State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction.

RNAs are essential molecules involved in numerous biological functions. Understanding RNA functions requires the knowledge of their 3D structures. Computational methods have been developed for over two decades to predict the 3D conformations from RNA sequences. These computational methods have been widely used and are usually categorised as either ab initio or template-based. The performances remain to be improved. Recently, the rise of deep learning has changed the sight of novel approaches. Deep learning methods are promising, but their adaptation to RNA 3D structure prediction remains difficult. In this paper, we give a brief review of the ab initio, template-based and novel deep learning approaches. We highlight the different available tools and provide a benchmark on nine methods using the RNA-Puzzles dataset. We provide an online dashboard that shows the predictions made by benchmarked methods, freely available on the EvryRNA platform: https://evryrna.ibisc.univ-evry.fr/evryrna/state_of_the_rnart/.

RNAdvisor: a comprehensive benchmarking tool for the measure and prediction of RNA structural model quality.

RNA is a complex macromolecule that plays central roles in the cell. While it is well known that its structure is directly related to its functions, understanding and predicting RNA structures is challenging. Assessing the real or predictive quality of a structure is also at stake with the complex 3D possible conformations of RNAs. Metrics have been developed to measure model quality while scoring functions aim at assigning quality to guide the discrimination of structures without a known and solved reference. Throughout the years, many metrics and scoring functions have been developed, and no unique assessment is used nowadays. Each developed assessment method has its specificity and might be complementary to understanding structure quality. Therefore, to evaluate RNA 3D structure predictions, it would be important to calculate different metrics and/or scoring functions. For this purpose, we developed RNAdvisor, a comprehensive automated software that integrates and enhances the accessibility of existing metrics and scoring functions. In this paper, we present our RNAdvisor tool, as well as state-of-the-art existing metrics, scoring functions and a set of benchmarks we conducted for evaluating them. Source code is freely available on the EvryRNA platform: https://evryrna.ibisc.univ-evry.fr.

Proteomic analysis of Acanthamoeba castellanii response to Legionella pneumophila infection.

Legionella pneumophila is an opportunistic pathogen responsible for Legionnaires' disease or Legionellosis. This bacterium is found in the environment interacting with free-living amoebae such as Acanthamoeba castellanii. Until now, proteomic analyses have been done in amoebae infected with L. pneumophila but focused on the Legionella-containing vacuole. In this study, we propose a global proteomic analysis of the A. castellanii proteome following infection with L. pneumophila wild-type (WT) or with an isogenic ΔdotA mutant strain, which is unable to replicate intracellularly. We found that infection with L. pneumophila WT leads to reduced levels of A. castellanii proteins associated with lipid homeostasis/metabolism, GTPase regulation, and kinase. The levels of organelle-associated proteins were also decreased during infection. Legionellapneumophila WT infection leads to increased levels of proteins associated with polyubiquitination, folding or degradation, and antioxidant activities. This study reinforces our knowledge of this too little explored but so fundamental interaction between L. pneumophila and A. castellanii, to understand how the bacterium could resist amoeba digestion.

A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment.

Encystment is a common stress response of most protists, including free-living amoebae. Cyst formation protects the amoebae from eradication and can increase virulence of the bacteria they harbor. Here, we mapped the global molecular changes that occur in the facultatively pathogenic amoeba Acanthamoeba castellanii during the early steps of the poorly understood process of encystment. By performing transcriptomic, proteomic, and phosphoproteomic experiments during encystment, we identified more than 150,000 previously undescribed transcripts and thousands of protein sequences absent from the reference genome. These results provide molecular details to the regulation of expected biological processes, such as cell proliferation shutdown, and reveal new insights such as a rapid phospho-regulation of sites involved in cytoskeleton remodeling and translation regulation. This work constitutes the first time-resolved molecular atlas of an encysting organism and a useful resource for further investigation of amoebae encystment to allow for a better control of pathogenic amoebae.

Can Leaves and Stems of Rubus idaeus L. Handle Candida albicans Biofilms?

Candida albicans is an opportunistic pathogen involved in many infections, especially linked to implanted medical devices. Its ability to form biofilms complicates the treatment of these infections as few molecules are active against sessile C. albicans. The aim of this study was to evaluate the potential of leaves, three-month-old and one-year-old stems of Rubus idaeus L. against C. albicans biofilm growth. Extractions with a polarity gradient were carried out on hydroacetonic extracts and followed by fractionation steps. The obtained extracts and fractions were tested for their anti-biofilm growth activity against C. albicans using XTT method. Compounds of active subfractions were identified by LC-MS. The hexane extracts from leaves and stems were the most active against the fungus with IC50 at 500 and 250 µg/mL. Their bioguided fractionation led to 4 subfractions with IC50 between 62.5 and 125 µg/mL. Most of the components identified in active subfractions were fatty acids and terpenoïds.

Nanovectorized Microalgal Extracts to Fight Candida albicans and Cutibacterium acnes Biofilms: Impact of Dual-Species Conditions.

Biofilm-related infections are a matter of concern especially because of the poor susceptibility of microorganisms to conventional antimicrobial agents. Innovative approaches are needed. The antibiofilm activity of extracts of cyanobacteria Arthrospira platensis, rich in free fatty acids, as well as of extract-loaded copper alginate-based nanocarriers, were studied on single- and dual-species biofilms of Candida albicans and Cutibacterium acnes. Their ability to inhibit the biofilm formation and to eradicate 24 h old biofilms was investigated. Concentrations of each species were evaluated using flow cytometry. Extracts prevented the growth of C. acnes single-species biofilms (inhibition > 75% at 0.2 mg/mL) but failed to inhibit preformed biofilms. Nanovectorised extracts reduced the growth of single-species C. albicans biofilms (inhibition > 43% at 0.2 mg/mL) while free extracts were weakly or not active. Nanovectorised extracts also inhibited preformed C. albicans biofilms by 55% to 77%, whereas the corresponding free extracts were not active. In conclusion, even if the studied nanocarrier systems displayed promising activity, especially against C. albicans, their efficacy against dual-species biofilms was limited. This study highlighted that working in such polymicrobial conditions can give a more objective view of the relevance of antibiofilm strategies by taking into account interspecies interactions that can offer additional protection to microbes.

Anti-biofilm activity of a semi-synthetic molecule obtained from resveratrol against Candida albicans biofilm.

Candida albicans can form biofilm on tissues and medical devices, becoming, in that case, less susceptible to antifungal agents. Treatment of candidiasis associated with the formation of C. albicans biofilms is restricted to echinocandins and lipid forms of amphotericin B. This study investigated the activity of micafungin and resveratrol modified molecule (EB487) against C. albicans biofilms. The anti-biofilm growth (Bgrowth) and anti-preformed biofilm (Bpreformed) activities of micafungin (0 to 3.94 µM) and EB487 (0 to 20.32 mM) were comparatively studied separately and combined, using XTT, flow cytometry and cell counts approaches. Concentrations causing 50% inhibition of the studied steps (IC50) were evaluated. When tested separately, IC50 Bgrowth was obtained for 4.8 mM and 0.13 µM of EB487 and micafungin respectively, and IC50 Bpreformed for 3.6 mM and 0.06 µM of EB487 and micafungin respectively. Micafungin used alone was not able to totally eradicate fungi. Micafungin combined with EB487 displayed synergistic activity (both anti-growth- and anti-preformed biofilm-activities). Optimal combination concentrations were EB487 (≤9.12 mM -strain ATCC 28367™ or ≤8.12 mM -strain CAI4-p), micafungin (≤0.05 µM for both) and caused a total eradication of fungi. Dose reduction indexes obtained using these concentrations were at least 9 (micafungin) and 3.2 (EB487) for both anti-biofilm growth- and anti-preformed biofilm-activities. Combinations indexes were consistently below one, demonstrating a synergistic relationship between micafungin and EB487 in these conditions. This study demonstrated the strong anti-biofilm activity of EB487 and highlighted its synergistic potential when combined with micafungin. EB487 is a promising semi-synthetic molecule with prophylactic and curative interests in fighting C. albicans biofilms.

Candida albicans enhances initial biofilm growth of Cutibacterium acnes under aerobic conditions.

Candida albicans and Cutibacterium acnes are opportunistic pathogens that co-colonize the human body. They are involved in biofilm-related infections of implanted medical devices. The objective of this study was to evaluate the ability of these species to interact and form polymicrobial biofilms. SEM imaging and adhesion assays showed that C. acnes adhesion to C. albicans did not have a preference for a specific morphological state of C. albicans; bacteria adhered to both hyphal and yeast forms of C. albicans. C. albicans did not influence growth of C. acnes under anaerobic growth conditions, however under aerobic growth condition, C. albicans enhanced early C. acnes biofilm formation. This favorable impact of C. albicans was not mediated by secreted compounds accumulating in the medium, but required the presence of metabolically active C. albicans. The ability of these microorganisms to interact together could modulate the physiopathology of infections.

Do raspberry extracts and fractions have antifungal or anti-adherent potential against Candida spp.?

Candida spp., especially Candida albicans, is one of the main colonisers of the oral cavity. Due to its ability to form biofilms, it can be implicated in dental caries, periodontal disease and denture stomatitis. Microbial cells in biofilms are minimally impacted by conventional drugs. The aim of this study was to find new substances able to inhibit the adhesion of Candida spp. in order to prevent biofilm formation in the oral cavity. This study focused on the red raspberry (Rubus idaeus) fruit, known for its richness in potentially antimicrobial tannins. Extraction with a polarity gradient was performed on acetone extracts from frozen ripe and unripe fruits, resulting in eight extracts. The antifungal and anti-adhesion effects of the extracts were determined using broth microdilution and XTT methods, respectively, against C. albicans, Candida glabrata and Candida parapsilosis strains. Interestingly, four extracts (hexane and ethyl acetate) displayed anti-adhesion activity against C. albicans at low concentrations [50% inhibitory concentration (IC50) 15.6-62.5 µg/mL]. Bioassay-guided fractionation by chromatographic methods of the most active extract obtained from ripe fruit (ethyl acetate extract) led to two subfractions enriched in anti-adhesion compounds, identified by mass spectrometry analysis as hydrolysable and condensed tannins. Their activities were dose-dependent with maximum inhibition at 80% (IC50 = 25 µg/mL and 12.5 µg/mL). Regarding antifungal activity, no extract was active against planktonic cells of the tested strains. This work highlights for the first time the potential of raspberries to prevent oral C. albicans biofilms.

Cutibacterium acnes protects Candida albicans from the effect of micafungin in biofilms.

The aim of this study was to investigate the ability of Candida albicans and Cutibacterium acnes to grow together as a polymicrobial biofilm in vitro and to examine the influence of C. acnes on C. albicans susceptibility to micafungin. Mature 72-h-old single-species biofilms of C. albicans and polymicrobial biofilms involving both C. albicans and C. acnes were formed in brain-heart infusion and were observed by scanning electronic microscopy. Moreover, 24-h-old single-species and polymicrobial biofilms were treated for 24 h with micafungin (concentrations ranging from 0.75 mg/L to 12 mg/L) and the antibiofilm activity of micafungin was evaluated on fungal cells by flow cytometry following addition of propidium iodide. The results showed that C. albicans and C. acnes formed a polymicrobial biofilm in the tested conditions and that bacterial presence did not modify fungal viability. Micafungin induced a fungal mortality rate ranging from 70-95% in C. albicans single-species biofilms and from 35-40% in C. acnes-C. albicans polymicrobial biofilms. Mortality induced by micafungin was significantly reduced (P < 0.05 for micafungin at 6 mg/L and P < 0.001 for other micafungin concentrations) in polymicrobial conditions compared with single-species biofilms. In conclusion, this study showed that C. albicans and C. acnes are able to form polymicrobial biofilms together in a synergistic way and that this organisation increases yeast resistance to micafungin.

Assessing and managing the risks of hypoxia in transitional waters: a case study in the tidal Garonne River (South-West France).

The Gironde estuary (S-W France) is one of the largest European macrotidal estuaries. In the tidal Garonne River, its main tributary, episodes of low (<5 mg L-1) to hypoxic (<2 mg L-1) dissolved oxygen (DO) concentrations have been occasionally recorded close to Bordeaux, about 100 km from the mouth. Projected long-term environmental changes (increase in temperature and population, decrease in river discharge) suggest the establishment of summer chronic oxygen deficiency in the tidal Garonne River in the next decades. Assessing and managing the risk of hypoxia on such a large, hyper-turbid fluvio-estuarine system is complex, due to the different forcing factors (temperature, river discharge, turbidity, urban wastes) acting over a wide range of temporal and spatial scales. In this context, we show the interest of a real-time, high-frequency monitoring of the water quality, the MAGEST network, which continuously records since 2005 temperature, salinity, turbidity, and dissolved oxygen in surface waters in Bordeaux. Through the analysis of the 10-year DO records, we demonstrate the interest of a high-frequency, long-term database to better document DO variability and to define the controlling factors of DO concentrations. This real-time monitoring is also of great interest for the development of manager's oriented tools and the follow-up of DO objectives in the tidal Garonne River.

Systematic study of subcellular localization of Arabidopsis PPR proteins confirms a massive targeting to organelles.

Four hundred and fifty-eight genes coding for PentatricoPeptide Repeat (PPR) proteins are annotated in the Arabidopsis thaliana genome. Over the past 10 years, numerous reports have shown that many of these proteins function in organelles to target specific transcripts and are involved in post-transcriptional regulation. Therefore, they are thought to be important players in the coordination between nuclear and organelle genome expression. Only four of these proteins have been described to be addressed outside organelles, indicating that some PPRs could function in post-transcriptional regulations of nuclear genes. In this work, we updated and improved our current knowledge on the localization of PPR proteins of Arabidopsis within the plant cell. We particularly investigated the subcellular localization of 166 PPR proteins whose targeting predictions were ambiguous, using a combination of high-throughput cloning and microscopy. Through systematic localization experiments and data integration, we confirmed that PPR proteins are largely targeted to organelles and showed that dual targeting to both the mitochondria and plastid occurs more frequently than expected. These results allow us to speculate that dual-targeted PPR proteins could be important for the fine coordination of gene expressions in both organelles.