Mechanism of mycobacterial ATP synthase inhibition by squaramides and second generation diarylquinolines.

Mycobacteria, such as Mycobacterium tuberculosis, depend on the activity of adenosine triphosphate (ATP) synthase for growth. The diarylquinoline bedaquiline (BDQ), a mycobacterial ATP synthase inhibitor, is an important medication for treatment of drug-resistant tuberculosis but suffers from off-target effects and is susceptible to resistance mutations. Consequently, both new and improved mycobacterial ATP synthase inhibitors are needed. We used electron cryomicroscopy and biochemical assays to study the interaction of Mycobacterium smegmatis ATP synthase with the second generation diarylquinoline TBAJ-876 and the squaramide inhibitor SQ31f. The aryl groups of TBAJ-876 improve binding compared with BDQ, while SQ31f, which blocks ATP synthesis ~10 times more potently than ATP hydrolysis, binds a previously unknown site in the enzyme's proton-conducting channel. Remarkably, BDQ, TBAJ-876, and SQ31f all induce similar conformational changes in ATP synthase, suggesting that the resulting conformation is particularly suited for drug binding. Further, high concentrations of the diarylquinolines uncouple the transmembrane proton motive force while for SQ31f they do not, which may explain why high concentrations of diarylquinolines, but not SQ31f, have been reported to kill mycobacteria.

Structure of mycobacterial ATP synthase bound to the tuberculosis drug bedaquiline.

Tuberculosis-the world's leading cause of death by infectious disease-is increasingly resistant to current first-line antibiotics1. The bacterium Mycobacterium tuberculosis (which causes tuberculosis) can survive low-energy conditions, allowing infections to remain dormant and decreasing their susceptibility to many antibiotics2. Bedaquiline was developed in 2005 from a lead compound identified in a phenotypic screen against Mycobacterium smegmatis3. This drug can sterilize even latent M. tuberculosis infections4 and has become a cornerstone of treatment for multidrug-resistant and extensively drug-resistant tuberculosis1,5,6. Bedaquiline targets the mycobacterial ATP synthase3, which is an essential enzyme in the obligate aerobic Mycobacterium genus3,7, but how it binds the intact enzyme is unknown. Here we determined cryo-electron microscopy structures of M. smegmatis ATP synthase alone and in complex with bedaquiline. The drug-free structure suggests that hook-like extensions from the α-subunits prevent the enzyme from running in reverse, inhibiting ATP hydrolysis and preserving energy in hypoxic conditions. Bedaquiline binding induces large conformational changes in the ATP synthase, creating tight binding pockets at the interface of subunits a and c that explain the potency of this drug as an antibiotic for tuberculosis.

A simple assay for inhibitors of mycobacterial oxidative phosphorylation.

Oxidative phosphorylation, the combined activities of the electron transport chain (ETC) and ATP synthase, has emerged as a valuable target for antibiotics to treat infection with Mycobacterium tuberculosis and related pathogens. In oxidative phosphorylation, the ETC establishes a transmembrane electrochemical proton gradient that powers ATP synthesis. Monitoring oxidative phosphorylation with luciferase-based detection of ATP synthesis or measurement of oxygen consumption can be technically challenging and expensive. These limitations reduce the utility of these methods for characterization of mycobacterial oxidative phosphorylation inhibitors. Here, we show that fluorescence-based measurement of acidification of inverted membrane vesicles (IMVs) can detect and distinguish between inhibition of the ETC, inhibition of ATP synthase, and nonspecific membrane uncoupling. In this assay, IMVs from Mycobacterium smegmatis are acidified either through the activity of the ETC or ATP synthase, the latter modified genetically to allow it to serve as an ATP-driven proton pump. Acidification is monitored by fluorescence from 9-amino-6-chloro-2-methoxyacridine, which accumulates and quenches in acidified IMVs. Nonspecific membrane uncouplers prevent both succinate- and ATP-driven IMV acidification. In contrast, the ETC Complex III2IV2 inhibitor telacebec (Q203) prevents succinate-driven acidification but not ATP-driven acidification, and the ATP synthase inhibitor bedaquiline prevents ATP-driven acidification but not succinate-driven acidification. We use the assay to show that, as proposed previously, lansoprazole sulfide is an inhibitor of Complex III2IV2, whereas thioridazine uncouples the mycobacterial membrane nonspecifically. Overall, the assay is simple, low cost, and scalable, which will make it useful for identifying and characterizing new mycobacterial oxidative phosphorylation inhibitors.

Design and synthesis of zinc protoporphyrin IX-adamantane/cyclodextrin/cellulose nanocrystals complexes for anticancer photodynamic therapy.

Two protoporphyrin IX (PpIX) adamantane derivatives were synthesized and then metallated with zinc. The Zn-PpIX derivatives, exhibiting a high singlet oxygen quantum yield, were tested for their photodynamic activity against the HT-29 cell line. In order to enhance their water-solubility and their cellular bioavailability, these photosensitizers were encapsulated into the hydrophobic cavity of cyclodextrins (CD) previously attached to cellulose nanocrystals (CNCs) via electrostatic interactions. Under illumination, the encapsulated adamantanyl-porphyrins exerted an enhanced in vitro cytotoxicity, as compared with the corresponding free photosensitizers.

Enhancement of hydrosolubility and in vitro antiproliferative properties of chalcones following encapsulation into ß-cyclodextrin/cellulose-nanocrystal complexes.

This paper describes the preparation of two chalcone/ß-cyclodextrin/cellulose-nanocrystals complexes and the study of their antiproliferative activities against two colorectal and two prostatic cancer cell lines. The aim of this work was to enhance hydrosolubility of chalcones thanks to the hydrophilic character of cellulose nanocrystals. These latter were linked, through ionic interactions, to a cationic derivative of ß-cyclodextrins whose lipophilic cavity allowed the encapsulation of hydrophobic chalcones: 3-hydroxy-3',4,4',5'-tetramethoxychalcone (1) and 3',4,4',5'-tetramethoxychalcone (2). First, we showed that encapsulation allowed hydrosolubilization of chalcones. Then, chalcone/ß-cyclodextrin/cellulose-nanocrystals complexes demonstrated enhanced in vitro antiproliferative activities, compared to the corresponding free-chalcones.

Bacterial diversity on stainless steel surfaces of egg processing companies and potential of selected isolates to spoil liquid whole egg products.

AIMS: To assess the bacterial diversity in the French egg processing industry and to explore the adhesion and spoilage potential of selected bacteria. METHODS AND RESULTS: Sterile stainless steel chips were suspended for 2 months inside the pipelines of seven egg processing companies, before and after the pasteurizer, at warm and cold seasons. After exposure, the bacterial diversity was assessed by 16S rDNA sequencing. The 231 collected isolates were mainly facultative anaerobic Gram positive bacteria, such as Streptococcus, Staphylococcus, Bacillus and Kocuria. Sixty-five representative isolates were further characterized in vitro regarding the potential for adhesion and egg product spoilage. A high diversity was observed from one genus to another. Kocuria and Rothia isolates showed significantly higher adhesion than the isolates of the other genera. Only the isolates belonging to the genera Bacillus and Lysinibacillus, associated with high enzymatic activities on a solid egg-based medium, were able to induce spoilage of liquid whole egg. CONCLUSIONS: Bacteria collected on stainless steel surfaces placed in egg processing industries could be associated to liquid egg product spoilage. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provides new insights on the bacterial contamination in egg processing companies and represents a first step for the effective control of undesirable bacteria in liquid egg products.

Deciphering the demographic history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa.

Understanding the processes of adaptive divergence, which may ultimately lead to speciation, is a major question in evolutionary biology. Allochronic differentiation refers to a particular situation where gene flow is primarily impeded by temporal isolation between early and late reproducers. This process has been suggested to occur in a large array of organisms, even though it is still overlooked in the literature. We here focused on a well-documented case of incipient allochronic speciation in the winter pine processionary moth Thaumetopoea pityocampa. This species typically reproduces in summer and larval development occurs throughout autumn and winter. A unique, phenologically shifted population (SP) was discovered in 1997 in Portugal. It was proved to be strongly differentiated from the sympatric "winter population" (WP), but its evolutionary history could only now be explored. We took advantage of the recent assembly of a draft genome and of the development of pan-genomic RAD-seq markers to decipher the demographic history of the differentiating populations and develop genome scans of adaptive differentiation. We showed that the SP diverged relatively recently, that is, few hundred years ago, and went through two successive bottlenecks followed by population size expansions, while the sympatric WP is currently experiencing a population decline. We identified outlier SNPs that were mapped onto the genome, but none were associated with the phenological shift or with subsequent adaptations. The strong genetic drift that occurred along the SP lineage certainly challenged our capacity to reveal functionally important loci.

Study of aggregation in surface sludge deposits from 14 full-scale French constructed wetlands using particle size distribution and dynamic vapor sorption analyses.

French vertical flow constructed wetlands (French VFCWs) are widely used for the treatment of wastewaters from small communities. In the system, unsettled wastewater is percolated through two successive stages of filter-cells planted with reeds. This causes the formation of a surface sludge layer. This layer plays positive roles in the treatment performance, but also leads to clogging. The objective of this study was to contribute to the description of the sludge deposits characteristics and their dynamics of evolution, which may control the development of clogging. Representative samples of sludge deposits were taken from 14 French VFCWs full-scale plants and analyzed for particle size, dynamic vapor sorption and other parameters of composition to compare their structure and evaluate the factors of influence. Results showed that ageing of the surface deposits layer over the years of operation in each plant induced the formation and integration of microaggregates within the initial macrostructure of fresh organic matter (OM). The humification process of the OM was found to play a key role in the aggregation process. The injection of FeCl3 operated to precipitate phosphates before filtration was found to accelerate the aggregation process in the early phase (<1 year) of operation of the sludge.

A model-based approach to characterize individual inbreeding at both global and local genomic scales.

Inbreeding results from the mating of related individuals and may be associated with reduced fitness because it brings together deleterious variants in one individual. In general, inbreeding is estimated with respect to an arbitrary base population consisting of ancestors that are assumed unrelated. We herein propose a model-based approach to estimate and characterize individual inbreeding at both global and local genomic scales by assuming the individual genome is a mosaic of homozygous-by-descent (HBD) and non-HBD segments. The HBD segments may originate from ancestors tracing back to different periods in the past defining distinct age-related classes. The lengths of the HBD segments are exponentially distributed with class-specific parameters reflecting that inbreeding of older origin generates on average shorter stretches of observed homozygous markers. The model is implemented in a hidden Markov model framework that uses marker allele frequencies, genetic distances, genotyping error rates and the sequences of observed genotypes. Note that genotyping errors, low-fold sequencing or genotype-by-sequencing data are easily accommodated under this framework. Based on simulations under the inference model, we show that the genomewide inbreeding coefficients and the parameters of the model are accurately estimated. In addition, when several inbreeding classes are simulated, the model captures them if their ages are sufficiently different. Complementary analyses, either on data sets simulated under more realistic models or on human, dog and sheep real data, illustrate the range of applications of the approach and how it can reveal recent demographic histories among populations (e.g., very recent bottlenecks or founder effects). The method also allows to clearly identify individuals resulting from extreme consanguineous matings.

Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida.

Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaVvrn , has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of this study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan. We performed a whole-genome resequencing of pools of individuals (Pool-Seq) belonging to G. pallida lineages derived from two independent populations having experimentally evolved on susceptible and resistant potato cultivars. About 1.6 million SNPs were used to perform the genome scan using a recent model testing for adaptive differentiation and association to population-specific covariables. We identified 275 outliers and 31 of them, which also showed a significant reduction in diversity in adapted lineages, were investigated for their genic environment. Some candidate genomic regions contained genes putatively encoding effectors and were enriched in SPRYSECs, known in cyst nematodes to be involved in pathogenicity and in (a)virulence. Validated candidate SNPs will provide a useful molecular tool to follow frequencies of virulence alleles in natural G. pallida populations and define efficient strategies of use of potato resistances maximizing their durability.

Effect of genetic European taurine ancestry on milk yield of Ankole-Holstein crossbred dairy cattle in mixed smallholders system of Burundi highlands.

Different breeding systems associated with specific bovine genetic resources have coexisted in Burundi. To prepare for the development of a national action plan for the improvement of bovine genetic resources in Burundi, we aimed at performing genetic characterization of Ankole and Ankole × European crossbred individuals and assessing the effect of European ancestry on milk productivity of cows kept under the mixed crops livestock system. To that end, we genotyped 37 Ankole and 138 crossbred individuals on 42 636 SNPs and combined these genotypes with those from 21 cattle breeds, representative of the bovine genetic diversity. We also measured milk yield not suckled and estimated suckled milk. Given the results, we confirmed the indicine × African taurine admixed origin of the Ankole in Burundi and showed that crossbred individuals present a high proportion of European ancestry (i.e. 57% on average). As the proportion of European ancestry increased, milk yield increased by 0.03 ± 0.01 l/day, at a lower extent than expected. We also observed that breeders were unable to correctly evaluate the European proportion in their livestock. Our results may provide useful information for objective dairy breeding in Burundi. As an example, an ex-situ conservation program of Ankole within the framework of value chains is proposed as an accompanying strategy to improve the sustainability of the crossbreeding program.

Development of curcumin-cyclodextrin/cellulose nanocrystals complexes: New anticancer drug delivery systems.

The synthesis of curcumin-cyclodextrin/cellulose nanocrystals (CNCx) nano complexes was performed. CNCx were functionalized by ionic association with cationic ß-cyclodextrin (CD) and CD/CNCx complexes were used to encapsulate curcumin. Preliminary in vitro results showed that the resulting curcumin-CD/CNCx complexes exerted antiproliferative effect on colorectal and prostatic cancer cell lines, with IC50s lower than that of curcumin alone.

Easy clip to treat anal fistula tracts: a word of caution.

BACKGROUND AND AIMS: Closing the internal opening by a clip ovesco has been recently proposed for healing the fistula tract, but, to date, data on benefit are poorly analyzed. The aim was to report a preliminary multicenter experience. MATERIALS AND METHODS: Retrospective study was undertaken in six different French centers: surgical procedure, immediate complications, and follow-up have been collected. RESULTS: Nineteen clips were inserted in 17 patients (M/F, 4/13; median age, 42 years [29-54]) who had an anal fistula: 12 (71%) high fistulas (including 4 rectovaginal fistulas), 5 (29%) lower fistulas (with 3 rectovaginal fistulas), and 6 (35%) Crohn's fistulas. Out of 17 patients, 15 had a seton drainage beforehand. The procedure was easy in 8 (47%) patients and the median operative time was 27.5 min (20-36.5). Postoperative period was painful for 11 (65%) patients. A clip migration was noted in 11 patients (65%) after a median follow-up of 10 days (5.5-49.8). Eleven patients (65%) who failed had reoperation including 10 new drainages within the first month (0.5-5). After a mean follow-up of 4 months (2-7),, closing the tract was observed in 2 patients (12%) following the first insertion of the clip and in another one after a second insertion. CONCLUSION: Treatment of anal fistula by placing a clip on the internal opening is disappointing and deleterious for some patients. A better assessment before dissemination is recommended.

Pilot-scale study of vertical flow constructed wetland combined with trickling filter and ferric chloride coagulation: influence of irregular operational conditions.

The aim of this study was to characterize the efficiency of an intensified process of vertical flow constructed wetland having the following particularities: (i) biological pretreatment by trickling filter, (ii) FeCl3 injection for dissolved phosphorus removal and (iii) succession of different levels of redox conditions along the process line. A pilot-scale set-up designed to simulate a real-scale plant was constructed and operated using real wastewater. The influences of FeCl3 injection and water saturation level within the vertical flow constructed wetland stage on treatment performances were studied. Three different water saturation levels were compared by monitoring: suspended solids (SS), total phosphorus (TP), dissolved chemical oxygen demand (COD), ammonium, nitrate, phosphate, iron, and manganese. The results confirmed the good overall efficiency of the process and the contribution of the trickling filter pretreatment to COD removal and nitrification. The effects of water saturation level and FeCl3 injection on phosphorus removal were evaluated by analysis of the correlations between the variables. Under unsaturated conditions, good nitrification and no denitrification were observed. Under partly saturated conditions, both nitrification and denitrification were obtained, along with a good retention of SSs. Finally, under saturated conditions, the performance was decreased for almost all parameters.

Global overview of the risk linked to the Bacillus cereus group in the egg product industry: identification of food safety and food spoilage markers.

AIMS: To evaluate the food safety and spoilage risks associated with psychrotrophic Bacillus cereus group bacteria for the egg product industry and to search for relevant risk markers. METHODS AND RESULTS: A collection of 68 psychrotrophic B. cereus group isolates, coming from pasteurized liquid whole egg products, was analysed through a principal component analysis (PCA) regarding their spoilage and food safety risk potentials. The principal component analysis showed a clear differentiation between two groups within the collection, one half of the isolates representing a safety risk and the other half a spoilage risk. CONCLUSIONS: Relevant risk markers were highlighted by PCA, that is (i) for the food safety risk, the presence of the specific 16S rDNA-1m genetic signature and the ability to grow at 43°C on solid medium and (ii) for the spoilage risk, the presence of the cspA genetic signature. SIGNIFICANCE AND IMPACT OF THE STUDY: This work represents a first step in the development of new diagnostic technologies for the assessment of the microbiological quality of foods likely to be contaminated with psychrotrophic B. cereus group bacteria.

High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles.

Intercellular communication in the nervous system occurs through the release of neurotransmitters into the synaptic cleft between neurons. In the presynaptic neuron, the proton pumping vesicular- or vacuolar-type ATPase (V-ATPase) powers neurotransmitter loading into synaptic vesicles (SVs), with the V1 complex dissociating from the membrane region of the enzyme before exocytosis. We isolated SVs from rat brain using SidK, a V-ATPase-binding bacterial effector protein. Single-particle electron cryomicroscopy allowed high-resolution structure determination of V-ATPase within the native SV membrane. In the structure, regularly spaced cholesterol molecules decorate the enzyme's rotor and the abundant SV protein synaptophysin binds the complex stoichiometrically. ATP hydrolysis during vesicle loading results in a loss of the V1 region of V-ATPase from the SV membrane, suggesting that loading is sufficient to induce dissociation of the enzyme.

Non-purged voltammetry explored with AGNES.

The reduction of oxygen increases pH in the surroundings of an electrode. A theoretical model estimates the steady-state pH profile from the surface of the electrode up to the bulk solution. A very simple formula predicts that, in non-deaerated solutions, for bulk pH-values between 4.0 and 10.0, the corresponding surface pH could be as high as 10.3, regardless of the thickness of the diffusion layer and composition of the sample (except if it has a buffering capacity). For bulk pH lower than 3.0 or higher than 10, pH increases are negligible. Less steep pH-profiles are obtained using buffers (such as MOPS 0.01 M or MES 0.01 M). The change in surface pH modifies the local speciation and hinders the standard interpretation of voltammetric responses. The electroanalytical technique Absence of Gradients and Nernstian Equilibrium Stripping (AGNES), implemented with Screen Printed Electrodes (SPE), provides experimental insights into this phenomenon. AGNES probes the free metal concentration at the electrode surface, from which the surface pH can be estimated for systems of known composition. These estimations agree with the theoretical model for the assayed systems. Additionally, the quantification of the bulk free Zn(2+) and Cd(2+) concentrations with specific modifications of AGNES for non-purged synthetic solutions is discussed. In general, more accurate determinations of the bulk free metal concentrations in non-purged solutions are expected: (i) when the calibration is performed in a medium where the pH increase induces similar changes in the surface free metal concentration and in the sample solution and (ii) when the system is more buffered.

Identification of large selective sweeps associated with major genes in cattle.

Selection for new favorable variants can lead to selective sweeps. However, such sweeps might be rare in the evolution of different species for which polygenic adaptation or selection on standing variation might be more common. Still, strong selective sweeps have been described in domestic species such as chicken lines or dog breeds. The goal of our study was to use a panel of individuals from 12 different cattle breeds genotyped at high density (800K SNPs) to perform a whole-genome scan for selective sweeps defined as unexpectedly long stretches of reduced heterozygosity. To that end, we developed a hidden Markov model in which one of the hidden states corresponds to regions of reduced heterozygosity. Some unexpectedly long regions were identified. Among those, six contained genes known to affect traits with simple genetic architecture such as coat color or horn development. However, there was little evidence for sweeps associated with genes underlying production traits.

Identifying risk factors for eggshell contamination by Bacillus cereus group bacteria in French laying farms.

1. The growth of Bacillus cereus group bacteria often limits the shelf-life of pasteurised liquid egg products and is also a putative toxin producer. This study was performed to better understand the route of contamination by B. cereus in egg products by studying the factors affecting eggshell contamination on-farm. 2. Eggs were collected in warm and cold seasons in 50 conventional laying farms in Western France. Egg surfaces were analysed for the presence of B. cereus group bacteria, environmental measurements were recorded and production practices were identified through a questionnaire filled out by the farmers. 3. A total of 44% of the farms were contaminated by mesophilic and 10% by psychrotrophic B. cereus group bacteria. No significant effect of the season was observed, whatever the thermal type. Several procedures were associated with reduced eggshell contamination by mesophilic bacteria, including the limitation of dust formation from manure and feeding and efficient disinfection of the silo, houses and the sanitary wall between houses. 4. The research highlights the need to promote prevention strategies, from farm to fork, for the control of eggshell and putative subsequent egg product contamination by B. cereus group bacteria.

Physical-chemical characterization of sludge and granular materials from a vertical flow constructed wetland for municipal wastewater treatment.

The use of vertical flow constructed wetlands (VFCWs) is well developed in France and other countries for the treatment of wastewaters from small communities. The patented Azoé® process has been developed by a French company, SCIRPE, in order to improve denitrification and phosphorus removal as compared to classical VFCWs. It includes a biological trickling filter pretreatment followed by two stages of partially flooded VFCW. The performances of partially flooded VFCW are well demonstrated for the removal of organic matter and nitrogen. The system is now being considered for phosphorus removal as well. In this article, sludge and granular materials sampled from the filters of a municipal plant where the Azoé® system has been operated for 8 years were analyzed in order to provide data that may contribute to a better understanding of the dynamics of phosphorus retention. Elemental analyses showed that phosphorus was predominantly captured in the sludge layer accumulated at the surface of the first stage. The progressive mineralization of the sludge over time was also clearly highlighted. The phosphate phases were mainly associated with iron and calcium. The transport of phosphorus via the migration of fine particles through the porous medium in the first stage was also observed.