Comparative Study of Single-stranded Oligonucleotides Secondary Structure Prediction Tools.

BACKGROUND: Single-stranded nucleic acids (ssNAs) have important biological roles and a high biotechnological potential linked to their ability to bind to numerous molecular targets. This depends on the different spatial conformations they can assume. The first level of ssNAs spatial organisation corresponds to their base pairs pattern, i.e. their secondary structure. Many computational tools have been developed to predict the ssNAs secondary structures, making the choice of the appropriate tool difficult, and an up-to-date guide on the limits and applicability of current secondary structure prediction tools is missing. Therefore, we performed a comparative study of the performances of 9 freely available tools (mfold, RNAfold, CentroidFold, CONTRAfold, MC-Fold, LinearFold, UFold, SPOT-RNA, and MXfold2) on a dataset of 538 ssNAs with known experimental secondary structure. RESULTS: The minimum free energy-based tools, namely mfold and RNAfold, and some tools based on artificial intelligence, namely CONTRAfold and MXfold2, provided the best results, with [Formula: see text] of exact predictions, whilst MC-fold seemed to be the worst performing tool, with only [Formula: see text] of exact predictions. In addition, UFold and SPOT-RNA are the only options for pseudoknots prediction. Including in the analysis of mfold and RNAfold results 5-10 suboptimal solutions further improved the performances of these tools. Nevertheless, we could observe issues in predicting particular motifs, such as multiple-ways junctions and mini-dumbbells, or the ssNAs whose structure has been determined in complex with a protein. In addition, our benchmark shows that some effort has to be paid for ssDNA secondary structure predictions. CONCLUSIONS: In general, Mfold, RNAfold, and MXfold2 seem to currently be the best choice for the ssNAs secondary structure prediction, although they still show some limits linked to specific structural motifs. Nevertheless, actual trends suggest that artificial intelligence has a high potential to overcome these remaining issues, for example the recently developed UFold and SPOT-RNA have a high success rate in predicting pseudoknots.

Lyme borreliosis diagnosis: state of the art of improvements and innovations.

With almost 700 000 estimated cases each year in the United States and Europe, Lyme borreliosis (LB), also called Lyme disease, is the most common tick-borne illness in the world. Transmitted by ticks of the genus Ixodes and caused by bacteria Borrelia burgdorferi sensu lato, LB occurs with various symptoms, such as erythema migrans, which is characteristic, whereas others involve blurred clinical features such as fatigue, headaches, arthralgia, and myalgia. The diagnosis of Lyme borreliosis, based on a standard two-tiered serology, is the subject of many debates and controversies, since it relies on an indirect approach which suffers from a low sensitivity depending on the stage of the disease. Above all, early detection of the disease raises some issues. Inappropriate diagnosis of Lyme borreliosis leads to therapeutic wandering, inducing potential chronic infection with a strong antibody response that fails to clear the infection. Early and proper detection of Lyme disease is essential to propose an adequate treatment to patients and avoid the persistence of the pathogen. This review presents the available tests, with an emphasis on the improvements of the current diagnosis, the innovative methods and ideas which, ultimately, will allow more precise detection of LB.

Evaluation of performance and validity limits of gas chromatography electron ionisation with Orbitrap detection for fatty acid methyl ester analyses.

RATIONALE: While the GC-Orbitrap, marketed in 2015, represents a technological breakthrough in terms of sensitivity, resolution and mass stability, many studies have reported ion ratio modification in mass spectra using the standard 70 eV electron ionisation. METHODS: We studied the influence of the acquisition and sample parameters leading to these modifications on fatty acid methyl esters (FAMEs). RESULTS: FAMEs showed that these variations in relative intensities of ions were related to the acquisition parameters such as the mass range and the offset values of the C-TRAP, but also directly related to the column concentration of the sample, and especially that it was molecule-dependent. Advantageously, it is possible to use this feature to promote the molecular ions of FAMEs sometimes not present in a spectrum under electron ionisation at 70 eV. CONCLUSIONS: The 70 eV electron ionisation mass spectra from the GC-Orbitrap were clearly molecule-dependent and could be due to metastable ions during storage states in the C-TRAP.

A gas chromatography full scan high resolution Orbitrap mass spectrometry method for separation and characterization of 3-hydroxymethyl pyridine ester of fatty acids at low levels.

Fatty acid methyl esters (FAMEs), which are commonly used to characterize lipids, have several limitations to conclude on many structures. 3-Pyridylcarbinol esters (3-PCE) are used to characterize fatty acid structures [1], in particular, to identify ring and double bond positions on the carbon chain. Chromatographic separation of these esters is complex due to their polarity and high boiling points. In this study, we used a column with high resolutive power based on ionic liquids to increase the separation quality in gas chromatography (GC). In addition, we used a high-resolution detector (Orbitrap) to limit non-specific signals and improve the detection limits. This detector could be used with a mass filter at 5 ppm for the rapid determination of 3-PCE from its characteristic ions (m/z = 108.0441 and 92.0495). This filter allowed the identification of derivative fatty acids with good sensibility. Thus, it was possible to characterize 3-PCE by measuring the exact fragment masses to confirm structures such as C19:2n12cycloΔ9.

Cysteine: A multifaceted amino acid involved in signaling, plant resistance and antifungal development.

Early effects induced by cysteine were monitored using the model of Mimosa pudica pulvinar cells. Rapid dose-dependent membrane depolarization (within seconds) and modification of proton secretion (within minutes) were triggered at cysteine concentrations higher than 0.1 mM. These effects did not result from a modification of the plasma membrane H+-ATPase activity nor from a protonophore effect as shown by assays on plasma membrane vesicles isolated from pulvinar tissues. In a 0.5-10 mM range, cysteine inhibited the ion-driven turgor-mediated seismonastic reaction of Mimosa pudica primary pulvini and the dark-induced movement of Cassia fasciculata leaflets. At concentrations higher than 1 mM, it induced a long-lasting leaflet necrosis dependent on the concentration and treatment duration. Electron microscopy showed that cysteine induced important damage in the nucleus, mitochondria, endoplasmic reticulum and Golgi of the M. pudica motor cell. Cysteine inhibited in a concentration-dependent manner, from 0.5 to 20 mM, both the mycelial growth and the spore germination of the fungal pathogens Phaeomoniella chlamydospora and Phaeoacremonium minimum implicated in esca disease of grapevines. Using [35S] cysteine, we showed that the amino acid was absorbed following leaf spraying, translocated from leaves to other parts of grapevine cuttings and accumulated within trunks and roots. Therefore, cysteine showed relevant properties to be a candidate able to control fungal diseases either by acting as an early signal directing plant host reaction or/and by acting directly on fungal development.

Influence of temperature and nutritional requirements for mycelial growth of Eutypa lata, a vineyard pathogenic fungus.

Eutypa dieback (dying arm disease, eutypiosis) is a very devastating disease in many grape-producing areas around the world. This vascular disease is induced by the ascomycete Eutypa lata Pers. Fr. Tul & C. Tul. invading the trunk by pruning wounds. The environmental factors and the nutritional requirements regulating fungus development are yet poorly known. This work shows that the isolated strain of E. lata was able to grow in a large temperature range (2-30 degrees C). However, a higher temperature (35 degrees C) presented inhibitory effects on mycelial growth. E. lata was able to use various osidic molecules (C5, C6, C12, C18, C24, and starch); showing thus a large adaptation to the carbon source supplied. As nitrogen source, it used salts and numerous natural amino acids. A significant result was obtained with cysteine presenting obvious antifungal properties. This effect can further be used with the aim of setting up a curative treatment of the disease.

Antifungal effects of cysteine towards Eutypa lata, a pathogen of vineyards.

Cysteine inhibited mycelial growth of the pathogenic fungus affecting grapevines Eutypa lata Pers. Fr. Tul. and C. Tul. in a concentration-dependent manner. The threshold value (defined by the concentration inducing a growth inhibition higher than 5%) was 0.5 mM. A 10 mM concentration induced a complete inhibition of growth and triggered necrotic processes as evidenced by an increasing number of nuclei stained by propidium iodide. In conditions mimicking the plant environment (in particular, a pH near the apoplastic value, i.e. 5.5), 6 mM cysteine induced dramatic modifications in the structural organization of the mycelium (wall, mitochondria, vacuoles and nucleus) leading to death of the hyphae. The antifungal effect of the molecule increased at the acidic experimental pH (pH 4.1). The effect was highly specific to cysteine since modifying the molecular arrangement or masking the SH-function hindered the antifungal efficiency. Cysteine spectrum of action was broad among the various strains of E. lata tested. However, a lower efficiency was observed against fungal species intervening in other grapevine diseases (esca, black dead arm). Besides its direct antifungal effect, the role of cysteine presents particular interest in the fight against fungal pathogens since it triggered an excretion of ergosterol, a compound with elicitor properties. Therefore, cysteine may indirectly increase plant defense reactions.

Biorefinery: Toward an industrial metabolism.

Fossil fuel reserves are running out, global warming is becoming a reality, waste recycling is becoming ever more costly and problematic, and unrelenting population growth will require more and more energy and consumer products. There is now an alternative to the 100% oil economy; it is a renewable resource based on agroresources by using the whole plant. Production and development of these new products are based on biorefinery concept. Each constituent of the plant can be extracted and functionalized in order to produce non-food and food fractions, intermediate agro-industrial products and synthons. Three major industrial domains can be concerned: molecules, materials and energy. Molecules can be used as solvent surfactants or chemical intermediates in substitution of petrol derivatives. Fibers can be valorized in materials like composites. Sugars and oils are currently used to produce biofuels like bioethanol or biodiesel, but second-generation biofuels will use lignocellulosic biomass as raw material. Lipids can be used to produce a large diversity of products like solvent, lubricants, pastes or surfactants. Industrial biorefinery will be linked to the creation of new processes based on the twelve principles of green chemistry (clean processes, atom economy, renewable feedstocks...). Biotechnology, especially white biotechnology, will take a major part into these new processes with biotransformations (enzymology, micro-organisms...) and fermentation. The substitution of oil products by biobased products will develop a new bioeconomy and new industrial processes respecting the sustainable development concept. Industrial biorefinery can be developed on the principle that any residues of one can then be exploited as raw material by others in an industrial metabolism.

Polypeptide metabolites secreted by the fungal pathogen Eutypa lata participate in Vitis vinifera cell structure damage observed in Eutypa dieback.

Eutypa dieback is a devastating disease of Vitis vinifera L. caused by the fungal pathogen Eutypa lata. This wood-inhabiting fungus degrades tissues in the trunk and cordons of infected vines and induces symptoms in the foliage. These symptoms have been attributed to the production of toxic metabolites by the pathogen, in particular eutypine. Recently, we have isolated polypeptide compounds secreted by the fungus in artificial culture. The aims of this study were to examine the effects induced in leaves by applying polypeptides and eutypine to detached canes and to compare this to the changes in leaf structure induced by E. lata in the vineyard. In leaves taken from vines infected with E. lata, the changes in mesophyll cells indicate that the fungus has an effect on tissue remote from the infected area. The size of mesophyll cells decreased by more than half, starch content was reduced and tannins were abundant. Plastids, mitochondria and cell walls were highly modified. In leaves taken from healthy canes treated with polypeptides of E. lata, the structure of mesophyll cells was also modified. The cell size did not change, but the tannin content increased and modifications in plastids and mitochondria were similar to those observed in leaves taken from infected vines. The major effect was the complete disorganisation of cell walls. Eutypine had less effect on organelle structure and did not modify the cell wall. In canes treated with polypeptides, vessel-associated cells (VACs) were also damaged. Abundant tannins occurred in the vacuoles of VACs and marked changes were noted in mitochondria, plastids and the protective layer, in particular in the pit at the vessel interface. In these pits, the protective layer, the primary wall and the middle lamella were all highly modified. In contrast, treatment with eutypine induced the development of a large transfer apparatus bordering the unmodified pectocellulose wall. These results illustrate that treatment with polypeptides produced by E. lata may cause changes in mesophyll cells in leaves and VACs in canes, that resemble changes observed in naturally infected vines. Comparatively, the differences with eutypine action were stressed. Both types of toxins may co-operate in vivo to produce the degeneration observed during the disease.

Structural modifications induced by Eutypa lata in the xylem of trunk and canes of Vitis vinifera.

Eutypa dieback, a devastating disease in grapevines, is caused by the fungal pathogen Eutypa lata, a wood-inhabiting fungus. E. lata acts by degrading wood tissues in the colonisation areas, and produces foliar symptoms. These striking symptoms have been attributed to the production of toxic metabolites by the pathogen, the most widely studied being eutypine. The aims of the study were to compare the effects of E. lata on xylem structure at the site of infection and in remote tissues. In healthy Vitis vinifera, the vessel-associated cells (VACs) in the trunk have a protective layer that covers the entire lignified wall and forms a transfer apparatus in pits located at the VAC / vessel interface. This apparatus occurs similarly in VACs in the basal part of canes but is less developed in the apical part. In the presence of E. lata, which is found only in the trunk and the cordons, the VACs initiated a program of secretory activity that led to the enlargement of the transfer apparatus, which is formed by tightly associated fibrils. This secretory activity was followed by VAC death. Furthermore, the hypertrophy of the transfer apparatus spread according to an acropetal gradient in the canes. Treatment with eutypine also induced the development of the transfer apparatus in VACs of basal and apical parts of canes excised from healthy vines. However, this apparatus was formed by loosely packed fibrils in VACs that were not completely damaged. Therefore, metabolites other than eutypine are expected to be involved in the VAC degeneration observed in infected vines.