogenic (CA) and rosmarinic (RA) acids are two natural bioactive hydroxycinnamic acids whose antioxidant properties can be modulated by the chelation of metal ions. In this work, the interactions of these two carboxylic phenols with calcium ions and the impact of such interactions on their antioxidant activity were investigated. UV-Vis absorbance, mass spectroscopy and 1H and 13C liquid NMR were used to identify complexes formed by CA and RA with calcium. Antioxidant activities were measured by the Bois method. Density functional theory (DFT) calculations were performed to evaluate the most stable configurations and correlated with NMR data. Taken together, these data suggest that calcium ions mainly interact with the carboxylate groups of both molecules but that this interaction modifies the reactivity of the catechol groups, especially for RA. These results highlight the complex interplay between metal chelation and antioxidant properties of natural carboxylic phenols.

Metabolic reprograming of LPS-stimulated human lung macrophages involves tryptophan metabolism and the aspartate-arginosuccinate shunt

Lung macrophages (LM) are in the first line of defense against inhaled pathogens and can undergo phenotypic polarization to the proinflammatory M1 after stimulation with Toll-like receptor agonists. The objective of the present work was to characterize the metabolic alterations occurring during the experimental M1 LM polarization. Human LM were obtained from resected lungs and cultured for 24 hrs in medium alone or with 10 ng.mL-1 lipopolysaccharide. Cells and culture supernatants were subjected to extraction for metabolomic analysis with high-resolution LC-MS (HILIC and reverse phase -RP- chromatography in both negative and positive ionization modes) and GC-MS. The data were analyzed with R and the Worklow4Metabolomics and MetaboAnalyst online infrastructures. A total of 8,741 and 4,356 features were detected in the intracellular and extracellular content, respectively, after the filtering steps. Pathway analysis showed involvement of arachidonic acid metabolism, tryptophan metabolism and Krebs cycle in the response of LM to LPS, which was confirmed by the specific quantitation of selected compounds. This refined analysis highlighted a regulation of the kynurenin pathway as well as the serotonin biosynthesis pathway, and an involvement of aspartate-arginosuccinate shunt in the malate production. Macrophages M1 polarization is accompanied by changes in the cell metabolome, with the differential expression of metabolites involved in the promotion and regulation of inflammation and antimicrobial activity. The analysis of this macrophage immunometabolome may be of interest for the understanding of the pathophysiology of lung inflammatory disesases.

Quaternization of Composite Algal/PEI Beads for Enhanced Uranium Sorption-Application to Ore Acidic Leachate

The necessity to recover uranium from dilute solutions (for environmental/safety and resource management) is driving research towards developing new sorbents. This study focuses on the enhancement of U(VI) sorption properties of composite algal/Polyethylenimine beads through the quaternization of the support (by reaction with glycidyltrimethylammonium chloride). The sorbent is fully characterized by FTIR, XPS for confirming the contribution of protonated amine and quaternary ammonium groups on U(VI) binding (with possible contribution of hydroxyl and carboxyl groups, depending on the pH). The sorption properties are investigated in batch with reference to pH effect (optimum value: pH 4), uptake kinetics (equilibrium: 40 min) and sorption isotherms (maximum sorption capacity: 0.86 mmol U g-1). Metal desorption (with 0.5 M NaCl/0.5 M HCl) is highly efficient and the sorbent can be reused for five cycles with limited decrease in performance. The sorbent is successfully applied to the selective recovery of U(VI) from acidic leachate of uranium ore, after pre-treatment (cementation of copper, precipitation of rare earth elements with oxalate, and precipitation of iron). A pure yellow cake is obtained after precipitation of the eluate.

Social intolerance is a consequence, not a cause, of dispersal in spiders

From invertebrates to vertebrates, a wealth of species display transient sociality during their life cycle. Investigating the causes of dispersal in temporary associations is important to better understand population dynamics. It is also essential to identify possible mechanisms involved in the evolutionary transition from transient to stable sociality, which has been documented repeatedly across taxa and typically requires the suppression of dispersal. In many animals, the onset of dispersal during ontogeny coincides with a sharp decline in social tolerance, but the causal relationship still remains poorly understood. Spiders offer relevant models to explore this question, because the adults of the vast majority of species (>48,000) are solitary and aggressive, but juveniles of most (if not all) species are gregarious and display amicable behaviors. We deployed a combination of behavioral, chemical, and modelling approaches in spiderlings of a solitary species to investigate the mechanisms controlling the developmental switch leading to the decline of social cohesion and the loss of tolerance. We show that maturation causes an increase in mobility that is sufficient to elicit dispersal without requiring any change in social behaviors. Our results further demonstrate that social isolation following dispersal triggers aggressiveness in altering the processing of conspecifics’ cues. We thus provide strong evidence that aggression is a consequence, not a cause, of dispersal in spiderlings. Overall, this study highlights the need of extended social interactions to preserve tolerance, which opens new perspectives for understanding the routes to permanent sociality.

Behavioral experiments with the spider Agelena labyrinthica, coupled to computational modelling, show that an increase in mobility with age drives dispersal in gregarious spiderlings of a solitary species and that the subsequent social isolation triggers aggression.

WhoGEM: an admixture-based prediction machine accurately predicts quantitative functional traits in plants

The explosive growth of genomic data provides an opportunity to make increased use of sequence variations for phenotype prediction. We have developed a prediction machine for quantitative phenotypes (WhoGEM) that overcomes some of the bottlenecks limiting the current methods. We demonstrated its performance by predicting quantitative disease resistance and quantitative functional traits in the wild model plant species, Medicago truncatula, using geographical locations as covariates for admixture analysis. The method's prediction reliability equals or outperforms all existing algorithms for quantitative phenotype prediction. WhoGEM analysis produces evidence that variation in genome admixture proportions explains most of the phenotypic variation for quantitative phenotypes.

Music training with Démos program positively influences cognitive functions in children from low socio-economic backgrounds

This study aimed at evaluating the impact of a classic music training program (Démos) on several aspects of the cognitive development of children from low socio-economic backgrounds. We were specifically interested in general intelligence, phonological awareness and reading abilities, and in other cognitive abilities that may be improved by music training such as auditory and visual attention, working and short-term memory and visuomotor precision. We used a longitudinal approach with children presented with standardized tests before the start and after 18 months of music training. To test for pre-to-post training improvements while discarding maturation and developmental effects, raw scores for each child and for each test were normalized relative to their age group. Results showed that Démos music training improved musicality scores, total IQ and Symbol Search scores as well as concentration abilities and reading precision. In line with previous results, these findings demonstrate the positive impact of an ecologically-valid music training program on the cognitive development of children from low socio-economic backgrounds and strongly encourage the broader implementation of such programs in disadvantaged school-settings.

Lipo-chitooligosaccharide signalling blocks a rapid pathogen-induced ROS burst without impeding immunity

Molecular signals released by microbes at the surface of plant roots and leaves largely determine host responses, notably by triggering either immunity or symbiosis. How these signalling pathways cross-talk upon coincident perception of pathogens and symbionts is poorly described in plants forming symbiosis. Nitrogen fixing symbiotic Rhizobia spp. and arbuscular mycorrhizal fungi produce lipo-chitooligosaccharides (LCOs) to initiate host symbiotic programmes. In Medicago truncatula roots, the perception of LCOs leads to reduced efflux of reactive oxygen species (ROS). By contrast, pathogen perception generally triggers a strong ROS burst and activates defence gene expression. Here we show that incubation of M. truncatula seedlings with culture filtrate (CF) of the legume pathogen Aphanomyces euteiches alone or simultaneously with Sinorhizobium meliloti LCOs, resulted in a strong ROS release. However, this response was completely inhibited if CF was added after pre-incubation of seedlings with LCOs. By contrast, expression of immunity-associated genes in response to CF and disease resistance to A. euteiches remained unaffected by LCO treatment of M. truncatula roots. Our findings suggest that symbiotic plants evolved ROS inhibition response to LCOs to facilitate early steps of symbiosis whilst maintaining a parallel defence mechanisms toward pathogens.

Partially Reversible Thermal-Induced Oxidation During a Dehydration Process in an H-bonded Supramolecular System

The thermal behaviour of an H-bonded molecular network A based on [FeII (CN)6 ]4- anions and organic bisamidium cations 12+ was investigated. Heating was found to induce the partial oxidation of [FeII (CN)6 ]4- into [FeIII (CN)6 ]3- , together with a thermochromic effect and also a loss of crystallinity was evidenced from mid and far FT-IR spectroscopic data, XRPD and DSC/TGA analysis. Rehydration also partially reversed the redox reaction and its colour, and after that, a mixture of A with an amorphous phases was observed. FT-IR spectroscopy revealed that the oxidation of Fe(II) was accompanied by a deprotonation of the cation.

bric à brac (bab), a central player in the gene regulatory network that mediates thermal plasticity of pigmentation in Drosophila melanogaster

Drosophila body pigmentation has emerged as a major Evo-Devo model. Using two Drosophila melanogaster lines, Dark and Pale, selected from a natural population, we analyse here the interaction between genetic variation and environmental factors to produce this complex trait. Indeed, pigmentation varies with genotype in natural populations and is sensitive to temperature during development. We demonstrate that the bric à brac (bab) genes, that are differentially expressed between the two lines and whose expression levels vary with temperature, participate in the pigmentation difference between the Dark and Pale lines. The two lines differ in a bab regulatory sequence, the dimorphic element (called here bDE). Both bDE alleles are temperature-sensitive, but the activity of the bDE allele from the Dark line is lower than that of the bDE allele from the Pale line. Our results suggest that this difference could partly be due to differential regulation by AbdB. bab has been previously reported to be a repressor of abdominal pigmentation. We show here that one of its targets in this process is the pigmentation gene tan (t), regulated via the tan abdominal enhancer (t_MSE). Furthermore, t expression is strongly modulated by temperature in the two lines. Thus, temperature sensitivity of t expression is at least partly a consequence of bab thermal transcriptional plasticity. We therefore propose that a gene regulatory network integrating both genetic variation and temperature sensitivity modulates female abdominal pigmentation. Interestingly, both bDE and t_MSE were previously shown to have been recurrently involved in abdominal pigmentation evolution in drosophilids. We propose that the environmental sensitivity of these enhancers has turned them into evolutionary hotspots.

Complex traits such as size or disease susceptibility are typically modulated by both genetic variation and environmental conditions. Model organisms such as fruit flies (Drosophila) are particularly appropriate to analyse the interactions between genetic variation and environmental factors during the development of complex phenotypes. Natural populations carry high genetic variation and can be grown in controlled conditions in the laboratory. Here, we use Drosophila melanogaster female abdominal pigmentation, which is both genetically variable and modulated by the environment (temperature) to dissect this kind of interaction. We show that the pigmentation difference between two inbred fly lines is caused by genetic variation in an enhancer of the bab locus, which encodes two transcription factors controlling abdominal pigmentation. Indeed, this enhancer drives differential expression between the two lines. Interestingly, this enhancer is sensitive to temperature in both lines. We show that the effect of bab on pigmentation is mediated by the pigmentation gene tan (t) that is repressed by bab. Thus, the previously reported temperature-sensitive expression of t is a direct consequence of bab transcriptional plasticity.

Expression of the inactivating deiodinase, Deiodinase 3, in the pre-metamorphic tadpole retina

Thyroid hormone (TH) orchestrates amphibian metamorphosis. Thus, this developmental phase is often used to study TH-dependent responses in specific tissues. However, TH signaling appears early in development raising the question of the control of TH availability in specific cell types prior to metamorphosis. TH availability is under strict temporal and tissue-specific control by deiodinases. We examined the expression of the TH-inactivating enzyme, deiodinase type 3 (D3), during early retinal development. To this end we created a Xenopus laevis transgenic line expressing GFP from the Xenopus dio3 promoter region (pdio3) and followed pdio3-GFP expression in pre-metamorphic tadpoles. To validate retinal GFP expression in the transgenic line as a function of dio3 promoter activity, we used in situ hybridization to compare endogenous dio3 expression to reporter-driven GFP activity. Retinal expression of dio3 increased during pre-metamorphosis through stages NF41, 45 and 48. Both sets of results show dio3 to have cell-specific, dynamic expression in the pre-metamorphic retina. At stage NF48, dio3 expression co-localised with markers for photoreceptors, rods, Opsin-S cones and bipolar neurons. In contrast, in post-metamorphic juveniles dio3 expression was reduced and spatially confined to certain photoreceptors and amacrine cells. We compared dio3 expression at stages NF41 and NF48 with TH-dependent transcriptional responses using another transgenic reporter line: THbZIP-GFP and by analyzing the expression of T3-regulated genes in distinct TH availability contexts. At stage NF48, the majority of retinal cells expressing dio3 were negative for T3 signaling. Notably, most ganglion cells were virtually both dio3-free and T3-responsive. The results show that dio3 can reduce TH availability at the cellular scale. Further, a reduction in dio3 expression can trigger fine-tuned T3 action in cell-type specific maturation at the right time, as exemplified here in photoreceptor survival in the pre-metamorphic retina.

Whole exome sequencing in three families segregating a pediatric case of sarcoidosis

BACKGROUND

Sarcoidosis (OMIM 181000) is a multi-systemic granulomatous disorder of unknown origin. Despite multiple genome-wide association (GWAS) studies, no major pathogenic pathways have been identified to date. To find out relevant sarcoidosis predisposing genes, we searched for de novo and recessive mutations in 3 young probands with sarcoidosis and their healthy parents using a whole-exome sequencing (WES) methodology.

METHODS

From the SARCFAM project based on a national network collecting familial cases of sarcoidosis, we selected three families (trios) in which a child, despite healthy parents, develop the disease before age 15 yr. Each trio was genotyped by WES (Illumina HiSEQ 2500) and we selected the gene variants segregating as 1) new mutations only occurring in affected children and 2) as recessive traits transmitted from each parents. The identified coding variants were compared between the three families. Allelic frequencies and in silico functional results were analyzed using ExAC, SIFT and Polyphenv2 databases. The clinical and genetic studies were registered by the ClinicalTrials.gov - Protocol Registration and Results System (PRS) ( https://clinicaltrials.gov ) receipt under the reference NCT02829853 and has been approved by the ethical committee (CPP LYON SUD EST - 2 - REF IRB 00009118 - September 21, 2016).

RESULTS

We identified 37 genes sharing coding variants occurring either as recessive mutations in at least 2 trios or de novo mutations in one of the three affected children. The genes were classified according to their potential roles in immunity related pathways: 9 to autophagy and intracellular trafficking, 6 to G-proteins regulation, 4 to T-cell activation, 4 to cell cycle and immune synapse, 2 to innate immunity. Ten of the 37 genes were studied in a bibliographic way to evaluate the functional link with sarcoidosis.

CONCLUSIONS

Whole exome analysis of case-parent trios is useful for the identification of genes predisposing to complex genetic diseases as sarcoidosis. Our data identified 37 genes that could be putatively linked to a pediatric form of sarcoidosis in three trios. Our in-depth focus on 10 of these 37 genes may suggest that the formation of the characteristic lesion in sarcoidosis, granuloma, results from combined deficits in autophagy and intracellular trafficking (ex: Sec16A, AP5B1 and RREB1), G-proteins regulation (ex: OBSCN, CTTND2 and DNAH11), T-cell activation (ex: IDO2, IGSF3), mitosis and/or immune synapse (ex: SPICE1 and KNL1). The significance of these findings needs to be confirmed by functional tests on selected gene variants.

Formation of large viroplasms and virulence of Cauliflower mosaic virus in turnip plants depend on the N-terminal EKI sequence of viral protein TAV

Cauliflower mosaic virus (CaMV) TAV protein (TransActivator/Viroplasmin) plays a pivotal role during the infection cycle since it activates translation reinitiation of viral polycistronic RNAs and suppresses RNA silencing. It is also the major component of cytoplasmic electron-dense inclusion bodies (EDIBs) called viroplasms that are particularly evident in cells infected by the virulent CaMV Cabb B-JI isolate. These EDIBs are considered as virion factories, vehicles for CaMV intracellular movement and reservoirs for CaMV transmission by aphids. In this study, focused on different TAV mutants in vivo, we demonstrate that three physically separated domains collectively participate to the formation of large EDIBs: the N-terminal EKI motif, a sequence of the MAV domain involved in translation reinitiation and a C-terminal region encompassing the zinc finger. Surprisingly, EKI mutant TAVm3, corresponding to a substitution of the EKI motif at amino acids 11-13 by three alanines (AAA), which completely abolished the formation of large viroplasms, was not lethal for CaMV but highly reduced its virulence without affecting the rate of systemic infection. Expression of TAVm3 in a viral context led to formation of small irregularly shaped inclusion bodies, mild symptoms and low levels of viral DNA and particles accumulation, despite the production of significant amounts of mature capsid proteins. Unexpectedly, for CaMV-TAVm3 the formation of viral P2-containing electron-light inclusion body (ELIB), which is essential for CaMV aphid transmission, was also altered, thus suggesting an indirect role of the EKI tripeptide in CaMV plant-to-plant propagation. This important functional contribution of the EKI motif in CaMV biology can explain the strict conservation of this motif in the TAV sequences of all CaMV isolates.

Knowledge-based prediction of protein backbone conformation using a structural alphabet

Libraries of structural prototypes that abstract protein local structures are known as structural alphabets and have proven to be very useful in various aspects of protein structure analyses and predictions. One such library, Protein Blocks, is composed of 16 standard 5-residues long structural prototypes. This form of analyzing proteins involves drafting its structure as a string of Protein Blocks. Predicting the local structure of a protein in terms of protein blocks is the general objective of this work. A new approach, PB-kPRED is proposed towards this aim. It involves (i) organizing the structural knowledge in the form of a database of pentapeptide fragments extracted from all protein structures in the PDB and (ii) applying a knowledge-based algorithm that does not rely on any secondary structure predictions and/or sequence alignment profiles, to scan this database and predict most probable backbone conformations for the protein local structures. Though PB-kPRED uses the structural information from homologues in preference, if available. The predictions were evaluated rigorously on 15,544 query proteins representing a non-redundant subset of the PDB filtered at 30% sequence identity cut-off. We have shown that the kPRED method was able to achieve mean accuracies ranging from 40.8% to 66.3% depending on the availability of homologues. The impact of the different strategies for scanning the database on the prediction was evaluated and is discussed. Our results highlight the usefulness of the method in the context of proteins without any known structural homologues. A scoring function that gives a good estimate of the accuracy of prediction was further developed. This score estimates very well the accuracy of the algorithm (R2 of 0.82). An online version of the tool is provided freely for non-commercial usage at http://www.bo-protscience.fr/kpred/.

Spatial regulation of monolignol biosynthesis and laccase genes control developmental and stress-related lignin in flax

BACKGROUND

Bast fibres are characterized by very thick secondary cell walls containing high amounts of cellulose and low lignin contents in contrast to the heavily lignified cell walls typically found in the xylem tissues. To improve the quality of the fiber-based products in the future, a thorough understanding of the main cell wall polymer biosynthetic pathways is required. In this study we have carried out a characterization of the genes involved in lignin biosynthesis in flax along with some of their regulation mechanisms.

RESULTS

We have first identified the members of the phenylpropanoid gene families through a combination of in silico approaches. The more specific lignin genes were further characterized by high throughput transcriptomic approaches in different organs and physiological conditions and their cell/tissue expression was localized in the stems, roots and leaves. Laccases play an important role in the polymerization of monolignols. This multigenic family was determined and a miRNA was identified to play a role in the posttranscriptional regulation by cleaving the transcripts of some specific genes shown to be expressed in lignified tissues. In situ hybridization also showed that the miRNA precursor was expressed in the young xylem cells located near the vascular cambium. The results obtained in this work also allowed us to determine that most of the genes involved in lignin biosynthesis are included in a unique co-expression cluster and that MYB transcription factors are potentially good candidates for regulating these genes.

CONCLUSIONS

Target engineering of cell walls to improve plant product quality requires good knowledge of the genes responsible for the production of the main polymers. For bast fiber plants such as flax, it is important to target the correct genes from the beginning since the difficulty to produce transgenic material does not make possible to test a large number of genes. Our work determined which of these genes could be potentially modified and showed that it was possible to target different regulatory pathways to modify lignification.