C-reactive protein is more suitable than Serum Amyloid A to monitor crises and attack-free periods in Systemic Auto-Inflammatory Diseases.

BACKGROUND: With their broad presentations and no global biomarker to discriminate crises and attack-free periods, Systemic Auto-Inflammatory Diseases (SAID) are difficult to manage. This study assessed Serum Amyloid A (SAA), C-reactive protein (CRP) and serum calprotectin as potential biomarkers to monitor patients with SAID. METHOD: SAA (already studied in Familial Mediterranean Fever (FMF)), CRP and serum calprotectin were measured on SAID adult patients from Juvenile Inflammatory Rheumatism (JIR) cohort during their follow-up visits between 2020 and 2022. Crises and attack-free periods were clinically determined. RESULTS: 96 measures, mainly from FMF (43 %) and Unclassified SAID (USAID) (37 %) patients were included. Using ROC curves, a threshold with sensitivity and specificity of/over 75 % was determined for SAA (9 mg/L) and CRP (9 mg/L) but not for serum calprotectin, not investigated further. With this threshold, the results were similar in FMF and USAID patients' subgroups. SAA and CRP showed a positive correlation with crises and attack-free periods in SAID patients (r = 0.4796, p < 0.001 and r = 0.5525, p < 0.001, respectively) as in FMF and USAID patients, with no significant difference between both markers in diagnosis value and ROC curves Area Under Curve (AUC) (p = 0.32). Only the CRP results were not influenced by obesity. CONCLUSION: SAA and CRP can discriminate crisis and attack-free periods in our cohort of SAID patients mainly composed of FMF and USAID patients. However, only CRP can be used regardless of body mass index. It is the first report of common biomarkers for all SAID, including USAID patients, with CRP widely accessible in routine worldwide.

Pervasive translation of Xrn1-sensitive unstable long noncoding RNAs in yeast.

Despite being predicted to lack coding potential, cytoplasmic long noncoding (lnc)RNAs can associate with ribosomes. However, the landscape and biological relevance of lncRNA translation remain poorly studied. In yeast, cytoplasmic Xrn1-sensitive unstable transcripts (XUTs) are targeted by nonsense-mediated mRNA decay (NMD), suggesting a translation-dependent degradation process. Here, we report that XUTs are pervasively translated, which impacts their decay. We show that XUTs globally accumulate upon translation elongation inhibition, but not when initial ribosome loading is impaired. Ribo-seq confirmed ribosomes binding to XUTs and identified ribosome-associated 5'-proximal small ORFs. Mechanistically, the NMD-sensitivity of XUTs mainly depends on the 3'-untranslated region length. Finally, we show that the peptide resulting from the translation of an NMD-sensitive XUT reporter exists in NMD-competent cells. Our work highlights the role of translation in the posttranscriptional metabolism of XUTs. We propose that XUT-derived peptides could be exposed to natural selection, while NMD restricts XUT levels.

Bile-induced biofilm formation in Bacteroides thetaiotaomicron requires magnesium efflux by an RND pump.

Bacteroides thetaiotaomicron is a prominent member of the human gut microbiota contributing to nutrient exchange, gut function, and maturation of the host's immune system. This obligate anaerobe symbiont can adopt a biofilm lifestyle, and it was recently shown that B. thetaiotaomicron biofilm formation is promoted by the presence of bile. This process also requires a B. thetaiotaomicron extracellular DNase, which is not, however, regulated by bile. Here, we showed that bile induces the expression of several Resistance-Nodulation-Division (RND) efflux pumps and that inhibiting their activity with a global competitive efflux inhibitor impaired bile-dependent biofilm formation. We then showed that, among the bile-induced RND-efflux pumps, only the tripartite BT3337-BT3338-BT3339 pump, re-named BipABC [for Bile Induced Pump A (BT3337), B (BT3338), and C (BT3339)], is required for biofilm formation. We demonstrated that BipABC is involved in the efflux of magnesium to the biofilm extracellular matrix, which leads to a decrease of extracellular DNA concentration. The release of magnesium in the biofilm matrix also impacts biofilm structure, potentially by modifying the electrostatic repulsion forces within the matrix, reducing interbacterial distance and allowing bacteria to interact more closely and form denser biofilms. Our study therefore, identified a new molecular determinant of B. thetaiotaomicron biofilm formation in response to bile salts and provides a better understanding on how an intestinal chemical cue regulates biofilm formation in a major gut symbiont.IMPORTANCEBacteroides thetaiotaomicron is a prominent member of the human gut microbiota able to degrade dietary and host polysaccharides, altogether contributing to nutrient exchange, gut function, and maturation of the host's immune system. This obligate anaerobe symbiont can adopt a biofilm community lifestyle, providing protection against environmental factors that might, in turn, protect the host from dysbiosis and dysbiosis-related diseases. It was recently shown that B. thetaiotaomicron exposure to intestinal bile promotes biofilm formation. Here, we reveal that a specific B. thetaiotaomicron membrane efflux pump is induced in response to bile, leading to the release of magnesium ions, potentially reducing electrostatic repulsion forces between components of the biofilm matrix. This leads to a reduction of interbacterial distance and strengthens the biofilm structure. Our study, therefore, provides a better understanding of how bile promotes biofilm formation in a major gut symbiont, potentially promoting microbiota resilience to stress and dysbiosis events.

Genome sequence of PSonyx, a singleton bacteriophage infecting Corynebacterium glutamicum.

PSonyx is a newly isolated phage that infects Corynebacterium glutamicum. This siphovirus was isolated from a French pond in the south of Paris by students from Paris-Saclay University. Its 80,277-bp singleton genome carries 136 protein-coding genes and 5 tRNAs.

Lung ultrasound: A potential tool in the diagnosis of ventilator-associated pneumonia in pediatric intensive care units.

PURPOSE: Ventilator-associated pneumonia (VAP) is a common healthcare-associated infection in pediatric intensive care unit (PICU), increasing mortality, antibiotics use and duration of ventilation and hospitalization. VAP diagnosis is based on clinical and chest X-ray (CXR) signs defined by the 2018 Center for Disease Control (gold standard). However, CXR induces repetitive patients' irradiation and technical limitations. This study aimed to investigate if lung ultrasound (LUS) can substitute CXR in the VAP diagnosis. METHODS: A monocentric and prospective study was conducted in a French tertiary care hospital. Patients under 18-year-old admitted to PICU between November 2018 and July 2020 with invasive mechanical ventilation for more than 48 h were included. The studied LUS signs were consolidations, dynamic air bronchogram, subpleural consolidations (SPC), B-lines, and pleural effusion. The diagnostic values of each sign associated with clinical signs (cCDC) were compared to the gold standard approach. LUS, chest X-ray, and clinical score were performed daily. RESULTS: Fifty-seven patients were included. The median age was 8 [3-34] months. Nineteen (33%) children developed a VAP. In patients with VAP, B-Lines, and consolidations were highly frequent (100 and 68.8%) and, associated with cCDC, were highly sensitive (100 [79-100] % and 88 [62-98] %, respectively) and specific (95.5 [92-98] % and 98 [95-99] %, respectively). Other studied signs, including SPC, showed high specificity (>97%) but low sensibility (<50%). CONCLUSION: LUS seems to be a powerful tool for VAP diagnosis in children with a clinical suspicion, efficiently substituting CXR, and limiting children's exposure to ionizing radiations.

Clinical Manifestation of Cytomegalovirus-Associated Protein-Losing Enteropathy in Children.

In children, CMV-associated protein-losing enteropathy (PLE) is characterised by a benign course and spontaneous healing but can lead to generalised oedema. Poorly defined, it is diagnosed after unnecessary invasive tests. Children with CMV-associated PLE between 2009 and 2019 in two French hospitals are retrospectively described. Clinical and biological signs, CMV identification, endoscopy and histological findings, disease management and course are analysed. CMV-associated PLE is proven in 21 immunocompetent and 22 immunosuppressed patients, with ages consistent with primo-infection and reactivation, respectively. The digestive symptoms prevail in immunocompetent children, mainly with vomiting (85.7% versus 50%, CI [1.2; 39.2], p = 0.02). Immunocompetent patients show more oedema (61.9% versus 4.5%, CI [3.6; 1502.4], p < 0.001), linked to more severe hypoalbuminemia (21.2 g/L [17.6-25.7] versus 29.6 g/L [24.9-33.9], p = 0.01). A severe course is observed in 23.8% of the immunocompetent patients and 54.5% of the immunosuppressed ones (p = 0.06). Evidence of CMV infection based on non-invasive methods is found on 88.9% of immunocompetent and 95.5% of immunosuppressed patients (p = 0.58), while endoscopy was performed on 95.2% and 100% of them, respectively (p = 0.48), without any therapeutic change. Thus, CMV-associated PLE should be suspected in children with generalised oedema. Not as benign as previously described, it can be confirmed using non-invasive tests.

Risk Analysis by Failure Modes, Effects and Criticality Analysis and Biosafety Management During Collective Air Medical Evacuation of Critically Ill Coronavirus Disease 2019 Patients.

In March 2020, coronavirus disease 2019 (COVID-19) caused an overwhelming pandemic. To relieve overloaded intensive care units in the most affected regions, the French Ministry of Defence triggered collective air medical evacuations (medevacs) on board an Airbus A330 Multi Role Tanker Transport of the French Air Force. Such a collective air medevac is a big challenge regarding biosafety; until now, only evacuations of a single symptomatic patient with an emergent communicable disease, such as Ebola virus disease, have been conducted. However, the COVID-19 pandemic required collective medevacs for critically ill patients and involved a virus that little is known about still. Thus, we performed a complete risk analysis using a process map and FMECA (Failure Modes, Effects and Criticality Analysis) to assess the risk and implement mitigation measures for health workers, flight crew, and the environment. We report the biosafety management experienced during 6 flights with a total of 36 critically ill COVID-19-positive patients transferred with no casualties while preserving both staffs and aircraft.

SURFMAP: A Software for Mapping in Two Dimensions Protein Surface Features.

Molecular cartography using two-dimensional (2D) representation of protein surfaces has been shown to be very promising for protein surface analysis. Here, we present SURFMAP, a free standalone and easy-to-use software that enables the fast and automated 2D projection of either predefined features of protein surface (i.e., electrostatic potential, hydrophobicity, stickiness, and surface relief) or any descriptor encoded in the temperature factor column of a PDB file. SURFMAP proposes three different "equal-area" projections that have the advantage of preserving the area measures. It provides the user with (i) 2D maps that enable the easy and visual analysis of protein surface features of interest and (ii) maps in a text file format allowing the fast and straightforward quantitative comparison of 2D maps of homologous proteins.

Exploring the Peptide Potential of Genomes.

Recent studies attribute a central role to the noncoding genome in the emergence of novel genes. The widespread transcription of noncoding regions and the pervasive translation of the resulting RNAs offer to the organisms a vast reservoir of novel peptides. Although the majority of these peptides are anticipated as deleterious or neutral, and thereby expected to be degraded right away or short-lived in evolutionary history, some of them can confer an advantage to the organism. The latter can be further subjected to natural selection and be established as novel genes. In any case, characterizing the structural properties of these pervasively translated peptides is crucial to understand (1) their impact on the cell and (2) how some of these peptides, derived from presumed noncoding regions, can give rise to structured and functional de novo proteins. Therefore, we present a protocol that aims to explore the potential of a genome to produce novel peptides. It consists in annotating all the open reading frames (ORFs) of a genome (i.e., coding and noncoding ones) and characterizing the fold potential and other structural properties of their corresponding potential peptides. Here, we apply our protocol to a small genome and show how to apply it to very large genomes. Finally, we present a case study which aims to probe the fold potential of a set of 721 translated ORFs in mouse lncRNAs, identified with ribosome profiling experiments. Interestingly, we show that the distribution of their fold potential is different from that of the nontranslated lncRNAs and more generally from the other noncoding ORFs of the mouse.

Bacteroides thetaiotaomicron uses a widespread extracellular DNase to promote bile-dependent biofilm formation.

Bacteroides thetaiotaomicron is a gut symbiont that inhabits the mucus layer and adheres to and metabolizes food particles, contributing to gut physiology and maturation. Although adhesion and biofilm formation could be key features for B. thetaiotaomicron stress resistance and gut colonization, little is known about the determinants of B. thetaiotaomicron biofilm formation. We previously showed that the B. thetaiotaomicron reference strain VPI-5482 is a poor in vitro biofilm former. Here, we demonstrated that bile, a gut-relevant environmental cue, triggers the formation of biofilm in many B. thetaiotaomicron isolates and common gut Bacteroidales species. We determined that bile-dependent biofilm formation involves the production of the DNase BT3563 or its homologs, degrading extracellular DNA (eDNA) in several B. thetaiotaomicron strains. Our study therefore shows that, although biofilm matrix eDNA provides a biofilm-promoting scaffold in many studied Firmicutes and Proteobacteria, BT3563-mediated eDNA degradation is required to form B. thetaiotaomicron biofilm in the presence of bile.

Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution.

The noncoding genome plays an important role in de novo gene birth and in the emergence of genetic novelty. Nevertheless, how noncoding sequences' properties could promote the birth of novel genes and shape the evolution and the structural diversity of proteins remains unclear. Therefore, by combining different bioinformatic approaches, we characterized the fold potential diversity of the amino acid sequences encoded by all intergenic open reading frames (ORFs) of S. cerevisiae with the aim of (1) exploring whether the structural states' diversity of proteomes is already present in noncoding sequences, and (2) estimating the potential of the noncoding genome to produce novel protein bricks that could either give rise to novel genes or be integrated into pre-existing proteins, thus participating in protein structure diversity and evolution. We showed that amino acid sequences encoded by most yeast intergenic ORFs contain the elementary building blocks of protein structures. Moreover, they encompass the large structural state diversity of canonical proteins, with the majority predicted as foldable. Then, we investigated the early stages of de novo gene birth by reconstructing the ancestral sequences of 70 yeast de novo genes and characterized the sequence and structural properties of intergenic ORFs with a strong translation signal. This enabled us to highlight sequence and structural factors determining de novo gene emergence. Finally, we showed a strong correlation between the fold potential of de novo proteins and one of their ancestral amino acid sequences, reflecting the relationship between the noncoding genome and the protein structure universe.

Lysine-specific acetylated proteome from the archaeon Thermococcus gammatolerans reveals the presence of acetylated histones.

Thermococcus gammatolerans EJ3 is an extremophile archaeon which was revealed as one of the most radioresistant organisms known on Earth, withstanding up to 30 kGy gamma-ray radiations. While its theoretical proteome is rather small, T. gammatolerans may enhance its toolbox by post-translational modification of its proteins. Here, we explored its extent of Nε-acetylation of lysines. For this, we immunopurified with two acetylated-lysine antibodies the acetylated peptides resulting from a proteolysis of soluble proteins with trypsin. The comparison of acetylated proteomes of two archaea highlights some common acetylation patterns but only 4 out of 26 orthologous proteins found to be acetylated in both species, are acetylated on the same lysine site. We evidenced that histone B is acetylated in T. gammatolerans at least at two different sites (K27 and K36), and a peptide common at the C-terminus of histones A and B is also acetylated. We verified that acetylation of histones is a common trait among Thermococcales after recording data on Thermococcus kodakaraensis histones and identifying three acetylated sites. This discovery reinforces the strong evolutionary link between Archaea and Eukaryotes and should be an incentive for further investigation on the extent and role of acetylation of histones in Archaea. SIGNIFICANCE: Acetylation is an important post-translational modification of proteins that has been extensively described in Eukaryotes, and more recently in Bacteria. Here, we report for the first time ever that histones in Archaea are also modified by acetylation after a systematic survey of acetylated peptides in Thermococcus gammatolerans. Structural models of histones A and B indicates that acetylation of the identified modified residues may play an important role in histone assembly and/or interaction with DNA. The in-depth protein acetylome landscape in T. gammatolerans includes at least 181 unique protein sequences, some of them being modified on numerous residues. Proteins involved in metabolic processes, information storage and processing mechanisms are over-represented categories in this dataset, highlighting the ancient role of this protein post-translational modification in primitive cells.

Febrile young infants with abnormal urine dipstick at low risk of invasive bacterial infection.

OBJECTIVES: To develop and validate a prediction rule to identify well-appearing febrile infants aged ≤90 days with an abnormal urine dipstick at low risk of invasive bacterial infections (IBIs, bacteraemia or bacterial meningitis). DESIGN: Ambispective, multicentre study. SETTING: The derivation set in a single paediatric emergency department (ED) between 2003 and 2017. The validation set in 21 European EDs between December 2017 and November 2019. PATIENTS: Two sets of well-appearing febrile infants aged ≤90 days with an abnormal urine dipstick (either leucocyte esterase and/or nitrite positive test). MAIN OUTCOME: Prevalence of IBI in low-risk infants according to the RISeuP score. RESULTS: We included 662 infants in the derivation set (IBI rate:5.2%). After logistic regression, we developed a score (RISeuP score) including age (≤15 days old), serum procalcitonin (≥0.6 ng/mL) and C reactive protein (≥20 mg/L) as risk factors. The absence of any risk factor had a sensitivity of 96.0% (95% CI 80.5% to 99.3%), a negative predictive value of 99.4% (95% CI 96.4% to 99.9%) and a specificity of 32.9% (95% CI 28.8% to 37.3%) for ruling out an IBI. Applying it in the 449 infants of the validation set (IBI rate 4.9%), sensitivity, negative predictive value and specificity were 100% (95% CI 87.1% to 100%), 100% (95% CI 97.3% to 100%) and 29.7% (95% CI 25.8% to 33.8%), respectively. CONCLUSION: This prediction rule accurately identified well-appearing febrile infants aged ≤90 days with an abnormal urine dipstick at low risk of IBI. This score can be used to guide initial clinical decision-making in these patients, selecting infants suitable for an outpatient management.

Protein Interaction Energy Landscapes are Shaped by Functional and also Non-functional Partners.

In the crowded cell, a strong selective pressure operates on the proteome to limit the competition between functional and non-functional protein-protein interactions. We developed an original theoretical framework in order to interrogate how this competition constrains the behavior of proteins with respect to their partners or random encounters. Our theoretical framework relies on a two-dimensional (2D) representation of interaction energy landscapes, with 2D energy maps, which reflect in a synthetic way the spatial distribution of the interaction propensity of a protein surface for another protein. We realized the interaction propensity mapping of proteins' surfaces in interaction with functional and arbitrary partners and asked whether the distribution of their interaction propensity is conserved during evolution. Therefore, we performed several thousands of cross-docking simulations to systematically characterize the energy landscapes of 103 proteins interacting with different sets of homologs, corresponding to their functional partner's family or arbitrary protein families. Then, we systematically compared the energy maps resulting from the docking of each protein with the different protein families of the dataset. Strikingly, we show that the interaction propensity not only of the binding sites but also of the rest of the surface is conserved for docking partners belonging to the same protein family. Interestingly, this observation holds for docked proteins corresponding to true but also arbitrary partners. Our theoretical framework enables the characterization of the energy behavior of a protein in interaction with hundreds of proteins and opens the way for the characterization of the behavior of proteins in a specific environment.

Roles of lytic transglycosylases in biofilm formation and ß-lactam resistance in methicillin-resistant Staphylococcus aureus.

Staphylococcus aureus is responsible for numerous community outbreaks and is one of the most frequent causes of nosocomial infections with significant morbidity and mortality. While the function of lytic transglycosylases (LTs) in relation to cell division, biofilm formation, and antibiotic resistance has been determined for several bacteria, their role in S. aureus remains largely unknown. The only known LTs in S. aureus are immunodominant staphylococcal antigen A (IsaA) and Staphylococcus epidermidis D protein (SceD). Our study demonstrates that, in a strain of methicillin-resistant S. aureus (MRSA), IsaA and SceD contribute differently to biofilm formation and ß-lactam resistance. Deletion of isaA, but not sceD, led to decreased biofilm formation. Additionally, in isaA-deleted strains, ß-lactam resistance was significantly decreased compared to that of wild-type strains. Plasmid-based expression of mecA, a major determinant of ß-lactam resistance in MRSA, in an isaA-deleted strain did not restore ß-lactam resistance, demonstrating that the ß-lactam susceptibility phenotype is exhibited by isaA mutant regardless of the production level of PBP2a. Overall, our results suggest that IsaA is a potential therapeutic target for MRSA infections.

Nutrition of Preterm Infants and Raw Breast Milk-Acquired Cytomegalovirus Infection: French National Audit of Clinical Practices and Diagnostic Approach.

Raw breast milk is the optimal nutrition for infants, but it is also the primary cause of acquired cytomegalovirus (CMV) infection. Thus, many countries have chosen to contraindicate to feed raw breast milk preterm infants from CMV-positive mothers before a corrected age of 32 weeks or under a weight of 1500 g. French national recommendations have not been updated since 2005. An audit of the French practices regarding the nutrition with raw breast milk in preterm infants was carried out using a questionnaire sent to all neonatal care units. Diagnosed postnatal milk-acquired CMV infections have been analysed using hospitalisation reports. Seventy-five percent of the neonatal units responded: 24% complied with the French recommendations, 20% contraindicated raw breast milk to all infants before 32 weeks regardless of the mothers' CMV-status, whereas 25% fed all preterm infants unconditionally with raw breast milk. Thirty-five cases of infants with milk-acquired CMV infections have been reported. The diagnosis was undeniable for five patients. In France, a high heterogeneity marks medical practices concerning the use of raw breast milk and the diagnostic approach for breast milk-acquired CMV infection is often incomplete. In this context, updated national recommendations and monitored CMV infections are urgently needed.

Meet-U: Educating through research immersion.

We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4-5 people and have to realize a project from A to Z that answers a challenging question in biology. Meet-U promotes "coopetition," as the students collaborate within and across the teams and are also in competition with each other to develop the best final product. Meet-U fosters interactions between different actors of education and research through the organization of a meeting day, open to everyone, where the students present their work to a jury of researchers and jury members give research seminars. This very unique combination of education and research is strongly motivating for the students and provides a formidable opportunity for a scientific community to unite and increase its visibility. We report on our experience with Meet-U in two French universities with master's students in bioinformatics and modeling, with protein-protein docking as the subject of the course. Meet-U is easy to implement and can be straightforwardly transferred to other fields and/or universities. All the information and data are available at www.meet-u.org.

Avaliação da autoeficácia materna em amamentar no puerpério imediato / Assessment of maternal self-efficacy in breastfeeding in the immediate puerperium

Objetivo: avaliar a autoeficácia materna em amamentar no puerpério imediato. Métodos: estudo transversal que envolveu 132 puérperas. No alojamento conjunto, foi aplicado formulário com dados sociodemográficos e obstétricos e a Breastfeeding Self-Efficacy Scale ­ Short Form. Resultados: a maioria das mulheres entrevistadas apresentou elevada (90,9%) e média (9,1%) autoeficácia em amamentar. Não houve associação entre os escores da Breastfeeding Self-Efficacy Scale ­ Short Form e as variáveis sociodemográficas e obstétricas. Conclusão: as mulheres apresentaram elevada autoeficácia em amamentar, o que remete à expectativa favorável ao aleitamento materno, sendo necessário acompanhamento do profissional enfermeiro para garantir assistência mais efetiva no apoio à amamentação (AU).

Erratum: Clinical Findings and Autopsy of a Preterm Infant with Breast Milk-Acquired Cytomegalovirus Infection.

[This corrects the article DOI: 10.1055/s-0035-1566249.].