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ABSTRACTIntratumoral bacteria flexibly contribute to cellular and molecular tumor heterogeneity for supporting cancer recurrence through poorly understood mechanisms. Using spatial metabolomic profiling technologies and 16SrRNA sequencing, we herein report that right-sided colorectal tumors are predominantly populated with Colibactin-producing Escherichia coli (CoPEC) that are locally establishing a high-glycerophospholipid microenvironment with lowered immunogenicity. It coincided with a reduced infiltration of CD8+ T lymphocytes that produce the cytotoxic cytokines IFN-γ where invading bacteria have been geolocated. Mechanistically, the accumulation of lipid droplets in infected cancer cells relied on the production of colibactin as a measure to limit genotoxic stress to some extent. Such heightened phosphatidylcholine remodeling by the enzyme of the Land’s cycle supplied CoPEC-infected cancer cells with sufficient energy for sustaining cell survival in response to chemotherapies. This accords with the lowered overall survival of colorectal patients at stage III-IV who were colonized by CoPEC when compared to patients at stage I-II. Accordingly, the sensitivity of CoPEC-infected cancer cells to chemotherapies was restored upon treatment with an acyl-CoA synthetase inhibitor. By contrast, such metabolic dysregulation leading to chemoresistance was not observed in human colon cancer cells that were infected with the mutant strain that did not produce colibactin (11G5∆ClbQ). This work revealed that CoPEC locally supports an energy trade-off lipid overload within tumors for lowering tumor immunogenicity. This may pave the way for improving chemoresistance and subsequently outcome of CRC patients who are colonized by CoPEC.

Field Portable X-Ray Fluorescence (FPXRF) was investigated as an alternative analysis tool for the detection and quantification of gold in hyperaccumulator plants in the field. First, synthetic gold standards were prepared with materials chosen to best simulate plant material, using microcrystalline cellulose (mcc) or ash by adding known amounts of gold. Powder samples were obtained containing gold in amounts ranging from 10 to 1000 ppm of gold. They were analysed, as well as blank samples of mcc and ash, using a NITON xl3t GOLDD+ FPXRF spectrometer in AllGeo and Soil modes with an analysis time of 60 s. Results were compared to Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES) analysis of the synthetic gold standards after digestion in aqua regia. Gold was detected and accurately quantified in synthetic gold standards containing more than 25 ppm of gold in AllGeo mode. At lower concentration, results were much more inaccurate, with no gold being detected at 10 ppm. In Soil mode, similar results to AllGeo mode were obtained with mcc synthetic standards. However, with ash synthetic standard gold quantification was very poor over the whole concentration range and gold was detected in the blank ash sample, which was confirmed as a false positive by the subsequent ICP analysis. Samples of Phyllanthus stipulatus, suspected gold hyperaccumulators, collected on gold-bearing sites in French Guiana were then analysed following the same protocol. The same false positive phenomenon was observed in some of them, with gold being detected by FPXRF in Soil mode but not by ICP analysis. Furthermore, analysis of the FPXRF spectra revealed that none of the characteristic gold emission ray was present. This false positive was attributed to an interference caused by zinc, present in significant amount in the ash of the synthetic standard and the collected plants.

Precision Medicine is being increasingly used in the developed world to improve health care. While several Precision Medicine (PM) initiatives have been launched worldwide, their implementations have proven to be more challenging particularly in low- and middle-income countries. To address this issue, the “Personalized Medicine in North Africa” initiative (PerMediNA) was launched in three North African countries namely Tunisia, Algeria and Morocco. PerMediNA is coordinated by Institut Pasteur de Tunis together with the French Ministry for Europe and Foreign Affairs, with the support of Institut Pasteur in France. The project is carried out along with Institut Pasteur d’Algérie and Institut Pasteur du Maroc in collaboration with national and international leading institutions in the field of PM including Institut Gustave Roussy in Paris. PerMediNA aims to assess the readiness level of PM implementation in North Africa, to strengthen PM infrastructure, to provide workforce training, to generate genomic data on North African populations, to implement cost effective, affordable and sustainable genetic testing for cancer patients and to inform policy makers on how to translate research knowledge into health products and services. Gender equity and involvement of young scientists in this implementation process are other key goals of the PerMediNA project.In this paper, we are describing PerMediNA as the first PM implementation initiative in North Africa. Such initiatives contribute significantly in shortening existing health disparities and inequities between developed and developing countries and accelerate access to innovative treatments for global health.

The stability of beams of laser wakefield accelerated electrons in dielectric capillary tubes is experimentally investigated. These beams are found to be more stable in charge and pointing than the corresponding beams of electrons accelerated in a gas jet. Electron beams with an average charge of 43 pC and a standard deviation of 14% are generated. The fluctuations in charge are partly correlated to fluctuations in laser pulse energy. The pointing scatter of the electron beams is measured to be as low as 0.8 mrad (rms). High laser beam pointing stability improved the stability of the electron beams.

The degradation of a mixture of ibuprofen, naproxen, and diclofenac in various effluents by UVC/H2O2 or UVC/S2O82− was studied to assess the impact of the matrix composition and of the oxidant precursor on process efficiency. Experiments were carried out in a 20-L laboratory pilot (a scaled-down version of a full-scale pilot). In effluents collected during dry weather, the rural constructed wetland effluent allowed faster degradation than the urban conventional WWTP effluent, regardless of the nature of the targets or of the oxidant precursor. This was mainly attributed to a three-times higher chemical oxygen demand in the urban effluent, likely to quench the oxidative species. UV fluences to reach 90% degradation of the three compounds were 3,800 and 5,500 mJ cm−2 in the rural effluent, whereas they were 6,600 and 6,100 mJ cm−2 in the urban effluent with H2O2 and S2O82−, respectively. After a rainfall event, the rural effluent composition was not significantly affected compared to that of the urban effluent that underwent the dilution effect. Therefore, the stability of the rural effluent composition allowed comparable degradation efficiency, whereas the dilution effect led to a significant increase in the degradation rate constants in the urban effluent (up to four times higher). HIGHLIGHTS UVC-based process efficiency varies with weather and effluent composition.; Downstream effluent composition seems more consistent in a rural constructed wetland than in an urban WWTP.; UVC-based AOPs are more appropriate to treat effluents with low and consistent organic matter concentration.; allows for faster degradation of NAP and H2O2 for faster degradation of IBU.;

In New Caledonia, a French archipelago situated in the Pacific Ocean and benefiting from a large autonomy, the population, which included natives and non-natives, is diverse depending on how long they have been settled in the territory. Non-natives, who have settled in successive waves since 1855 in the context of colonization and then of the 1960s nickel boom, can be divided between Caldoches, metropolitans and other minorities (especially Asians and Oceanians), despite widespread interbreeding. This diversity is reflected in the territory by a division between inalienable Kanak customary lands and lands transferable to other populations, and by the maintenance of a customary system which was institutionalized in 1999 with the establishment of a customary Senate. The Matignon-Oudinot agreements (1988) thus ratified a division of the archipelago between the Kanaks (Northern Province and the islands) and the Caldoches (Southern Province).

Abstract Background Bacteria and their viruses, bacteriophages, are the most abundant entities of the gut microbiota, a complex community of microorganisms associated with human health and disease. In this ecosystem, the interactions between these two key components are still largely unknown. In particular, the impact of the gut environment on bacteria and their associated prophages is yet to be deciphered. Results To gain insight into the activity of lysogenic bacteriophages within the context of their host genomes, we performed proximity ligation-based sequencing (Hi-C) in both in vitro and in vivo conditions on the 12 bacterial strains of the OMM12 synthetic bacterial community stably associated within mice gut (gnotobiotic mouse line OMM12). High-resolution contact maps of the chromosome 3D organization of the bacterial genomes revealed a wide diversity of architectures, differences between environments, and an overall stability over time in the gut of mice. The DNA contacts pointed at 3D signatures of prophages leading to 16 of them being predicted as functional. We also identified circularization signals and observed different 3D patterns between in vitro and in vivo conditions. Concurrent virome analysis showed that 11 of these prophages produced viral particles and that OMM12 mice do not carry other intestinal viruses. Conclusions The precise identification by Hi-C of functional and active prophages within bacterial communities will unlock the study of interactions between bacteriophages and bacteria across conditions (healthy vs disease). Video Abstract

Abstract The ability of bacterial pathogens to establish recurrent and persistent infections is frequently associated with their ability to form biofilms. Clostridioides difficile infections have a high rate of recurrence and relapses and it is hypothesized that biofilms are involved in its pathogenicity and persistence. Biofilm formation by C. difficile is still poorly understood. It has been shown that specific molecules such as deoxycholate (DCA) or metronidazole induce biofilm formation, but the mechanisms involved remain elusive. In this study, we describe the role of the C. difficile lipoprotein CD1687 during DCA-induced biofilm formation. We showed that the expression of CD1687, which is part of an operon within the CD1685-CD1689 gene cluster, is controlled by multiple transcription starting sites and some are induced in response to DCA. Only CD1687 is required for biofilm formation and the overexpression of CD1687 is sufficient to induce biofilm formation. Using RNAseq analysis, we showed that CD1687 affects the expression of transporters and metabolic pathways and we identified several potential binding partners by pull-down assay, including transport-associated extracellular proteins. We then demonstrated that CD1687 is surface exposed in C. difficile, and that this localization is required for DCA-induced biofilm formation. Given this localization and the fact that C. difficile forms eDNA-rich biofilms, we confirmed that CD1687 binds DNA in a non-specific manner. We thus hypothesize that CD1687 is a component of the downstream response to DCA leading to biofilm formation by promoting interaction between the cells and the biofilm matrix by binding eDNA.

Summary: Investigations of cellular responses to viral infection are commonly performed on mixed populations of infected and uninfected cells or using single-cell RNA sequencing, leading to inaccurate and low-resolution gene expression interpretations. Here, we performed deep polyA+ transcriptome analyses and novel RNA profiling of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected lung epithelial cells, sorted based on the expression of the viral spike (S) protein. Infection caused a massive reduction in mRNAs and long non-coding RNAs (lncRNAs), including transcripts coding for antiviral factors, such as interferons (IFNs). This absence of IFN signaling probably explained the poor transcriptomic response of bystander cells co-cultured with S+ ones. NF-κB pathway and the inflammatory response escaped the global shutoff in S+ cells. Functional investigations revealed the proviral function of the NF-κB pathway and the antiviral activity of CYLD, a negative regulator of the pathway. Thus, our transcriptomic analysis on sorted cells revealed additional genes that modulate SARS-CoV-2 replication in lung cells.

Abstract Since the beginning of the SARS-CoV-2 coronavirus pandemic, genome sequencing is essential to monitor viral mutations over time and by territory. This need for complete genetic information is further reinforced by the rapid spread of variants of concern. In this paper, we assess the ability of the hybridization technique, Capture-Seq, to detect the SARS-CoV-2 genome, either partially or in its integrity on patients samples. We studied 20 patient nasal swab samples broken down into five series of four samples of equivalent viral load from CT25 to CT36+ . For this, we tested 3 multi-virus panel as well as 2 SARS-CoV-2 only panels. The panels were chosen based on their specificity, global or specific, as well as their technological difference in the composition of the probes: ssRNA, ssDNA and dsDNA. The multi-virus panels are able to capture high-abundance targets but fail to capture the lowest-abundance targets, with a high percentage of off-target reads corresponding to the abundance of the host sequences. Both SARS-CoV-2-only panels were very effective, with high percentage of reads corresponding to the target. Overall, capture followed by sequencing is very effective for the study of SARS-CoV-2 in low-abundance patient samples and is suitable for samples with CT values up to 35.

Bismuth vanadate – bismuth molybdate solid-solution was prepared to elaborate ceramics with different amounts of cation vacancies. Dense ceramics with similar microstructures were obtained and the evolution of their melting point, specific heat, thermal diffusivity, and conductivity as a function of the amount of vacancy was evaluated. At room temperature, the thermal conductivity decreases from 1.74 W m−1 K−1 for BiVO4 (x=0) to 1.12 W m−1 K−1 for Bi0.867□0.133Mo0.4V0.6O4 (x=0.4). Moreover, we show that a very small amount of vacancy (1.7%, x=0.05) is enough to provide a large decrease in thermal conductivity by more than 15%, in agreement with a mass fluctuation scattering model. However, the temperature of the melting point also decreases with increasing amount of vacancy. Our results suggest adding only a very small amount of vacancy as the best strategy to obtain superior materials for thermal barriers and thermoelectric devices, with ultra-low thermal conductivity and high-temperature stability.

A dicationic PdII dimer, bis{2-[(diisopropylphosphanyl)methyl]quinoline-8-thiolato}palladium(II) bis(hexafluoridoantimonate) dichloromethane monosolvate, [Pd2(C32H42N2P2S2)](SbF6)2·CH2Cl2, containing a 2-[(diisopropylphosphanyl)methyl]quinoline-8-thiolate pincer ligand, was isolated and its crystal structure determined. The title compound crystallizes in the orthorhombic space group Pbca. A dimeric structure is formed by bridging coordination of the S atoms. The geometry of the butterfly-shaped Pd2S2 core is bent, with a hinge angle of 108.0 (1)° and a short Pd...Pd distance of 2.8425 (7) Å. These values are the lowest measured compared to ten dicationic dimers with a Pd2S2 core featuring sulfur atoms embedded in a chelating ligand. One of the two hexafluoridoantimonate anions is disordered over two sets of positions with site-occupancy factors of 0.711 (5) and 0.289 (5). The crystal structure is stabilized by many C—H...F and C—H...π interactions, forming a supramolecular network.

Oropouche fever is a zoonotic dengue-like syndrome caused by Oropouche virus. In August–September 2020, dengue-like syndrome developed in 41 patients in a remote rainforest village in French Guiana. By PCR or microneutralization, 23 (82.1%) of 28 tested patients were positive for Oropouche virus, documenting its emergence in French Guiana.

Orthohantaviruses are rodent-borne emerging viruses that may cause severe diseases in humans but no apparent pathology in their small mammal reservoirs. However, the mechanisms leading to tolerance or pathogenicity in humans and persistence in rodent reservoirs are poorly understood, as is the manner in which they spread within and between organisms. Here, we used a range of cellular and molecular approaches to investigate the interactions of three different orthohantaviruses-Puumala virus (PUUV), responsible for a mild to moderate form of hemorrhagic fever with renal syndrome in humans, Tula virus (TULV) with low pathogenicity, and non-pathogenic Prospect Hill virus (PHV)-with human and rodent host cell lines. Besides the fact that cell susceptibility to virus infection was shown to depend on the cell type and virus strain, the three orthohantaviruses were able to infect Vero E6 and HuH7 human cells, but only the former secreted infectious particles. In cells derived from PUUV reservoir, the bank vole (Myodes glareolus), PUUV achieved a complete viral cycle, while TULV did not enter the cells and PHV infected them but did not produce infectious particles, reflecting differences in host specificity. A search for mature virions by electron microscopy (EM) revealed that TULV assembly occurred in part at the plasma membrane, whereas PHV particles were trapped in autophagic vacuoles in cells of the heterologous rodent host. We described differential interactions of orthohantaviruses with cellular factors, as supported by the cellular distribution of viral nucleocapsid protein with cell compartments, and proteomics identification of cellular partners. Our results also showed that interferon (IFN) dependent gene expression was regulated in a cell and virus species dependent manner. Overall, our study highlighted the complexity of the host-virus relationship and demonstrated that orthohantaviruses are restricted at different levels of the viral cycle. In addition, the study opens new avenues to further investigate how these viruses differ in their interactions with cells to evade innate immunity and how it depends on tissue type and host species.

Abstract Interactions between the prokaryotic microbiome and eukaryotic parasites in the vertebrate gut may affect overall host health and disease. While intertropical areas exhibit a high rate of parasites carriers, such interactions are understudied in these populations. Our objectives were to (1) describe the gut microbiome of individuals living in Madagascar, (2) identify potential associations between bacterial taxa and parasites colonizing the digestive tract and (3) highlight main determinants of the gut microbiota composition in this developing country. Metadata (socioeconomic, diet, clinical) and fecal samples were collected from 219 volunteers from North-West Madagascar (Mahajanga). Fecal microbiome was assessed through 16S rRNA gene sequencing and metabolomics, and related to dietary habits and parasites carriage. We highlight important Malagasy gut microbiome peculiarities. Out of three detected enterotypes, only one is similar to that observed in Westernized countries (Ruminococcus-driven). Functions associated with the two others (Clostridium sensu stricto-driven and Escherichia/Shigella-driven) are mostly directed toward amino acids biosynthesis and degradation, respectively. Diet and protozoan carriage were the main drivers of microbiota composition. High protozoan carriage was associated with higher diversity, richness and microbial functionalities. The gut microbiome of Malagasy strongly differs from that of Westernized countries. Asymptomatic protozoan carriage and dietary habits are the external factors with the deepest impact on gut microbiome. Further studies are needed to understand whether gut microbial richness constitute a predilection niche for protozoans colonization, due to their gazing features, or whether the parasites themselves induce a higher bacterial richness.

Abstract Viruses that infect bacteria (phages) are increasingly recognized for their importance in diverse ecosystems but identifying and annotating them in large-scale sequence datasets is still challenging. Although efficient scalable virus identification tools are emerging, defining the exact ends (termini) of phage genomes is still particularly difficult. The proper identification of termini is crucial, as it helps in characterizing the packaging mechanism of bacteriophages and provides information on various aspects of phage biology. Here, we introduce PhageTermVirome (PTV) as a tool for the easy and rapid high-throughput determination of phage termini and packaging mechanisms using modern large-scale metagenomics datasets. We successfully tested the PTV algorithm on a mock virome dataset and then used it on two real virome datasets to achieve the rapid identification of more than 100 phage termini and packaging mechanisms, with just a few hours of computing time. Because PTV allows the identification of free fully formed viral particles (by recognition of termini present only in encapsidated DNA), it can also complement other virus identification softwares to predict the true viral origin of contigs in viral metagenomics datasets. PTV is a novel and unique tool for high-throughput characterization of phage genomes, including phage termini identification and characterization of genome packaging mechanisms. This software should help researchers better visualize, map and study the virosphere. PTV is freely available for downloading and installation at https://gitlab.pasteur.fr/vlegrand/ptv .

Prematurity is a risk factor for dysbiosis of the gut microbiota due to particular birth conditions and frequent prolonged hospitalization of neonates. Although gut microbiota colonization after birth and its establishment during the hospitalization period have been studied in preterm infants, data on gut microbiota following discharge, particularly during early childhood, are scarce. The present study investigated the relationship between gut microbiota at 1 month after birth (hospitalization period) and 3.5 years of age in 159 preterm children belonging to the French EPIFLORE prospective observational cohort study. Analysis using bacterial 16S rRNA gene sequencing showed that the gut microbiota of preterm neonates at 1 month was highly variable and characterized by six distinct enterotypes. In contrast, the gut microbiota of the same children at 3.5 years of age showed less variability, with only two discrete enterotypes. An absence of association between enterotypes at 1 month and 3.5 years of age was observed. While the alpha diversity of gut microbiota significantly increased between 1 month and 3.5 years of age, for both alpha and beta diversities, there was no correlation between the 1-month and 3.5-years time points. Comparison at 3.5 years between children born either preterm (n = 159) or full-term (n = 200) showed no differences in terms of enterotypes, but preterm children harbored a lower Shannon diversity index and a different overall composition of microbiota than full-term children. This study suggests that the characteristics of the early gut microbiota of preterm children are not predictive of the microbial community composition at 3.5 years of age. However, the impact of gestational age is still noticeable on the gut microbiota up to 3.5 years of age.

Ionization-induced electron injection was investigated experimentally by focusing a driving laser pulse with a maximum normalized potential of 1.2 at different positions along the plasma density profile inside a gas cell, filled with a gas mixture composed of 99%H2+1%N2. Changing the laser focus position relative to the gas cell entrance controls the accelerated electron bunch properties, such as the spectrum width, maximum energy, and accelerated charge. Simulations performed using the 3D particle-in-cell code WARP with a realistic density profile give results that are in good agreement with the experimental ones. The interest of this regime for optimizing the bunch charge in a selected energy window is discussed.

SpoIIE is a phosphatase involved in the activation of the first sigma factor of the forespore, σF, during sporulation. A ΔspoIIE mutant of Clostridium beijerinckii NCIMB 8052, previously generated by CRISPR-Cas9, did not sporulate but still produced granulose and solvents. Microscopy analysis also showed that the cells of the ΔspoIIE mutant are elongated with the presence of multiple septa. This observation suggests that in C. beijerinckii, SpoIIE is necessary for the completion of the sporulation process, as seen in Bacillus and Clostridium acetobutylicum. Moreover, when grown in reactors, the spoIIE mutant produced higher levels of solvents than the wild type strain. The impact of the spoIIE inactivation on gene transcription was assessed by comparative transcriptome analysis at three time points (4 h, 11 h and 23 h). Approximately 5% of the genes were differentially expressed in the mutant compared to the wild type strain at all time points. Out of those only 12% were known sporulation genes. As expected, the genes belonging to the regulon of the sporulation specific transcription factors (σF, σE, σG, σK) were strongly down-regulated in the mutant. Inactivation of spoIIE also caused differential expression of genes involved in various cell processes at each time point. Moreover, at 23 h, genes involved in butanol formation and tolerance, as well as in cell motility, were up-regulated in the mutant. In contrast, several genes involved in cell wall composition, oxidative stress and amino acid transport were down-regulated. These results indicate an intricate interdependence of sporulation and stationary phase cellular events in C. beijerinckii.

The emerging human enteropathogen Clostridioides difficile is the main cause of diarrhea associated with antibiotherapy. Regulatory pathways underlying the adaptive responses remain understudied and the global view of C. difficile promoter structure is still missing. In the genome of C. difficile 630, 22 genes encoding sigma factors are present suggesting a complex pattern of transcription in this bacterium. We present here the first transcriptional map of the C. difficile genome resulting from the identification of transcriptional start sites (TSS), promoter motifs and operon structures. By 5′-end RNA-seq approach, we mapped more than 1000 TSS upstream of genes. In addition to these primary TSS, this analysis revealed complex structure of transcriptional units such as alternative and internal promoters, potential RNA processing events and 5′ untranslated regions. By following an in silico iterative strategy that used as an input previously published consensus sequences and transcriptomic analysis, we identified candidate promoters upstream of most of protein-coding and non-coding RNAs genes. This strategy also led to refine consensus sequences of promoters recognized by major sigma factors of C. difficile. Detailed analysis focuses on the transcription in the pathogenicity locus and regulatory genes, as well as regulons of transition phase and sporulation sigma factors as important components of C. difficile regulatory network governing toxin gene expression and spore formation. Among the still uncharacterized regulons of the major sigma factors of C. difficile, we defined the SigL regulon by combining transcriptome and in silico analyses. We showed that the SigL regulon is largely involved in amino-acid degradation, a metabolism crucial for C. difficile gut colonization. Finally, we combined our TSS mapping, in silico identification of promoters and RNA-seq data to improve gene annotation and to suggest operon organization in C. difficile. These data will considerably improve our knowledge of global regulatory circuits controlling gene expression in C. difficile and will serve as a useful rich resource for scientific community both for the detailed analysis of specific genes and systems biology studies.

Since the 1990s, the Christmas markets have become unavoidable festive events during the season of Advent in Alsace, and have staged “the magic of Christmas” to develop. Thanks to the transformation of a medieval German cultural tradition into event tourism, the region is now attracting a growing number of visitors during a slack period of the year. This form of event tourism uses specific temporalities and scales in the “ordinary” territories of the city centers, and gives international visibility to Alsace as a travel destination. But, more and more difficulties are raised by the saturation of space, increasing commodification and territorial conflicts.

In the Ile-de-France area, suburban forests still exist, but their size, uses and exploitations are different compared to other French forests. These suburban forests can in many respects be described as margins. First, they constitute “natural” spaces in an urban area. Moreover, they have a social, ecological and recreational role. The activities they are the site of are only marginal in the French productive system: forestry, hunting, mushroom picking. However the level of marginality increases from Paris to the periphery and from forest edges to forest interior.

Abstract The worrying rise of antibiotic resistance in pathogenic bacteria is leading to a renewed interest in bacteriophages as a treatment option. Novel sequencing technologies enable description of an increasing number of phage genomes, a critical piece of information to understand their life cycle, phage-host interactions, and evolution. In this work, we demonstrate how it is possible to recover more information from sequencing data than just the phage genome. We developed a theoretical and statistical framework to determine DNA termini and phage packaging mechanisms using NGS data. Our method relies on the detection of biases in the number of reads, which are observable at natural DNA termini compared with the rest of the phage genome. We implemented our method with the creation of the software PhageTerm and validated it using a set of phages with well-established packaging mechanisms representative of the termini diversity, i.e. 5′cos (Lambda), 3′cos (HK97), pac (P1), headful without a pac site (T4), DTR (T7) and host fragment (Mu). In addition, we determined the termini of nine Clostridium difficile phages and six phages whose sequences were retrieved from the Sequence Read Archive. PhageTerm is freely available (https://sourceforge.net/projects/phageterm), as a Galaxy ToolShed and on a Galaxy-based server (https://galaxy.pasteur.fr).

Clostridium difficile is an opportunistic entero-pathogen causing post-antibiotic and nosocomial diarrhea upon microbiota dysbiosis. Although biofilms could contribute to colonization, little is known about their development and physiology. Strain 630Δerm is able to form, in continuous-flow micro-fermentors, macro-colonies and submersed biofilms loosely adhesive to glass. According to gene expression data, in biofilm/planktonic cells, central metabolism is active and fuels fatty acid biosynthesis rather than fermentations. Consistently, succinate is consumed and butyrate production is reduced. Toxin A expression, which is coordinated to metabolism, is down-regulated, while surface proteins, like adhesins and the primary Type IV pili subunits, are over-expressed. C-di-GMP level is probably tightly controlled through the expression of both diguanylate cyclase-encoding genes, like dccA, and phosphodiesterase-encoding genes. The coordinated expression of genes controlled by c-di-GMP and encoding the putative surface adhesin CD2831 and the major Type IV pilin PilA1, suggests that c-di-GMP could be high in biofilm cells. A Bacillus subtilis SinR-like regulator, CD2214, and/or CD2215, another regulator co-encoded in the same operon as CD2214, control many genes differentially expressed in biofilm, and in particular dccA, CD2831 and pilA1 in a positive way. After growth in micro-titer plates and disruption, the biofilm is composed of robust aggregated structures where cells are embedded into a polymorphic material. The intact biofilm observed in situ displays a sparse, heterogeneous and high 3D architecture made of rods and micro-aggregates. The biofilm is denser in a mutant of both CD2214 and CD2215 genes, but it is not affected by the inactivation of neither CD2831 nor pilA1. dccA, when over-expressed, not only increases the biofilm but also triggers its architecture to become homogeneous and highly aggregated, in a way independent of CD2831 and barely dependent of pilA1. Cell micro-aggregation is shown to play a major role in biofilm formation and architecture. This thorough analysis of gene expression reprogramming and architecture remodeling in biofilm lays the foundation for a deeper understanding of this lifestyle and could lead to novel strategies to limit C. difficile spread.

ABSTRACT Clostridium difficile is an important nosocomial pathogen and the leading cause of hospital-acquired diarrhea. Antibiotic use is the primary risk factor for the development of C. difficile-associated disease because it disrupts normally protective gut flora and enables C. difficile to colonize the colon. C. difficile damages host tissue by secreting toxins and disseminates by forming spores. The toxin-encoding genes, tcdA and tcdB, are part of a pathogenicity locus, which also includes the tcdR gene that codes for TcdR, an alternate sigma factor that initiates transcription of tcdA and tcdB genes. We created a tcdR mutant in epidemic-type C. difficile strain R20291 in an attempt to identify the global role of tcdR. A site-directed mutation in tcdR affected both toxin production and sporulation in C. difficile R20291. Spores of the tcdR mutant were more heat sensitive than the wild type (WT). Nearly 3-fold more taurocholate was needed to germinate spores from the tcdR mutant than to germinate the spores prepared from the WT strain. Transmission electron microscopic analysis of the spores also revealed a weakly assembled exosporium on the tcdR mutant spores. Accordingly, comparative transcriptome analysis showed many differentially expressed sporulation genes in the tcdR mutant compared to the WT strain. These data suggest that regulatory networks of toxin production and sporulation in C. difficile strain R20291 are linked with each other. IMPORTANCE C. difficile infects thousands of hospitalized patients every year, causing significant morbidity and mortality. C. difficile spores play a pivotal role in the transmission of the pathogen in the hospital environment. During infection, the spores germinate, and the vegetative bacterial cells produce toxins that damage host tissue. Thus, sporulation and toxin production are two important traits of C. difficile. In this study, we showed that a mutation in tcdR, the toxin gene regulator, affects both toxin production and sporulation in epidemic-type C. difficile strain R20291.

NILE ("New Improvements for Lignocellulosic Ethanol") was an integrated European project (2005-2010) devoted to the conversion of lignocellulosic raw materials to ethanol. The main objectives were to design novel enzymes suitable for the hydrolysis of cellulose to glucose and new yeast strains able to efficiently converting all the sugars present in lignocellulose into ethanol. The project also included testing these new developments in an integrated pilot plant and evaluating the environmental and socio-economic impacts of implementing lignocellulosic ethanol on a large scale. Two model raw materials – spruce and wheat straw – both preconditioned with similar pretreatments, were used. Several approaches were explored to improve the saccharification of these pretreated raw materials such as searching for new efficient enzymes and enzyme engineering. Various genetic engineering methods were applied to obtain stable xylose- and arabinose-fermenting Saccharomyces cerevisiae strains that tolerate the toxic compounds present in lignocellulosic hydrolysates. The pilot plant was able to treat 2 tons of dry matter per day, and hydrolysis and fermentation could be run successively or simultaneously. A global model integrating the supply chain was used to assess the performance of lignocellulosic ethanol from an economical and environmental perspective. It was found that directed evolution of a specific enzyme of the cellulolytic cocktail produced by the industrial fungus, Trichoderma reesei, and modification of the composition of this cocktail led to improvements of the enzymatic hydrolysis of pretreated raw material. These results, however, were difficult to reproduce at a large scale. A substantial increase in the ethanol conversion yield and in specific ethanol productivity was obtained through a combination of metabolic engineering of yeast strains and fermentation process development. Pilot trials confirmed the good behaviour of the yeast strains in industrial conditions as well as the suitability of lignin residues as fuels. The ethanol cost and the greenhouse gas emissions were highly dependent on the supply chain but the best performing supply chains showed environmental and economic benefits. From a global standpoint, the results showed the necessity for an optimal integration of the process to co-develop all the steps of the process and to test the improvements in a flexible pilot plant, thus allowing the comparison of various configurations and their economic and environmental impacts to be determined. Le projet NILE, acronyme de "New Improvements for Lignocellulosic Ethanol", était un projet européen (2005-2010) consacré à la conversion des matières premières lignocellulosiques en éthanol. Ses principaux objectifs étaient de concevoir de nouvelles enzymes adaptées à l’hydrolyse de la cellulose en glucose et de nouvelles souches de levure capables de convertir efficacement tous les sucres présents dans la lignocellulose en éthanol. Une autre partie du projet consistait à tester ces nouveaux systèmes dans une installation pilote et à évaluer les impacts environnementaux et socio-économiques de la production et utilisation à grande échelle d’éthanol lignocellulosique. Deux matières premières modèles (l’épicéa et la paille de blé) prétraitées de façon semblable, ont été étudiées. Différentes approches ont été tentées pour améliorer la saccharification de ces matières premières, par exemple, la recherche de nouvelles enzymes efficaces ou l’ingénierie d’enzymes. Plusieurs stratégies d’ingénierie génétique ont été utilisées pour obtenir des souches stables de Saccharomyces cerevisiae capables de fermenter le xylose et l’arabinose, et de tolérer les composés toxiques présents dans les hydrolysats lignocellulosiques. L’installation pilote pouvait traiter 2 tonnes de matières sèches par jour, et l’hydrolyse et la fermentation pouvaient être menées successivement ou simultanément. Un modèle global intégrant la chaîne d’approvisionnement en matière première a servi à évaluer les performances économiques et environnementales de la production d’éthanol lignocellulosique. L’évolution dirigée d’une enzyme du cocktail cellulolytique produit par le champignon Trichoderma reesei, et la modification de la composition de ce cocktail améliorent l’hydrolyse enzymatique des matières premières prétraitées. Cependant, ces résultats n’ont pu être reproduits à grande échelle. Le rendement de conversion et la productivité spécifique en éthanol ont été sensiblement augmentés grâce à l’ingénierie métabolique des souches de levure et au développement d’un procédé optimal de fermentation. Les essais en pilote ont confirmé le bon comportement de ces souches de levure en conditions industrielles ainsi que la possibilité d’utiliser les résidus riches en lignine comme combustible. Le coût de production de l’éthanol et le bilan des émissions de gaz à effet de serre étaient très dépendants des sources d’énergie utilisées. D’un point de vue plus global, les résultats ont montré que l’optimisation du procédé nécessite de codévelopper toutes les étapes de façon intégrée et de valider les améliorations dans une installation pilote, afin notamment de pouvoir comparer différentes configurations et d’en déterminer les effets sur l’économie du procédé et ses impacts environnementaux.

Enzymatic hydrolysis of lignocellulose is one of the major bottlenecks in the development of biological conversion of lignocellulosic biomass to biofuels. One of the most efficient organisms for the production of cellulolytic enzymes is the fungus Trichoderma reesei, mainly thanks to its high secretion capacity. The conversion of cellulose to glucose involves three types of cellulases working in synergy: endoglucanases (EC 3.2.1.4) randomly cleave 13-1,4 glycosidic linkages of cellulose, cellobiohydrolases (EC 3.2.1.91) attack cellulose chain ends to produce cellobiose dimers which are converted into glucose by the 13-glucosidases (EC 3.2.1 21). Unexpectedly, the amount of l3-glucosidase (BGLI) from T. reesei hyperproducing strains represents a very low percentage of the total secreted proteins. A suboptimal content of this enzyme limits the performance of commercial cellulase preparations as cellobiose represents the main inhibitor of the cellulolysis reaction by cellobiohydrolases. This bottleneck can be alleviated either by overexpressing the f3-glucosidase in T. reesei or optimized its specific activity. After giving a brief overview of the main available technologies, this example will be used to illustrate the potential of directed evolution technologies to devolop enzymes tailored to fit industrial needs. We describe the L-ShuffiingTM strategy implemented with three parental genes originating from microbial biodiversity leading to identification of an efficient 13-glucosidase showing a 242 fold increase in specific activity for the pNPGIc substrate compared to WT (Wild Type) Cel3a beta-glucosidase of T. reesei. After expression of the best improved 13-glucosidase in T. reesei and secretion of a new enzymatic cocktail, improvement of the glucosidase activity allows a 4-fold decrease of cellulase loading for the saccharification of an industrial pretreated biomass compared to the parental cocktail. L’hydrolyse enzymatique de la lignocellulose est l’un des principaux goulets d’étranglement dans le développement de la conversion biologique de la biomasse lignocellulosique en biocarburants. L’un des organismes les plus efficaces pour la production d’enzymes cellulolytiques est le champignon Trichoderma reesei, principalement grâce à sa capacité importante de sécrétion. La conversion de la cellulose en glucose implique trois types de cellulases travaillant en synergie : les endoglucanases (EC 3.2.1.4) clivant de façon aléatoire les liaisons glycosidiques en (3-1,4, les cellobiohydrolases (EC 3.2.1.91) attaquant la chaîne de cellulose aux deux extrémités afin de produire le cellobiose, dimère qui sera converti en glucose par l’action des (3-glucosidases (EC 3.2.1.21). De façon inattendue, la quantité de 3-glucosidase (BGL1) sécrétée par les souches de T. reesei représente un très faible pourcentage de la quantité totale des protéines sécrétées qui en fait donc une activité limitante du cocktail. Cette faible activité limite d’autant plus les performances du cocktail que le cellobiose représente le principal inhibiteur de la réaction cellulolyse par les cellobiohydrolases. Ce goulot d’étranglement peut être atténué soit par une surexpression de la (3-glucosidase chez T. reesei, soit par une amélioration de son activité spécifique. Après un bref aperçu des principales technologies existantes, cet exemple sera utilisé dans cette revue pour illustrer le potentiel des technologies d’évolution dirigée pour développer des enzymes répondant aux besoins de l’industrie des biotechnologies. Nous décrivons comment la mise en oeuvre d’une stratégie d’évolution dirigée par le L-ShufflingTM avec trois gènes parentaux provenant de la biodiversité microbienne permet d’obtenir des activités (3-glucosidases très améliorées par rapport à la Cel3a (3-glucosidase de T. reesei (activité spécifique 242 fois plus élevée pour le substrat pNPGIc). Cette amélioration de l’activité glucosidasique, après expression du gène codant pour la 3-glucosidase améliorée chez T. reesei et sécrétion du nouveau cocktail, permet une diminution d’un facteur 4 de la quantité de cocktail nécessaire à la saccharification d’une biomasse industrielle prétraitée (paille de blé).

In situ formation of two cyclic (alkyl) (amino) carbenes (CAACs) followed by addition of BF3•Et2O provided the first two examples of CAAC–BF3 complexes: 1-(2,6-diisopropylphenyl)-3,5,5-trimethyl-3-phenylpyrrolidin-2-ylidene trifluoroborane, and 2-(2,6-diisopropylphenyl)-3,3-dimethyl-2-azaspiro[4.5]decan-1-ylidene trifluoroborane. These CAAC–BF3 complexes are robust compounds that are stable to ambient laboratory conditions and silica gel chromatography. They were characterized by spectroscopy and X-ray crystallography. In contrast, a CAAC complex with borane (BH3) was readily formed in situ according to 1H and 11B NMR analysis, but did not survive the workup conditions. These results set the stage for further studies of the chemistry of CAAC boranes.

ABSTRACT Clostridium difficile is the cause of most frequently occurring nosocomial diarrhea worldwide. As an enteropathogen, C. difficile must be exposed to multiple exogenous genetic elements in bacteriophage-rich gut communities. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems allow bacteria to adapt to foreign genetic invaders. Our recent data revealed active expression and processing of CRISPR RNAs from multiple type I-B CRISPR arrays in C. difficile reference strain 630. Here, we demonstrate active expression of CRISPR arrays in strain R20291, an epidemic C. difficile strain. Through genome sequencing and host range analysis of several new C. difficile phages and plasmid conjugation experiments, we provide evidence of defensive function of the CRISPR-Cas system in both C. difficile strains. We further demonstrate that C. difficile Cas proteins are capable of interference in a heterologous host, Escherichia coli. These data set the stage for mechanistic and physiological analyses of CRISPR-Cas-mediated interactions of important global human pathogen with its genetic parasites. IMPORTANCE Clostridium difficile is the major cause of nosocomial infections associated with antibiotic therapy worldwide. To survive in bacteriophage-rich gut communities, enteropathogens must develop efficient systems for defense against foreign DNA elements. CRISPR-Cas systems have recently taken center stage among various anti-invader bacterial defense systems. We provide experimental evidence for the function of the C. difficile CRISPR system against plasmid DNA and bacteriophages. These data demonstrate the original features of active C. difficile CRISPR system and bring important insights into the interactions of this major enteropathogen with foreign DNA invaders during its infection cycle.

L'environnement naturel des enzymes étant de nature aqueuse, leurs applications industrielles se sont en général limitées à des réactions mettant en jeu des substrats solubles dans l'eau. Depuis quelques années, la possibilité de faire fonctionner des enzymes dans des milieux hydrophobes (hydrocarbures, solvants organiques) a été mise en évidence, engendrant ainsi de nombreux travaux visant, d'une part à mieux comprendre les mécanismes permettant aux enzymes de rester actives dans un tel environnement et, d'autre part à explorer les nouvelles applications envisageables. Les produits pétroliers constituant par excellence le domaine des molécules hydrophobes, le présent article se propose de faire le point sur ces deux aspects, compréhension et intérêt de la catalyse enzymatique en milieu organique. Nous détaillerons ainsi les vues actuelles sur le fonctionnement des enzymes dans des solvants organiques, les différents modes de mise en oeuvre possibles et, à travers une revue de leurs applications potentielles, les principaux systèmes enzymatiques utilisés. The extension of enzymatic catalysis, classically carried out in aqueous media, to organic media can be first ascribed to the possibility of using substrates that are poorly soluble or insoluble in water. In biphasic media consisting of an aqueous phase containing the enzyme in solution and of a non water-miscible organic solvent, the enzyme is kept in a suitable aqueous environment. A variant biphasic system consists in creating reverse micelles by the addition of a surfactant in order to increase the interfacial area and thus to improve the transfers between the aqueous phase where the enzyme is located and the organic phase. In these two cases, the partition coefficient of the different reactants plays a crucial role by governing the rates and yields of reaction. Microaqueous media constitute a new system for biocatalysis in organic media. In this case, a solid enzyme is incorporated into an organic solvent, preferably a hydrophobic one, wherein it exhibits new properties, especially a higher stability and a modified selectivity. The enzymes the most studied in this type of medium are hydrolytic ones, such as lipases or proteases which can then catalyze synthesis reactions. Yet, other classes of enzymes have also been used in this way. As oil products are typical hydrophobic compounds, it was of interest in view of possible applications in the petroleum and petrochemical industries to report the present knowledge about the functioning of enzymes in organic media. The present and potential applications of the most studied enzymatic systems will be reviewed in order to point out the major points of interest of biocatalysis in organic media either for organic synthesis or for less investigated fields, such as, for instance, biodegradation of pollutants by whole cells.

The gut microbiota is a collection of symbiotic microorganisms in the gastrointestinal tract. Its sensitivity to chemicals with widespread exposure, such as phthalates, is little known. We aimed to investigate the impact of perinatal exposure to phthalates on the infant gut microbiota at 12 months of age. Within SEPAGES cohort (Suivi de l'Exposition à la Pollution Atmosphérique durant la Grossesse et Effet sur la Santé), we assessed 13 phthalate metabolites and 2 di(isononyl) cyclohexane-1,2-dicarboxylate (DINCH) metabolites in repeated urine samples collected in pregnant women and their offspring. We obtained stool samples from 356 children at 12 months of age and sequenced the V3-V4 region of the 16S rRNA gene, allowing gut bacterial profiling. We used single-chemical (linear regressions) and mixture (BKMR, Bayesian Kernel Machine Regression) models to examine associations of phthalates and DINCH metabolites, with gut microbiota indices of α-diversity (specific richness and Shannon diversity) and the relative abundances of the most abundant microbiota phyla and genera. After correction for multiple testing, di(2-ethylhexyl) phthalate (ΣDEHP), diethyl phthalate (DEP) and bis(2-propylheptyl) phthalate (DPHP) metabolites 12-month urinary concentrations were associated with higher Shannon α-diversity of the child gut microbiota in single-chemical models. The multiple-chemical model (BKMR) suggested higher α-diversity with exposure to the phthalate mixture at 12 months, driven by the same phthalates. There were no associations between phthalate and DINCH exposure biomarkers at other time points and α-diversity after correction for multiple testing. ΣDEHP metabolites concentration at 12 months was associated with higher Coprococcus genus. Finally, ΣDEHP exposure at 12 months tended to be associated with higher phylum Firmicutes, an association not maintained after correction for multiple testing. Infancy exposure to phthalate might disrupt children's gut microbiota. The observed associations were cross-sectional, so that reverse causality cannot be excluded. [Display omitted] • ΣDEHP, DEP and DPHP were associated with higher α-diversity in child gut microbiota. • The phthalates mixture was associated with higher α-diversity in child gut microbiota. • The mixture effect was mostly driven by DEP, ΣDEHP and DPHP metabolites. • DEHP metabolites were associated with higher abundance of Coprococcus in the microbiota. [ABSTRACT FROM AUTHOR]

The capability to simulate the transport of charged and/or high-energy hadrons (especially protons) is indispensable for a number of applications. This includes, among others, simulation studies concerned with radiation protection and decommissioning around accelerators and high-intensity laser facilities, as well as beam characterisation in spallation neutron sources. In the context of Monte-Carlo particle transport codes, solving these problems often requires the use of advanced variance-reduction techniques. TRIPOLI-4® is a reference Monte-Carlo particle transport code for the simulation of low-energy (≲ 20 MeV) neutrons and photons and offers a wide range of sophisticated variance-reduction schemes; however, it cannot be applied to the problems mentioned above because it lacks the capability to transport charged, high-energy hadrons. This limitation can be circumvented by coupling TRIPOLI-4r with the Geant4 particle-transport toolkit. We present here the first results of this coupling.