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Divergent evolution of genomes among closely related species is shaped by both neutral processes and ecological forces, such as local adaptation and reinforcement. These factors can drive accelerated evolution of sex chromosomes relative to autosomes. Comparative genomic analyses between allopatric and sympatric species with overlapping or divergent ecological niches offer insights into reinforcement and ecological specialization on genome evolution. In the butterfly genus Morpho, several species coexist in sympatry, with specialization across forest strata and temporal niches. We analyzed the genomes of eight Morpho species, along with previously published genomes of three others, to compare chromosomal rearrangements and signs of positive selection in the Z chromosome vs autosomes. We found extensive chromosomal rearrangements in Z chromosome, particularly in sympatric species with similar ecological niches, suggesting a role for inversions in restricting gene flow at a postzygotic level. Z-linked genes also exhibited significantly higher dN/dS ratios than autosomal genes across the genus, with pronounced differences in closely related species living in sympatry. Additionally, we examined the evolution of eight circadian clock genes, detecting positive selection in Period, located on the Z chromosome. Our findings suggest that the Z chromosome evolves more rapidly than autosomes, particularly among closely related species, raising questions about its role in pre- and post-zygotic isolation mechanisms., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Adaptation is usually explained by beneficial genetic mutations that are transmitted from parents to offspring and become fixed in the adapted population. However, genetic mutation analysis alone is not sufficient to fully explain the adaptive processes, and several studies report the existence of nongenetic (or epigenetic) inheritance that can enable adaptation to new environments. In the present work, we tested the hypothesis of the role of DNA methylation, a form of epigenetic modification, in adaptation of the plant pathogen Ralstonia pseudosolanacearum to the host during experimental evolution. Using SMRT-seq technology, we analyzed the methylomes of 31 experimentally evolved clones obtained after serial passages on 5 different plant species during 300 generations. Comparison with the methylome of the ancestral clone revealed a list of 50 differential methylated sites (DMSs) at the GTWWAC motif. Gene expression analysis of the 39 genes targeted by these DMSs revealed limited correlation between differential methylation and differential expression of the corresponding genes. Only 1 gene showed a correlation, the RSp0338 gene encoding the EpsR regulator protein. The MSRE-qPCR technology, used as an alternative approach for DNA methylation analysis, also found the 2 DMSs upstream RSp0338. Using site-directed mutagenesis, we demonstrated the contribution of these 2 DMSs in host adaptation. As these DMSs appeared very early in the experimental evolution, we hypothesize that such fast epigenetic changes can allow rapid adaptation to the plant stem environment. In addition, we found that the change in DNA methylation upstream RSp0338 remains stable at least for 100 generations outside the host and thus can contribute to long-term adaptation to the host plant. To our knowledge, this is the first study showing a direct link between bacterial epigenetic variation and adaptation to a new environment., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Gopalan-Nair et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The microbial contamination of eye drop tips and caps varies between 7.7% and 100%. In seeking patient protection and continuous improvement, the Pharmacy Department in the Sterile Ophthalmological and Oncological Preparations Unit at Cochin Hospital AP-HP, Paris, France, conducted a two-phase study to compare the antimicrobial efficiency and practical use of standard packaging and a marketed eye drop container incorporating a self-decontaminating antimicrobial green technology by Pylote SAS at the tip and cap sites. The first phase was conducted in situ to identify the microbial contaminants of eye drops used in the hospital and community settings. A total of 110 eye drops were included for testing. Staphylococcus species were the most prevalent bacteria. Candida parapsilosis was detected in only one residual content sample and, at the same time, on the cap and tip. The second phase was performed in vitro, according to JIS Z2801. Reductions above one log in Staphylococcus aureus and Pseudomonas aeruginosa counts were noted in Pylote SAS eye drop packaging after 24 h of contact. The practical tests showed satisfactory results. Pylote SAS antimicrobial mineral oxide technology exhibited promising effects that combined effectiveness, safety, and sustainability to protect the patient by preventing infections due to the contamination of eye drop containers.

Background: The honey bee reference genome, HAv3.1, was produced from a commercial line sample that was thought to have a largely dominant Apis mellifera ligustica genetic background. Apis mellifera mellifera, often referred to as the black bee, has a separate evolutionary history and is the original type in western and northern Europe. Growing interest in this subspecies for conservation and non-professional apicultural practices, together with the necessity of deciphering genome backgrounds in hybrids, triggered the necessity for a specific genome assembly. Moreover, having several high-quality genomes is becoming key for taking structural variations into account in pangenome analyses., Results: Pacific Bioscience technology long reads were produced from a single haploid black bee drone. Scaffolding contigs into chromosomes was done using a high-density genetic map. This allowed for re-estimation of the recombination rate, which was over-estimated in some previous studies due to mis-assemblies, which resulted in spurious inversions in the older reference genomes. The sequence continuity obtained was very high and the only limit towards continuous chromosome-wide sequences seemed to be due to tandem repeat arrays that were usually longer than 10 kb and that belonged to two main families, the 371 and 91 bp repeats, causing problems in the assembly process due to high internal sequence similarity. Our assembly was used together with the reference genome to genotype two structural variants by a pangenome graph approach with Graphtyper2. Genotypes obtained were either correct or missing, when compared to an approach based on sequencing depth analysis, and genotyping rates were 89 and 76% for the two variants., Conclusions: Our new assembly for the Apis mellifera mellifera honey bee subspecies demonstrates the utility of multiple high-quality genomes for the genotyping of structural variants, with a test case on two insertions and deletions. It will therefore be an invaluable resource for future studies, for instance by including structural variants in GWAS. Having used a single haploid drone for sequencing allowed a refined analysis of very large tandem repeat arrays, raising the question of their function in the genome. High quality genome assemblies for multiple subspecies such as presented here, are crucial for emerging projects using pangenomes., (© 2024. The Author(s).)

Background: The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems., Results: We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex-determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplicates (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been likely lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome 18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variations (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex-determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in the testis than in the ovary., Conclusions: Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species., (© 2024. The Author(s).)

The interaction of foreign implants with their surrounding environment is significantly influenced by the adsorption of proteins on the biomaterial surfaces, playing a role in microbial adhesion. Therefore, understanding protein adsorption on solid surfaces and its effect on microbial adhesion is essential to assess the associated risk of infection. The aim of this study is to evaluate the effect of conditioning by fibronectin (Fn) or bovine serum albumin (BSA) protein layers of silica (SiO 2 ) surfaces on the adhesion and detachment of two pathogenic microorganisms: Pseudomonas aeruginosa PAO1-Tn 7-gfp and Candida albicans CIP 48.72. Experiments are conducted under both static and hydrodynamic conditions using a shear stress flow chamber. Through the use of very low wall shear stresses, the study brings the link between the static and dynamic conditions of microbial adhesion. The results reveal that the microbial adhesion critically depends on: (i) the presence of a protein layer conditioning the SiO 2 surface, (ii) the type of protein and (iii) the protein conformation and organization in the conditioning layer. In addition, a very distinct adhesion behaviour of P. aeruginosa is observed towards the two tested proteins, Fn and BSA. This effect is reinforced by the amount of proteins adsorbed on the surface and their organization in the layer. The results are discussed in the light of atomic force microscopy analysis of the organization and conformation of proteins in the layers after adsorption on the SiO 2 surface, as well as the specificity in bacterial behaviour when interacting with these protein layers. The study also demonstrates the very distinctive behaviours of the prokaryote P. aeruginosa PAO1-Tn 7-gfp compared to the eukaryote C. albicans CIP 48.72. This underscores the importance of considering species-specific interactions between the protein conditioning layer and different pathogenic microorganisms, which appear crucial in designing tailored anti-adhesive surfaces.

Although originally primarily a system for functional biology, Arabidopsis thaliana has, owing to its broad geographical distribution and adaptation to diverse environments, developed into a powerful model in population genomics. Here we present chromosome-level genome assemblies of 69 accessions from a global species range. We found that genomic colinearity is very conserved, even among geographically and genetically distant accessions. Along chromosome arms, megabase-scale rearrangements are rare and typically present only in a single accession. This indicates that the karyotype is quasi-fixed and that rearrangements in chromosome arms are counter-selected. Centromeric regions display higher structural dynamics, and divergences in core centromeres account for most of the genome size variations. Pan-genome analyses uncovered 32,986 distinct gene families, 60% being present in all accessions and 40% appearing to be dispensable, including 18% private to a single accession, indicating unexplored genic diversity. These 69 new Arabidopsis thaliana genome assemblies will empower future genetic research., (© 2024. The Author(s).)

We present the first use of amperometric detection to assess the viability of mammalian cells in continuous mode, directly in the cell culture medium. Vero or HeLa cells were injected into electrochemical sensors equipped with a 3-electrode system and containing DCIP 50 µM used as the redox mediator. DCIP was reduced by the viable cells and the reduced form was detected amperometrically at 300 mV vs silver pseudo-reference. The continuous regeneration of the oxidized form of the mediator ensured a stable redox state of the cell environment, allowing the cells to survive during the measurement time. The electrochemical response was related to cell metabolism (no response with dead cells or lysed cells) and depended on both mediator concentration and cell density. The protocol was applied to both cells in suspension and adhered cells. It was also adapted to detect trans-plasma membrane electron transfer (tPMET) by replacing DCIP by ferricyanide 500 µM and using linear scan voltammetry (2 mV/s). The pioneering results described here pave the way to the development of routine electrochemical assays for cell viability and for designing a cell-based analytical platform., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Simon Guette-Marquet, Christine Roques and Alain Bergel are co-inventors of the patent FR 22 04472 “Procédé d’analyse de la viabilité de cellules animales par mesure électrochimique”, 11 May 2022., (Copyright © 2023 Elsevier B.V. All rights reserved.)

The size of body compartments is a determinant of several factors of blood viscosity. Red cell aggregation is proportional to fat mass while hematocrit is proportional to both fat-free mass and abdominal adiposity, but which parts of these body components are involved in this relationship is not known. Segmental bioelectrical impedance analysis (sBIA) provides a possibility to delineate the relationships more precisely between various subdivisions of the body and blood viscosity factors, going farther than preceding studies using non segmental BIA. In this study we investigated in 38 subjects undergoing a standardized breakfast test with mathematical modelling of glucose homeostasis and a segmental bioelectrical impedance analysis (sBIA) the relationships between the various compartments of the body and viscosity factors. Blood and plasma viscosity were measured with the Anton Paar rheometer and analyzed with Quemada's model. The parameters better correlated to hematocrit are fat free mass (r = 0.562) and its two components muscle mass (r = 0.516) and non-muscular fat-free mass (r = 0.452), and also trunk fat mass (r = 0.383) and waist-to hip ratio (r = 0.394). Red cell aggregation measurements were correlated with both truncal and appendicular fat mass (r ranging between 0.603 and 0.728). Weaker correlations of M and M1 are found with waist circumference and hip circumference. This study shows that the correlation between lean mass and hematocrit involves both muscle and non-muscle moieties of lean mass, and that both central and appendicular fat are determinants of red cell aggregation.

The oomycete Phytophthora capsici is a common pathogen of the Solanaceae and Cucurbitaceae families. An improved assembly for the reference isolate LT1534 was constructed using Oxford Nanopore Technologies and Illumina data. Additionally, an unpolished assembly was produced for the European isolate Pc285 collected on chili pepper using Oxford Nanopore reads., Competing Interests: The authors declare no conflict of interest.

The impact of host diversity on the genotypic and phenotypic evolution of broad-spectrum pathogens is an open issue. Here, we used populations of the plant pathogen Ralstonia pseudosolanacearum that were experimentally evolved on five types of host plants, either belonging to different botanical families or differing in their susceptibility or resistance to the pathogen. We investigated whether changes in transcriptomic profiles, associated with or independent of genetic changes, could occur during the process of host adaptation, and whether transcriptomic reprogramming was dependent on host type. Genomic and transcriptomic variations were established for 31 evolved clones that showed better fitness in their experimental host than the ancestral clone. Few genomic polymorphisms were detected in these clones, but significant transcriptomic variations were observed, with a large number of differentially expressed genes (DEGs). In a very clear way, a group of genes belonging to the network of regulation of the bacterial virulence such as efpR , efpH or hrpB , among others, were deregulated in several independent evolutionary lineages and appeared to play a key role in the transcriptomic rewiring observed in evolved clones. A double hierarchical clustering based on the 400 top DEGs for each clone revealed 2 major patterns of gene deregulation that depend on host genotype, but not on host susceptibility or resistance to the pathogen. This work therefore highlights the existence of two major evolutionary paths that result in a significant reorganization of gene expression during adaptive evolution and underscore clusters of co-regulated genes associated with bacterial adaptation on different host lines.

The sealing characteristics of the geological formation located above a CO 2 storage reservoir, the so-called caprock, are essential to ensure efficient geological carbon storage. If CO 2 were to leak through the caprock, temporal changes in fluid geochemistry can reveal fundamental information on migration mechanisms and induced fluid-rock interactions. Here, we present the results from a unique in-situ injection experiment, where CO 2 -enriched fluid was continuously injected in a faulted caprock analogue. Our results show that the CO 2 migration follows complex pathways within the fault structure. The joint analysis of noble gases, ion concentrations and carbon isotopes allow us to quantify mixing between injected CO 2 -enriched fluid and resident formation water and to describe the temporal evolution of water-rock interaction processes. The results presented here are a crucial complement to the geophysical monitoring at the fracture scale highlighting a unique migration of CO 2 in fault zones., (© 2023. Springer Nature Limited.)

Pseudomonas aeruginosa , Staphylococcus aureus , and Burkholderia cepacia are notorious pathogens known for their ability to form resilient biofilms, particularly within the lung environment of cystic fibrosis (CF) patients. The heightened concentration of NaCl, prevalent in the airway liquid of CF patients' lungs, has been identified as a factor that promotes the growth of osmotolerant bacteria like S. aureus and dampens host antibacterial defenses, thereby fostering favorable conditions for infections. In this study, we aimed to investigate how increased NaCl concentrations impact the development of multi-species biofilms in vitro , using both laboratory strains and clinical isolates of P. aeruginosa , S. aureus , and B. cepacia co-cultures. Employing a low-nutrient culture medium that fosters biofilm growth of the selected species, we quantified biofilm formation through a combination of adherent CFU counts, qPCR analysis, and confocal microscopy observations. Our findings reaffirmed the challenges faced by S. aureus in establishing growth within 1:1 mixed biofilms with P. aeruginosa when cultivated in a minimal medium. Intriguingly, at an elevated NaCl concentration of 145 mM, a symbiotic relationship emerged between S. aureus and P. aeruginosa , enabling their co-existence. Notably, this hyperosmotic environment also exerted an influence on the interplay of these two bacteria with B. cepacia . We demonstrated that elevated NaCl concentrations play a pivotal role in orchestrating the distribution of these three species within the biofilm matrix. Furthermore, our study unveiled the beneficial impact of NaCl on the biofilm growth of clinically relevant mucoid P. aeruginosa strains, as well as two strains of methicillin-sensitive and methicillin-resistant S. aureus . This underscores the crucial role of the microenvironment during the colonization and infection processes. The results suggest that hyperosmotic conditions could hold the key to unlocking a deeper understanding of the genesis and behavior of CF multi-species biofilms., Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Fatima El Garah reports financial support was provided by Regional Council of Occitanie., (© 2023 The Authors. Published by Elsevier B.V.)

Enterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering and mortality and requiring antimicrobial use in poultry. Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of disease-associated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last 10 years from 16 French broiler farms. Comparative genomics, genome-wide association studies, and the measured susceptibility to serum, biofilm-forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate the origin of the isolates or the phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically, and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones of E. cecorum cluster into a few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones of E. cecorum belong mainly to one phylogenetic clade. IMPORTANCE Enterococcus cecorum is an important pathogen of poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associated E. cecorum isolates. To address this need, we performed whole-genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first data set on the genetic diversity and resistome of E. cecorum strains circulating in France, we pinpoint an epidemic lineage that is probably also circulating elsewhere that should be targeted preferentially by preventive strategies in order to reduce the burden of E. cecorum -related diseases.

The antimicrobial activity of surfaces treated with zinc and/or magnesium mineral oxide microspheres is a patented technology that has been demonstrated in vitro against bacteria and viruses. This study aims to evaluate the efficiency and sustainability of the technology in vitro, under simulation-of-use conditions, and in situ. The tests were undertaken in vitro according to the ISO 22196:2011, ISO 20473:2013, and NF S90-700:2019 standards with adapted parameters. Simulation-of-use tests evaluated the robustness of the activity under worst-case scenarios. The in situ tests were conducted on high-touch surfaces. The in vitro results show efficient antimicrobial activity against referenced strains with a log reduction of >2. The sustainability of this effect was time-dependent and detected at lower temperatures (20 ± 2.5 °C) and humidity (46%) conditions for variable inoculum concentrations and contact times. The simulation of use proved the microsphere's efficiency under harsh mechanical and chemical tests. The in situ studies showed a higher than 90% reduction in CFU/25 cm 2 per treated surface versus the untreated surfaces, reaching a targeted value of <50 CFU/cm 2 . Mineral oxide microspheres can be incorporated into unlimited surface types, including medical devices, to efficiently and sustainably prevent microbial contamination.

It is now well established that biological pollution is a major cause of the degradation of indoor air quality. It has been shown that microbial communities from the outdoors may significantly impact the communities detected indoors. One can reasonably assume that the fungal contamination of the surfaces of building materials and their release into indoor air may also significantly impact indoor air quality. Fungi are well known as common contaminants of the indoor environment with the ability to grow on many types of building materials and to subsequently release biological particles into the indoor air. The aerosolization of allergenic compounds or mycotoxins borne by fungal particles or vehiculated by dust may have a direct impact on the occupant's health. However, to date, very few studies have investigated such an impact. The present paper reviewed the available data on indoor fungal contamination in different types of buildings with the aim of highlighting the direct connections between the growth on indoor building materials and the degradation of indoor air quality through the aerosolization of mycotoxins. Some studies showed that average airborne fungal spore concentrations were higher in buildings where mould was a contaminant than in normal buildings and that there was a strong association between fungal contamination and health problems for occupants. In addition, the most frequent fungal species on surfaces are also those most commonly identified in indoor air, regardless the geographical location in Europe or the USA. Some fungal species contaminating the indoors may be dangerous for human health as they produce mycotoxins. These contaminants, when aerosolized with fungal particles, can be inhaled and may endanger human health. However, it appears that more work is needed to characterize the direct impact of surface contamination on the airborne fungal particle concentration. In addition, fungal species growing in buildings and their known mycotoxins are different from those contaminating foods. This is why further in situ studies to identify fungal contaminants at the species level and to quantify their average concentration on both surfaces and in the air are needed to be better predict health risks due to mycotoxin aerosolization.

Accurate species phylogenies are a prerequisite for all evolutionary research. Teleosts are the largest and most diversified group of extant vertebrates, but relationships among their three oldest extant lineages remain unresolved. On the basis of seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (arapaima, elephantnose fish) in a monophyletic sister group to all other teleosts, i.e., the Clupeocephala lineage (zebrafish, medaka). This finding resolves more than 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies.

In this work, β-thiogalactoside mimetics bearing 1,1-diarylmethylene or benzophenone aglycons have been prepared and assayed for their affinity towards LecA, a lectin and virulence factor from Pseudomonas aeruginosa involved in bacterial adhesion and biofilm formation. The hit compound presents higher efficiency than previously described monovalent inhibitors and the crystal structure confirmed the occurrence of additional contacts between the aglycone and the protein surface. The highest affinity (160 nM) was obtained for a divalent ligand containing two galactosides. The monovalent high affinity compound (K d  = 1 μM) obtained through structure-activity relationship (SAR) showed efficient antibiofilm activity with no associated bactericidal activity., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Masson SAS. All rights reserved.)

Of American origin, a wide diversity of Xylella fastidiosa strains belonging to different subspecies have been reported in Europe since 2013 and its discovery in Italian olive groves. Strains from the subspecies multiplex (ST6 and ST7) were first identified in France in 2015 in urban and natural areas. To trace back the most probable scenario of introduction in France, the molecular evolution rate of this subspecies was estimated at 3.2165 × 10 -7 substitutions per site per year, based on heterochronous genome sequences collected worldwide. This rate allowed the dating of the divergence between French and American strains in 1987 for ST6 and in 1971 for ST7. The development of a new VNTR-13 scheme allowed tracing the spread of the bacterium in France, hypothesizing an American origin. Our results suggest that both sequence types were initially introduced and spread in Provence-Alpes-Côte d'Azur (PACA); then they were introduced in Corsica in two waves from the PACA bridgehead populations., (© 2023. The Author(s).)

Introduction: Osteoarthritis is a chronic pathology that involves multidisciplinary management. Self-management for patients is an essential element, present in all international guidelines. During the time of the spa therapy, the patient is receptive to take the advantage of self-management workshops. The aim of this study is to assess the effects of 18 days spa therapy associated with a self-management intervention in patients with knee osteoarthritis in comparison with spa therapy alone on a priority objective, personalized and determined with the patient, chosen in the list of 5 objectives determined during the self-management initial assessment., Methods and Analysis: Two hundred fifty participants with knee osteoarthritis will participate to this multicenter, prospective, randomized, controlled study. All patients will benefit 18 days of spa therapy and patients randomized in the intervention group will participate to 6 self-management workshops. Randomization will be centralized. The allocation ratio will be 1:1. Data analysts and assessor will be blinded. The primary outcome is the effectiveness of the educational workshops associated with spa therapy in comparison with spa therapy alone on a priority objective, measured by Goal Attainment Scaling (GAS). The secondary outcomes are disability, health-related quality of life, and pain intensity., Ethics and Dissemination: Ethics were approved by the CPP Sud-Méditerranée II. The results will be disseminated in a peer-reviewed journal and disseminated at PRM, rheumatology, and orthopedics conferences. The results will also be disseminated to patients., Trial Registration: Trial registration number NCT03550547. Registered 8 June 2018. Date and version identifier of the protocol. Version N°6 of March 12, 2018., (© 2022. The Author(s).)

An electrochemical protocol was designed to enable Vero cells to transfer electrons to an electrode without any added redox mediator. The cells were cultured on the surface of electrodes polarized at the optimal potential of 400 mV/silver pseudo-reference. Gold, carbon, and CNT-coated carbon electrodes displayed similar current record patterns. Extracellular electron transfer was sustained for several days. Its intensity, up to 1.5 pA.cell -1 , was in the range of the electron flows implemented by cell respiration. A large fraction of the current vanished as soon as anoxic conditions were established, which suggests a mitochondrial origin for a large proportion of the electrons. The current records always showed a two-phase pattern. The occurrence of the two phases was not due to an evolution of the cell mat structure, which was fully established during the first day of polarization and did not change significantly thereafter. Increasing the cell seeding density decreased the maximum current reached during the first phase and the duration of the phase. These observations put together lead us to propose a model, in which only the cells adhered on the electrode surface produced current by metabolizing glutamine during the first phase. The possible role of this extracellular electron transfer as an alternative cell respiration pathway is discussed. The key roles it could play in regulating pH and pO 2 gradients are considered, specifically to explain the pH gradient reversal observed in cancer cells. These pioneering results pave the way for electrochemical sensors to directly address cellular metabolic pathways., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Dental implants provide a good solution for the replacement of tooth roots. However, the full restoration of tooth functions relies on the bone-healing period before positioning the abutment and the crown on the implant, with the associated risk of post-operative infection. This study aimed at developing a homogeneous and adherent thin calcium phosphate antibacterial coating on titanium dental implants by electrodeposition to favor both implant osseointegration and to limit peri-implantitis. By combining global (XRD, FTIR-ATR, elemental titration) and local (SEM, Raman spectroscopy on the coating surface and thickness) characterization techniques, we determined the effect of electrodeposition time on the characteristics and phases content of the coating and the associated mechanism of its formation. The 1-min-electrodeposited CaP coating (thickness: 2 ± 1 μm) was mainly composed of nano-needles of octacalcium phosphate. We demonstrated its mechanical stability after screwing and unscrewing the dental implant in an artificial jawbone. Then, we showed that we can reach a high copper incorporation rate (up to a 27% Cu/(Cu+Ca) molar ratio) in this CaP coating by using an ionic exchange post-treatment with copper nitrate solution at different concentrations. The biological properties (antibiofilm activity and cytotoxicity) were tested in vitro using a model of mixed bacteria biofilm mimicking peri-implantitis and the EN 10993-5 standard (direct contact), respectively. An efficient copper-doping dose was determined, providing an antibiofilm property to the coating without cytotoxic side effects. By combining the electrodeposition and copper ionic exchange processes, we can develop an antibiofilm calcium phosphate coating on dental implants with a tunable thickness and phases content.

The sterility of eye drop content is a primary concern from manufacturing until opening, as well as during handling by end users, while microbial contamination of the dropper tip and cap are often disregarded. The contamination of these sites during drug administration represents a risk of microbial transmission and ocular infection. In this review, we aim to assess microbial contamination of the dropper tip and cap of in-use eye drops, the associated contributory factors, and the risk of infection. We conducted a literature search of the MEDLINE, PubMed, and Cochrane Central databases. A total of 31 out of 1503 studies were selected. All the studies conducted in different settings that documented microbiologically contaminated in-use eye drops were included. Our review showed that microbial contamination of the dropper tip and cap of in-use eye drops ranged from 7.7 to 100% of the total contaminated tested samples. Documented contributory factors were conflicting across the literature. Studies investigating the association between eye infection and microbial contamination of the dropper tip and cap were scarce. New technologies offer a promising potential for securing the long-term sterility of eye drop content, tips, and caps, which could benefit from more research and well-defined study protocols under real-life scenarios.

The Pacific halibut (Hippoglossus stenolepis) is a key species in the North Pacific Ocean and Bering Sea ecosystems, where it also supports important fisheries. However, the lack of genomic resources limits our understanding of evolutionary, environmental and anthropogenic forces affecting key life history characteristics of Pacific halibut and prevents the application of genomic tools in fisheries management and conservation efforts. In the present study, we report on the first generation of a high-quality chromosome-level assembly of the Pacific halibut genome, with an estimated size of 602 Mb, 24 chromosome-length scaffolds that contain 99.8% of the assembly and a N 50 scaffold length of 27.3 Mb. In the first application of this important resource, we conducted genome-wide analyses of sex-specific genetic variation by pool sequencing and characterized a potential sex-determining region in chromosome 9 with a high density of female-specific SNPs. Within this region, we identified the bmpr1ba gene as a potential candidate for master sex-determining (MSD) gene. bmpr1ba is a member of the TGF-β family that in teleosts has provided the largest number of MSD genes, including a paralogue of this gene in Atlantic herring. The genome assembly constitutes an essential resource for future studies on Pacific halibut population structure and dynamics, evolutionary history and responses to environmental and anthropogenic influences. Furthermore, the genomic location of the sex-determining region in Pacific halibut has been identified and a putative candidate MSD gene has been proposed, providing further support for the rapid evolution of sex-determining mechanisms in teleost fish., (© 2022 International Pacific Halibut Commission. Molecular Ecology Resources published by John Wiley & Sons Ltd.)

Vanilla planifolia, the species cultivated to produce one of the world's most popular flavors, is highly prone to partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report here the first molecular evidence of partial endoreplication at the chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. planifolia. Cytogenetic data demonstrated that the diploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid cells are frequently observed. Using PacBio HiFi and optical mapping, we assembled and phased a diploid genome of 3.4 Gb with a scaffold N50 of 1.2 Mb and 59 128 predicted protein-coding genes. The atypical k-mer frequencies and the uneven sequencing depth observed agreed with our expectation of unbalanced genome representation. Sixty-seven percent of the genes were scattered over only 30% of the genome, putatively linking gene-rich regions and the endoreplication phenomenon. By contrast, low-coverage regions (non-endoreplicated) were rich in repeated elements but also contained 33% of the annotated genes. Furthermore, this assembly showed distinct haplotype-specific sequencing depth variation patterns, suggesting complex molecular regulation of endoreplication along the chromosomes. This high-quality, anchored assembly represents 83% of the estimated V. planifolia genome. It provides a significant step toward the elucidation of this complex genome. To support post-genomics efforts, we developed the Vanilla Genome Hub, a user-friendly integrated web portal that enables centralized access to high-throughput genomic and other omics data and interoperable use of bioinformatics tools., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

Treatment of biofilm-associated infections has become a major challenge in biomedical and clinical fields due to the failure of conventional treatments in controlling this highly complex and tolerant structure. Therefore, the search for novel antibiofilm agents with increased efficacy as those provided by natural products, presents an urgent need. The aim of this study was to explore extracts derived from three algae (green Ulva lactuca , brown Stypocaulon scoparium , red Pterocladiella capillacea ) for their potential antibiofilm activity against Staphylococcus aureus , bacterium responsible for several acute and chronic infections. Seaweed extracts were prepared by successive maceration in various solvents (cyclohexane (CH), dichloromethane (DCM), ethyl acetate (EA), and methanol (MeOH)). The ability of the different extracts to inhibit S. aureus biofilm formation was assessed using colony-forming unit (CFU) counts method supported by epifluorescence microscopic analysis. Effects of active extracts on the biofilm growth cycle, as well as on S. aureus surface hydrophobicity were evaluated. Results revealed the ability of four extracts to significantly inhibit S. aureus biofilm formation. These findings were supported by microscopy analyses. The gradual increase in the number of adherent bacteria when the selected extracts were added at various times (t 0 , t 2h , t 4h , t 6h , and t 24h ) revealed their potential effect on the initial adhesion and proliferation stages of S. aureus biofilm development. Interestingly, a significant reduction in the surface hydrophobicity of S. aureus treated with dichloromethane (DCM) extract derived from U. lactuca was demonstrated. These findings present new insights into the exploration of seaweeds as a valuable source of antibiofilm agents with preventive effect by inhibiting and/or delaying biofilm formation.

The evolution of sex determination (SD) in teleosts is amazingly dynamic, as reflected by the variety of different master sex-determining genes identified. Pangasiids are economically important catfishes in South Asian countries, but little is known about their SD system. Here, we generated novel genomic resources for 12 Pangasiids and characterized their SD system. Based on a Pangasianodon hypophthalmus chromosome-scale genome assembly, we identified an anti-Müllerian hormone receptor type Ⅱ gene (amhr2) duplication, which was further characterized as being sex-linked in males and expressed only in testes. These results point to a Y chromosome male-specific duplication (amhr2by) of the autosomal amhr2a. Sequence annotation revealed that the P. hypophthalmus Amhr2by is truncated in its N-terminal domain, lacking the cysteine-rich extracellular part of the receptor that is crucial for ligand binding, suggesting a potential route for its neofunctionalization. Reference-guided assembly of 11 additional Pangasiids, along with sex-linkage studies, revealed that this truncated amhr2by duplication is a male-specific conserved gene in Pangasiids. Reconstructions of the amhr2 phylogeny suggested that amhr2by arose from an ancient duplication/insertion event at the root of the Siluroidei radiation that is dated to ~100 million years ago. Together these results bring multiple lines of evidence supporting that amhr2by is an ancient and conserved master sex-determining gene in Pangasiids, a finding that highlights the recurrent use of the transforming growth factor β pathway, which is often used for the recruitment of teleost master SD genes, and provides another empirical case towards firther understanding of dynamics of SD systems., (© 2022 John Wiley & Sons Ltd.)

MRG15/MORF4L1 is a highly conserved protein in eukaryotes that contains a chromodomain (CHD) recognizing methylation of lysine 36 on histone H3 (H3K36me3) in chromatin. Intriguingly, it has been reported in the literature to interact with several different factors involved in chromatin modifications, gene regulation, alternative mRNA splicing, and DNA repair by homologous recombination. To get a complete and reliable picture of associations in physiological conditions, we used genome editing and tandem affinity purification to analyze the stable native interactome of human MRG15, its paralog MRGX/MORF4L2 that lacks the CHD, and MRGBP (MRG-binding protein) in isogenic K562 cells. We found stable interchangeable association of MRG15 and MRGX with the NuA4/TIP60 histone acetyltransferase/chromatin remodeler, Sin3B histone deacetylase/demethylase, ASH1L histone methyltransferase, and PALB2-BRCA2 DNA repair protein complexes. These associations were further confirmed and analyzed by CRISPR tagging of endogenous proteins and comparison of expressed isoforms. Importantly, based on structural information, point mutations could be introduced that specifically disrupt MRG15 association with some complexes but not others. Most interestingly, we also identified a new abundant native complex formed by MRG15/X-MRGBP-BRD8-EP400NL (EP400 N-terminal like) that is functionally similar to the yeast TINTIN (Trimer Independent of NuA4 for Transcription Interactions with Nucleosomes) complex. Our results show that EP400NL, being homologous to the N-terminal region of NuA4/TIP60 subunit EP400, creates TINTIN by competing for BRD8 association. Functional genomics indicate that human TINTIN plays a role in transcription of specific genes. This is most likely linked to the H4ac-binding bromodomain of BRD8 along the H3K36me3-binding CHD of MRG15 on the coding region of transcribed genes. Taken together, our data provide a complete detailed picture of human MRG proteins-associated protein complexes, which are essential to understand and correlate their diverse biological functions in chromatin-based nuclear processes., Competing Interests: Conflict of interest The authors declare no competing interests., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

In the challenging quest for a solution to reduce the risk of implant-associated infections in bone substitution surgery, the use of silver ions is promising regarding its broad spectrum on planktonic, sessile as well as multiresistant bacteria. In view of controlling its delivery in situ at the desired dose, we investigated its encapsulation in carboxymethyl cellulose (CMC) microparticles by spray-drying and included the latter in the formulation of a self-setting calcium phosphate bone cement. We implemented an original step-by-step methodology starting from the in vitro study of the antibacterial properties and cytotoxicity of two silver salts of different solubility in aqueous medium and then in the cement to determine the range of silver loading able to confer anti-biofilm and non-cytotoxic properties to the biomaterial. A dose-dependent efficiency of silver was demonstrated on the main species involved in bone-implant infection (S. aureus and S. epidermidis). Loading silver in microspheres instead of loading it directly inside the cement permitted to avoid undesired silver-cement interactions during setting and led to a faster release of silver, i.e. to a higher dose released within the first days combining anti-biofilm activity and preserved cytocompatibility. In addition, a combined interest of the introduction of about 10% (w/w) silver-loaded CMC microspheres in the cement formulation was demonstrated leading to a fully injectable and highly porous (77%) cement, showing a compressive strength analogous to cancellous bone. This injectable silver-loaded biomimetic composite cement formulation constitutes a versatile bone substitute material with tunable drug delivery properties, able to fight against bone implant associated infection. STATEMENT OF SIGNIFICANCE: This study is based on two innovative scientific aspects regarding the literature: i) Choice of silver ions as antibacterial agent combined with their way of incorporation: Carboxymethylcellulose has never been tested into bone cement to control its drug loading and release properties. ii) Methodology to formulate an antibacterial and injectable bone cement: original and multidisciplinary step-by-step methodology to first define, through (micro)biological tests on two silver salts with different solubilities, the targeted range of silver dose to include in carboxymethylcellulose microspheres and, then optimization of silver-loaded microparticles processing to fulfill requirements (encapsulation efficiency and size). The obtained fully injectable composite controls the early delivery of active dose of silver (from 3 h and over 2 weeks) able to fight against bone implant-associated infections., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.)

Spa therapy is considered an add-on treatment for psoriasis, but without any objective evaluation in the absence of randomized trials. This multicenter, open-label, randomized trial compared immediate spa therapy versus a control group having usual treatments until study assessments at 4.5 months. Spa therapy was proposed in five French spa resorts with standardized programs. Inclusion criteria were adults with plaque psoriasis, Dermatology Life Quality Index (DLQI) > 10, and stable medical treatment in the last 6 months. The main objective was DLQI ≤ 10 at 4.5 months after inclusion. VQ-Dermato and EQ5D-3L also assessed quality of life (QoL), Perceived Stress Scale (PSS) stress, and visual analogue scales (VAS) pain and pruritus. Between January 2015 and November 2018, 128 patients were randomized to either immediate spa therapy (64) (within 34 days, median) or usual treatments (61) until assessment at 4.5 months. Most were first-time spa users (71.2%). Mean DLQI and Psoriasis Area and Severity Index at inclusion were 16.7 and 10.5, respectively. Immediate spa therapy patients achieved the primary objective for 66.1% [95% CI 52.6% > 77.9%] vs 41.4% [95% CI 28.6% > 55.1%] control group patients (p = 0.007). VQ-Dermato scores and pruritus VAS significantly improved. Outcomes at 12-month follow-up of the immediate spa therapy group showed persistent improvement of DLQI, VQ-Dermato, and pruritus. This randomized controlled trial demonstrated that a cure of spa therapy improves QoL and alleviates certain symptoms of psoriasis, in short and long terms. This justifies its integration in the therapeutic strategies for psoriasis. Trial registration number: ClinicalTrials.gov Identifier: NCT02098213., (© 2022. The Author(s).)

Both nanometer-sized CuO and MgO particles exhibit bactericidal activities against Staphylococcus aureus and Escherichia coli , two bacteria causing healthcare-associated infections. The solid solution Cu 1- x Mg x O is potentially interesting for biomedical applications as one of the compositions could have a much higher bactericidal activity than the parent CuO and MgO oxides considered separately. But, to date, no Vegard's law proves the real existence of such a solid solution. This study was aimed at shedding light on the solubility of Mg 2+ ions in CuO nanoparticles and its impact on the free oxygen radicals they produce, the quantity of which determines their bactericidal performance. The solid solution Cu 1- x Mg x O does exist and particles were synthesized as nanorods of 50-60 nm length by thermally decomposing at 400 °C the single source precursors Cu 1- x Mg x (OH) 2 . Vegard's laws exist only in the compositional range 0 ≤ x ≤ 0.1, due to the low capacity of the distorted NaCl-type structure to accommodate regular coordination [MgO 6 ] octahedra. Only neutron diffraction allowed the detection of the small amount of MgO nanoparticles present as impurity in a 10 g sample beyond the solubility limit of x = 0.1. In this series, CuO nanorods remain the most active against E. coli and S. aureus with reduction in viability of 99.998% and 98.7% after 180 min in water, respectively. Our synthesis route has significantly increased the activity of pure CuO nanoparticles beyond the values reported so far, especially against E. coli . The bactericidal performances of CuO and the magnesium-substituted counterparts ( i.e. Cu 1- x Mg x O) are not linked to cupric ions they release in water since their mass concentrations after 180 min are much lower than minimal concentrations inhibiting the growth of E. coli and S. aureus . These CuO nanorods kill bacteria in water because they produce a large quantity of free oxygen radicals in the presence of H 2 O 2 only, the majority of which are highly toxic HO˙ radicals. Mg 2+ ions have a detrimental effect on this production, thus explaining the lowest bactericidal performance of Cu 1- x Mg x O nanorods. Definitive knowledge of the toxicity of Cu 1- x Mg x O nanoparticles towards bacteria in water is now available.

The Nernst potential of the support/cell interface is suspected to play a key role in cell adhesion and proliferation. However, the studies that have addressed this topic have generally varied the electrochemical potential of the interface by comparing different materials or by varying the chemical composition of the surface coating. It is consequently hard to definitively separate the actual effect of the potential from possible side-effects due to differences in the surface composition or topography. Here, a 3-electrode set-up was used to apply different values of potential to identical carbon electrodes. Potentials were applied in the range -200 to 400 mV vs. silver pseudo-reference (SPR), i.e. 90 to 690 mV/SHE, to screen-printed carbon electrodes used to grow Vero or Raw 264.7 cell lines. Values up to 200 mV/SPR prohibited cell adhesion and even caused detachment of cells that were previously adhered. The value of 400 mV/DRP allowed cell adhesion and proliferation, leading to confluent and sometimes very compact mats. The zero charge potential, measured around 200 mV/DRP, showed that the drastic effect of the applied potential was probably due to the negative/positive switch of the surface charge., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Biofilm formation is considered a major cause of therapeutic failure because bacteria in biofilms have higher protection against antimicrobials. Thus, biofilm-related infections are extremely challenging to treat and pose major concerns for public health, along with huge economic impacts. Pseudomonas aeruginosa, in particular, is a “critical priority” pathogen, responsible for severe infections, especially in cystic fibrosis patients because of its capacity to form resistant biofilms. Therefore, new therapeutic approaches are needed to complete the pipeline of molecules offering new targets and modes of action. Biofilm formation is mainly controlled by Quorum Sensing (QS), a communication system based on signaling molecules. In the present study, we employed a molecular docking approach (Autodock Vina) to assess two series of chromones-based compounds as possible ligands for PqsR, a LuxR-type receptor. Most compounds showed good predicted affinities for PqsR, higher than the PQS native ligand. Encouraged by these docking results, we synthesized a library of 34 direct and 25 retro chromone carboxamides using two optimized routes from 2-chromone carboxylic acid as starting material for both series. We evaluated the synthesized carboxamides for their ability to inhibit the biofilm formation of P. aeruginosa in vitro. Overall, results showed several chromone 2-carboxamides of the retro series are potent inhibitors of the formation of P. aeruginosa biofilms (16/25 compound with % inhibition ≥ 50% at 50 μM), without cytotoxicity on Vero cells (IC50 > 1.0 mM). The 2,4-dinitro-N-(4-oxo-4H-chromen-2-yl) benzamide (6n) was the most promising antibiofilm compound, with potential for hit to lead optimization.

Stenotrophomonas maltophilia strain 1800 was isolated from the effluent of an industrial oil refinery in Algeria. Its genome was sequenced using Illumina MiSeq (2 × 150-bp read pairs) and Oxford Nanopore (long reads) technologies and assembled using Unicycler. It is composed of one chromosome of 4.83 Mb.

To date, there is still a lack of definite knowledge regarding the toxicity of Cu(OH) 2 nanoparticles towards bacteria. This study was aimed at shedding light on the role played by released cupric ions in the toxicity of nanoparticles. To address this issue, the bactericidal activity of Cu(OH) 2 was at first evaluated in sterile water, a medium in which particles are not soluble. In parallel, an isovalent substitution of cupric ions by Mg 2+ was attempted in the crystal structure of Cu(OH) 2 nanoparticles to increase their solubility and determine the impact on the bactericidal activity. For the first time, mixed Cu 1- x Mg x (OH) 2 nanorods ( x ≤ 0.1) of about 15 nm in diameter and a few hundred nanometers in length were successfully prepared by a simple co-precipitation at room temperature in mixed alkaline (NaOH/Na 2 CO 3 ) medium. For E. coli , 100% reduction of one million CFU per mL (6 log 10 ) occurs after only 180 min on contact with both Cu(OH) 2 and Cu 0.9 Mg 0.1 (OH) 2 nanorods. The entire initial inoculum of S. aureus is also killed by Cu(OH) 2 after 180 min (100% or 6 log 10 reduction), while 0.01% of these bacteria stay alive on contact with Cu 0.9 Mg 0.1 (OH) 2 (99.99% or 4 log 10 reduction). The bactericidal performances of Cu(OH) 2 and the magnesium-substituted counterparts ( i.e. Cu 1- x Mg x (OH) 2 ) are not linked to cupric ions they release in water since their mass concentrations after 180 min are much lower than minimal concentrations inhibiting the growth of E. coli and S. aureus . Finally, an EPR spin trapping study reveals how these nanorods kill bacteria in water: only the presence of hydrogen peroxide, a by-product of the normal metabolism of oxygen in aerobic bacteria, allows the Cu(OH) 2 and its magnesium-substituted counterparts to produce a lethal amount of free radicals, the majority of which are the highly toxic HO˙.

The history of antimicrobial resistance (AMR) evolution and the diversity of the environmental resistome indicate that AMR is an ancient natural phenomenon. Acquired resistance is a public health concern influenced by the anthropogenic use of antibiotics, leading to the selection of resistant genes. Data show that AMR is spreading globally at different rates, outpacing all efforts to mitigate this crisis. The search for new antibiotic classes is one of the key strategies in the fight against AMR. Since the 1980s, newly marketed antibiotics were either modifications or improvements of known molecules. The World Health Organization (WHO) describes the current pipeline as bleak, and warns about the scarcity of new leads. A quantitative and qualitative analysis of the pre-clinical and clinical pipeline indicates that few antibiotics may reach the market in a few years, predominantly not those that fit the innovative requirements to tackle the challenging spread of AMR. Diversity and innovation are the mainstays to cope with the rapid evolution of AMR. The discovery and development of antibiotics must address resistance to old and novel antibiotics. Here, we review the history and challenges of antibiotics discovery and describe different innovative new leads mechanisms expected to replenish the pipeline, while maintaining a promising possibility to shift the chase and the race between the spread of AMR, preserving antibiotic effectiveness, and meeting innovative leads requirements.

The organization of bacteria in biofilms is one of the adaptive resistance mechanisms providing increased protection against conventional treatments. Thus, the search for new antibiofilm agents for medical purposes, especially of natural origin, is currently the object of much attention. The objective of the study presented here was to explore the potential of extracts derived from three seaweeds: the green Ulva lactuca , the brown Stypocaulon scoparium , and the red Pterocladiella capillacea , in terms of their antibiofilm activity against P. aeruginosa . After preparation of extracts by successive maceration in various solvents, their antibiofilm activity was evaluated on biofilm formation and on mature biofilms. Their inhibition and eradication abilities were determined using two complementary methods: crystal violet staining and quantification of adherent bacteria. The effect of active extracts on biofilm morphology was also investigated by epifluorescence microscopy. Results revealed a promising antibiofilm activity of two extracts (cyclohexane and ethyl acetate) derived from the green alga by exhibiting a distinct mechanism of action, which was supported by microscopic analyses. The ethyl acetate extract was further explored for its interaction with tobramycin and colistin. Interestingly, this extract showed a promising synergistic effect with tobramycin. First analyses of the chemical composition of extracts by GC-MS allowed for the identification of several molecules. Their implication in the interesting antibiofilm activity is discussed. These findings suggest the ability of the green alga U. lactuca to offer a promising source of bioactive candidates that could have both a preventive and a curative effect in the treatment of biofilms.

Ecological baselines for the structure and functioning of ecosystems in the absence of human activity can provide essential information on their health status. The Glorieuses islands are located in the Western Indian Ocean (WIO) and can be considered as "pristine" ecosystems that have not been subjected to anthropogenic pressure. Their nutrient context and the microbial assemblages were assessed by determining the abundance of heterotrophic prokaryotes (archaea and bacteria), picocyanobacteria, picoeukaryotes, microphytoplankton and protozooplankton communities in five stations, during two contrasted periods (November 2015 and May 2016). Chlorophyll-a concentrations were always under 1 μg/L and associated to very low levels in orthophosphates, nitrate and dissolved organic carbon, revealing an ultra-oligotrophic status for the Glorieuses waters. Picocyanobacteria confirmed the ultra-oligotrophic status with a predominance of Synechococcus. Zeaxanthin associated with the presence of picocyanobacteria represented the major pigment in both surveys. Three indices of diversity (species richness, Shannon and Pielou indexes) from microscopy observations highlighted the difference of diversity in microphytoplankton between the surveys. A focus on a 16S metabarcoding approach showed a high dominance of picocyanobacteria, Alpha- and Gammaproteobacteria, regardless of station or period. Multivariate analyses (co-inertia analyses) revealed a strong variability of ecological conditions between the two periods, with (i) high nutrient concentrations and heterotrophic nanoflagellate abundance in November 2015, and (ii) high heterotrophic prokaryote and picoeukaryote abundance in May 2016. The impact of a category 5 tropical cyclone (Fantala) on the regional zone in April 2016 is also advanced to explain these contrasted situations. Relative importance of top-down factors between bacterial and heterotrophic nanoflagellates was observed in November 2015 with an active microbial food web. All the results indicate that three microbial indexes potentially can be considered to assess the ecological change in Glorieuses marine waters., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

The host range of parasites is an important factor in assessing the dynamics of disease epidemics. The evolution of pathogens to accommodate new hosts may lead to host range expansion, a process the molecular bases of which are largely enigmatic. The fungus Sclerotinia sclerotiorum has been reported to parasitize more than 400 plant species from diverse eudicot families while its close relative, S. trifoliorum, is restricted to plants from the Fabaceae family. We analyzed S. sclerotiorum global transcriptome reprogramming on hosts from six botanical families and reveal a flexible, host-specific transcriptional program. We generated a chromosome-level genome assembly for S. trifoliorum and found near-complete gene space conservation in two representative strains of broad and narrow host range Sclerotinia species. However, S. trifoliorum showed increased sensitivity to the Brassicaceae defense compound camalexin. Comparative analyses revealed a lack of transcriptional response to camalexin in the S. trifoliorum strain and suggest that regulatory variation in detoxification and effector genes at the population level may associate with the genetic accommodation of Brassicaceae in the Sclerotinia host range. Our work proposes transcriptional plasticity and the co-existence of signatures for generalist and polyspecialist adaptive strategies in the genome of a plant pathogen., (© 2021. The Author(s), under exclusive licence to International Society for Microbial Ecology.)

Sex chromosomes are generally derived from a pair of classical type-A chromosomes, and relatively few alternative models have been proposed up to now. 1 , 2 B chromosomes (Bs) are supernumerary and dispensable chromosomes with non-Mendelian inheritance found in many plant and animal species 3 , 4 that have often been considered as selfish genetic elements that behave as genome parasites. 5 , 6 The observation that in some species Bs can be either restricted or predominant in one sex 7-14 raised the interesting hypothesis that Bs could play a role in sex determination. 15 The characterization of putative B master sex-determining (MSD) genes, however, has not yet been provided to support this hypothesis. Here, in Astyanax mexicanus cavefish originating from Pachón cave, we show that Bs are strongly male predominant. Based on a high-quality genome assembly of a B-carrying male, we characterized the Pachón cavefish B sequence and found that it contains two duplicated loci of the putative MSD gene growth differentiation factor 6b (gdf6b). Supporting its role as an MSD gene, we found that the Pachón cavefish gdf6b gene is expressed specifically in differentiating male gonads, and that its knockout induces male-to-female sex reversal in B-carrying males. This demonstrates that gdf6b is necessary for triggering male sex determination in Pachón cavefish. Altogether these results bring multiple and independent lines of evidence supporting the conclusion that the Pachón cavefish B is a "B-sex" chromosome that contains duplicated copies of the gdf6b gene, which can promote male sex determination in this species., Competing Interests: Declaration of interests The authors declare no competing interests, (Copyright © 2021 Elsevier Inc. All rights reserved.)

Arapaima gigas is one of the largest freshwater fish species of high ecological and economic importance. Overfishing and habitat destruction are severe threats to the remaining wild populations. By incorporating a chromosomal Hi-C contact map, we improved the arapaima genome assembly to chromosome-level, revealing an unexpected high degree of chromosome rearrangements during evolution of the bonytongues (Osteoglossiformes). Combining this new assembly with pool-sequencing of male and female genomes, we identified id2bbY, a duplicated copy of the inhibitor of DNA binding 2b (id2b) gene on the Y chromosome as candidate male sex-determining gene. A PCR-test for id2bbY was developed, demonstrating that this gene is a reliable male-specific marker for genotyping. Expression analyses showed that this gene is expressed in juvenile male gonads. Its paralog, id2ba, exhibits a male-biased expression in immature gonads. Transcriptome analyses and protein structure predictions confirm id2bbY as a prime candidate for the master sex-determiner. Acting through the TGFβ signaling pathway, id2bbY from arapaima would provide the first evidence for a link of this family of transcriptional regulators to sex determination. Our study broadens our current understanding about the evolution of sex determination genetic networks and provide a tool for improving arapaima aquaculture for commercial and conservation purposes., (© 2021. The Author(s).)

Motivation: Long-read sequencing technologies can be employed to detect and map DNA modifications at the nucleotide resolution on a genome-wide scale. However, published software packages neglect the integration of genomic annotation and comprehensive filtering when analyzing patterns of modified bases detected using Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT) data. Here, we present DNA Modification Annotation (DNAModAnnot), a R package designed for the global analysis of DNA modification patterns using adapted filtering and visualization tools., Results: We tested our package using PacBio sequencing data to analyze patterns of the 6-methyladenine (6mA) in the ciliate Paramecium tetraurelia, in which high 6mA amounts were previously reported. We found P. tetraurelia 6mA genome-wide distribution to be similar to other ciliates. We also performed 5-methylcytosine (5mC) analysis in human lymphoblastoid cells using ONT data and confirmed previously known patterns of 5mC. DNAModAnnot provides a toolbox for the genome-wide analysis of different DNA modifications using PacBio and ONT long-read sequencing data., Availability and Implementation: DNAModAnnot is distributed as a R package available via GitHub (https://github.com/AlexisHardy/DNAModAnnot)., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2021. Published by Oxford University Press.)

To identify the environmental factors that drive plankton community composition and structure in coastal waters, a shallow northwestern Mediterranean lagoon was monitored from winter to spring in two contrasting years. The campaign was based on high-frequency recordings of hydrological and meteorological parameters and weekly samplings of nutrients and the plankton community. The collected data allowed the construction of correlation networks, which revealed that water temperature was the most important factor governing community composition, structure and succession at different trophic levels, suggesting its ubiquitous food web control. Temperature favoured phytoplanktonic flagellates (Cryptophyceae, Chrysophyceae, and Chlorophyceae) and ciliates during winter and early spring. In contrast, it favoured Bacillariophyceae, dinoflagellates, phytoplankton < 6 µm and aloricate Choreotrichida during spring. The secondary factors were light, which influenced phytoplankton, and wind, which may regulate turbidity and the nutrient supply from land or sediment, thus affecting benthic species such as Nitzschia sp. and Uronema sp. or salinity-tolerant species such as Prorocentrum sp. The central role of temperature in structuring the co-occurrence network suggests that future global warming could deeply modify plankton communities in shallow coastal zones, affecting whole-food web functioning., (© 2021. The Author(s).)

Adenoviral pancreatitis has been amply described for decades in guinea fowl. Although its pathologic picture has been characterized fairly well, its etiology still remains only partially clarified. Based on several outbreaks diagnosed on commercial guinea flocks raised in France since 2017, we performed direct whole-genome sequencing from pancreatic lesional tissue by using the Oxford Nanopore Technologies (ONT) sequencing method. We generated 4781 viral reads and assembled a whole genome of 43,509 bp, clustering within fowl adenovirus type 1 (FAdV-1). A phylogenetic analysis based on a partial sequence of the hexon and short fiber genes on viruses collected in France showed 98.7% and 99.8% nucleotide identity, respectively. Altogether, these results confirm that an FAdV-1 closely related to chicken and other avian strains is the agent of pancreatitis in guinea fowl. This study illustrates the potential of ONT sequencing method to achieve rapid whole-genome sequencing directly from pathologic material.

Objectives: The rising incidence of urinary tract infections (UTIs) attributable to Escherichia coli resistant isolates is becoming a serious public health concern. Although global rates of infection vary considerably by region, the growing prevalence of this uropathogen has been associated with a high economic burden and health strain. This study aims: (1) to estimate the differences in clinical and economic outcomes between 2 groups of adult hospitalized patients with UTIs from E. coli resistant and susceptible bacteria and (2) to investigate drivers of this cost from a payer's perspective., Methods: A prospective multicenter cohort study was conducted in 10 hospitals in Lebanon. The cost analysis followed a bottom-up microcosting approach; a linear regression was constructed to evaluate the predictors of hospitalization costs and a Cox proportional hazards model was used to estimate the impact of resistance on length of stay (LOS) and in-hospital mortality., Results: Out of 467 inpatients, 250 cases were because of resistant E. coli isolates. Results showed that patients with resistant uropathogens had 29% higher mean total hospitalization costs ($3429 vs $2651; P = .004), and an extended median LOS (6 days vs 5 days; P = .020) compared with susceptible cohorts. The selection of resistant bacteria and the Charlson comorbidity index predicted higher total hospitalization costs and in-hospital mortality., Conclusion: In an era of increased pressure for cost containment, this study showed the burden of treating UTIs resulting from resistant bacteria. The results can inform cost-effectiveness analyses that intend to evaluate the benefit of a national action plan aimed at decreasing the impact of antibiotic resistance., (Copyright © 2021. Published by Elsevier Inc.)

Several hypotheses explain the prevalence of undifferentiated sex chromosomes in poikilothermic vertebrates. Turnovers change the master sex determination gene, the sex chromosome or the sex determination system (e.g. XY to WZ). Jumping master genes stay main triggers but translocate to other chromosomes. Occasional recombination (e.g. in sex-reversed females) prevents sex chromosome degeneration. Recent research has uncovered conserved heteromorphic or even homomorphic sex chromosomes in several clades of non-avian and non-mammalian vertebrates. Sex determination in sturgeons (Acipenseridae) has been a long-standing basic biological question, linked to economical demands by the caviar-producing aquaculture. Here, we report the discovery of a sex-specific sequence from sterlet ( Acipenser ruthenus ). Using chromosome-scale assemblies and pool-sequencing, we first identified an approximately 16 kb female-specific region. We developed a PCR-genotyping test, yielding female-specific products in six species, spanning the entire phylogeny with the most divergent extant lineages ( A. sturio, A. oxyrinchus versus A. ruthenus, Huso huso ), stemming from an ancient tetraploidization. Similar results were obtained in two octoploid species ( A. gueldenstaedtii, A. baerii ). Conservation of a female-specific sequence for a long period, representing 180 Myr of sturgeon evolution, and across at least one polyploidization event, raises many interesting biological questions. We discuss a conserved undifferentiated sex chromosome system with a ZZ/ZW-mode of sex determination and potential alternatives. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.

Microfluidization has been investigated as a new, scalable, and basic component saving method to produce cationic lipid nanoparticles, in particular for the delivery of short interfering RNAs (siRNAs). The design of experiment (DoE) allowed to reach optimized characteristics in terms of nanocarrier size reduction and low polydispersity. The structure of cationic liposomes and siRNA-lipoplexes was characterized. The optimized preparation parameters were identified as three microfluidization passages at a pressure of 10,000 psi, with a thin film hydration volume of 4 ml. Microfluidized liposomes mean size was 160 nm, with a polydispersity index of 0.2-0.3 and a zeta potential of +40 mV to +60 mV. Positive versus negative charge ratio between the charges of the cationic lipid and the phosphate charges of the siRNAs is a key factor determining the structure and silencing efficacy of siRNA lipoplexes. At a (+/-) charge ratio of 8, a proportion of 88% of the siRNA was associated to microfluidized lipoplexes, which remained stable for one month. These lipoplexes exhibited moderate cytotoxicity and gene silencing efficacy, which should be further optimized., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding.