Multi-regulated GDP-l-galactose phosphorylase calls the tune in ascorbate biosynthesis

Ascorbate is involved in numerous vital processes, in particular in response to abiotic but also biotic stresses whose frequency and amplitude increase with climate change. Ascorbate levels vary greatly depending on species, tissues, or stages of development, but also in response to stress. Since its discovery, the ascorbate biosynthetic pathway has been intensely studied and it appears that GDP-l-galactose phosphorylase (GGP) is the enzyme with the greatest role in the control of ascorbate biosynthesis. Like other enzymes of this pathway, its expression is induced by various environmental and also developmental factors. Although mRNAs encoding it are among the most abundant in the transcriptome, the protein is only present in very small quantities. In fact, GGP translation is repressed by a negative feedback mechanism involving a small open reading frame located upstream of the coding sequence (uORF). Moreover, its activity is inhibited by a PAS/LOV type photoreceptor, the action of which is counteracted by blue light. Consequently, this multi-level regulation of GGP would allow fine control of ascorbate synthesis. Indeed, experiments varying the expression of GGP have shown that it plays a central role in response to stress. This new understanding will be useful for developing varieties adapted to future environmental conditions.

Phylogenetically diverse wild plant species use common biochemical strategies to thrive in the Atacama Desert

The best ideotypes are under mounting pressure due to increased aridity. Understanding the conserved molecular mechanisms that evolve in wild plants adapted to harsh environments is crucial in developing new strategies for agriculture. Yet our knowledge of such mechanisms in wild species is scant. We performed metabolic pathway reconstruction using transcriptome information from 32 Atacama and phylogenetically related species that do not live in Atacama (Sisters species). We analyzed reaction enrichment to understand the commonalities and differences of Atacama plants. To gain insights into the mechanisms that ensure survival, we compared expressed gene isoform numbers and gene expression patterns between the annotated biochemical reactions from 32 Atacama and Sister species. We found biochemical convergences characterized by reactions enriched in at least 50% of the Atacama species, pointing to potential advantages against drought and nitrogen starvation, for instance. These findings suggest that the adaptation in the Atacama Desert may result in part from shared genetic legacies governing the expression of key metabolic pathways to face harsh conditions. Enriched reactions corresponded to ubiquitous compounds common to extreme and agronomic species and were congruent with our previous metabolomic analyses. Convergent adaptive traits offer promising candidates for improving abiotic stress resilience in crop species.

Ecological and metabolic implications of the nurse effect of Maihueniopsis camachoi in the Atacama Desert

Plant-plant positive interactions are key drivers of community structure. Yet, the underlying molecular mechanisms of facilitation processes remain unexplored. We investigated the 'nursing' effect of Maihueniopsis camachoi, a cactus that thrives in the Atacama Desert between c. 2800 and 3800 m above sea level. We hypothesised that an important protective factor is thermal amelioration of less cold-tolerant species with a corresponding impact on molecular phenotypes. To test this hypothesis, we compared plant cover and temperatures within the cactus foliage with open areas and modelled the effect of temperatures on plant distribution. We combined eco-metabolomics and machine learning to test the molecular consequences of this association. Multiple species benefited from the interaction with M. camachoi. A conspicuous example was the extended distribution of Atriplex imbricata to colder elevations in association with M. camachoi (400 m higher as compared to plants in open areas). Metabolomics identified 93 biochemical markers predicting the interaction status of A. imbricata with 79% accuracy, independently of year. These findings place M. camachoi as a key species in Atacama plant communities, driving local biodiversity with an impact on molecular phenotypes of nursed species. Our results support the stress-gradient hypothesis and provide pioneer insights into the metabolic consequences of facilitation.

Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth-defence trade-off

Although primary metabolism is well conserved across species, it is useful to explore the specificity of its network to assess the extent to which some pathways may contribute to particular outcomes. Constraint-based metabolic modelling is an established framework for predicting metabolic fluxes and phenotypes and helps to explore how the plant metabolic network delivers specific outcomes from temporal series. After describing the main physiological traits during fruit development, we confirmed the correlations between fruit relative growth rate (RGR), protein content and time to maturity. Then a constraint-based method is applied to a panel of eight fruit species with a knowledge-based metabolic model of heterotrophic cells describing a generic metabolic network of primary metabolism. The metabolic fluxes are estimated by constraining the model using a large set of metabolites and compounds quantified throughout fruit development. Multivariate analyses showed a clear common pattern of flux distribution during fruit development with differences between fast- and slow-growing fruits. Only the latter fruits mobilise the tricarboxylic acid cycle in addition to glycolysis, leading to a higher rate of respiration. More surprisingly, to balance nitrogen, the model suggests, on the one hand, nitrogen uptake by nitrate reductase to support a high RGR at early stages of cucumber and, on the other hand, the accumulation of alkaloids during ripening of pepper and eggplant. Finally, building virtual fruits by combining 12 biomass compounds shows that the growth-defence trade-off is supported mainly by cell wall synthesis for fast-growing fruits and by total polyphenols accumulation for slow-growing fruits.

Enzyme-based kinetic modelling of ASC-GSH cycle during tomato fruit development reveals the importance of reducing power and ROS availability

The ascorbate-glutathione (ASC-GSH) cycle is at the heart of redox metabolism, linking the major redox buffers with central metabolism through the processing of reactive oxygen species (ROS) and pyridine nucleotide metabolism. Tomato fruit development is underpinned by changes in redox buffer contents and their associated enzyme capacities, but interactions between them remain unclear. Based on quantitative data obtained for the core redox metabolism, we built an enzyme-based kinetic model to calculate redox metabolite concentrations with their corresponding fluxes and control coefficients. Dynamic and associated regulations of the ASC-GSH cycle throughout the whole fruit development were analysed and pointed to a sequential metabolic control of redox fluxes by ASC synthesis, NAD(P)H and ROS availability depending on the developmental phase. Furthermore, we highlighted that monodehydroascorbate reductase and the availability of reducing power were found to be the main regulators of the redox state of ASC and GSH during fruit growth under optimal conditions. Our kinetic modelling approach indicated that tomato fruit development displayed growth phase-dependent redox metabolism linked with central metabolism via pyridine nucleotides and H2 O2 availability, while providing a new tool to the scientific community to investigate redox metabolism in fruits.

Multi-omics quantitative data of tomato fruit unveils regulation modes of least variable metabolites

BACKGROUND

The composition of ripe fruits depends on various metabolites which content evolves greatly throughout fruit development and may be influenced by the environment. The corresponding metabolism regulations have been widely described in tomato during fruit growth and ripening. However, the regulation of other metabolites that do not show large changes in content have scarcely been studied.

RESULTS

We analysed the metabolites of tomato fruits collected on different trusses during fruit development, using complementary analytical strategies. We identified the 22 least variable metabolites, based on their coefficients of variation. We first verified that they had a limited functional link with the least variable proteins and transcripts. We then posited that metabolite contents could be stabilized through complex regulations and combined their data with the quantitative proteome or transcriptome data, using sparse partial-least-square analyses. This showed shared regulations between several metabolites, which interestingly remained linked to early fruit development. We also examined regulations in specific metabolites using correlations with individual proteins and transcripts, which revealed that a stable metabolite does not always correlate with proteins and transcripts of its known related pathways.

CONCLUSIONS

The regulation of the least variable metabolites was then interpreted regarding their roles as hubs in metabolic pathways or as signalling molecules.

SPITFIR(e): a supermaneuverable algorithm for fast denoising and deconvolution of 3D fluorescence microscopy images and videos

Modern fluorescent microscopy imaging is still limited by the optical aberrations and the photon budget available in the specimen. A direct consequence is the necessity to develop flexible and "off-road" algorithms in order to recover structural details and improve spatial resolution, which is critical when restraining the illumination to low levels in order to limit photo-damages. Here, we report SPITFIR(e) a flexible method designed to accurately and quickly restore 2D-3D fluorescence microscopy images and videos (4D images). We designed a generic sparse-promoting regularizer to subtract undesirable out-of-focus background and we developed a primal-dual algorithm for fast optimization. SPITFIR(e) is a "swiss-knife" method for practitioners as it adapts to any microscopy techniques, to various sources of signal degradation (noise, blur), to variable image contents, as well as to low signal-to-noise ratios. Our method outperforms existing state-of-the-art algorithms, and is more flexible than supervised deep-learning methods requiring ground truth datasets. The performance, the flexibility, and the ability to push the spatiotemporal resolution limit of sub-diffracted fluorescence microscopy techniques are demonstrated on experimental datasets acquired with various microscopy techniques from 3D spinning-disk confocal up to lattice light sheet microscopy.

Sparse denoising and adaptive estimation enhances the resolution and contrast of fluorescence emission difference microscopy based on an array detector

An array detector allows a resolution gain for confocal microscopy by combining images sensed by a set of photomultipliers tubes (or sub-detectors). Several methods have been proposed to reconstruct a high-resolution image by linearly combining sub-detector images, especially the fluorescence emission difference (FED) technique. To improve the resolution and contrast of FED microscopy based on an array detector, we propose to associate sparse denoising with spatial adaptive estimation. We show on both calibration slides and real data that our approach applied to the full stack of spatially reassigned detector signals, enables us to achieve a higher reconstruction performance in terms of resolution, image contrast, and noise reduction.

Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience

Current crop yield of the best ideotypes is stagnating and threatened by climate change. In this scenario, understanding wild plant adaptations in extreme ecosystems offers an opportunity to learn about new mechanisms for resilience. Previous studies have shown species specificity for metabolites involved in plant adaptation to harsh environments. Here, we combined multispecies ecological metabolomics and machine learning-based generalized linear model predictions to link the metabolome to the plant environment in a set of 24 species belonging to 14 families growing along an altitudinal gradient in the Atacama Desert. Thirty-nine common compounds predicted the plant environment with 79% accuracy, thus establishing the plant metabolome as an excellent integrative predictor of environmental fluctuations. These metabolites were independent of the species and validated both statistically and biologically using an independent dataset from a different sampling year. Thereafter, using multiblock predictive regressions, metabolites were linked to climatic and edaphic stressors such as freezing temperature, water deficit and high solar irradiance. These findings indicate that plants from different evolutionary trajectories use a generic metabolic toolkit to face extreme environments. These core metabolites, also present in agronomic species, provide a unique metabolic goldmine for improving crop performances under abiotic pressure.

STracking: a free and open-source python library for particle tracking and analysis

SUMMARY

Analysis of intra and extra cellular dynamic like vesicles transport involves particle tracking algorithms. The design of a particle tracking pipeline is a routine but tedious task. Therefore, particle dynamics analysis is often performed by combining several pieces of software (filtering, detection, tracking…) requiring many manual operations, and thus leading to poorly reproducible results. Given the new segmentation tools based on deep learning, modularity and interoperability between software have become essential in particle tracking algorithms. A good synergy between a particle detector and a tracker is of paramount importance. In addition, a user-friendly interface to control the quality of estimated trajectories is necessary. To address these issues, we developed STracking, a python library that allows combining algorithms into standardized particle tracking pipelines.

AVAILABILITY AND IMPLEMENTATION

STracking is available as a python library using "pip install" and the source code is publicly available on GitHub (https://github.com/sylvainprigent/stracking). A graphical interface is available using two napari plugins: napari-stracking and napari-tracks-reader. These napari plugins can be installed via the napari plugins menu or using "pip install". The napari plugin source codes are available on GitHub (https://github.com/sylvainprigent/napari-tracks-reader, https://github.com/sylvainprigent/napari-stracking).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Identifying early metabolite markers of successful graft union formation in grapevine

Grafting is an important horticultural technique used for many crop species. However, some scion/rootstock combinations are considered as incompatible due to poor graft union formation and subsequently high plant mortality. The early identification of graft incompatibility could allow the selection of non-viable plants before planting and would have a beneficial impact on research and development in the nursery sector. In general, visible phenotypes of grafted plants (size, root number, etc.) are poorly correlated with grafting success, but some studies have suggested that some polyphenols could be used as markers of graft incompatibility several months or years after grafting. However, much of the previous studies into metabolite markers of grafting success have not included all the controls necessary to unequivocally validate the markers proposed. In this study, we quantified 73 primary and secondary metabolites in nine hetero-grafts and six homo-grafted controls 33 days after grafting at the graft interface and in both the scion and rootstock woody tissues. Certain biomarker metabolites typical of a high stress status (such as proline, GABA and pallidol) were particularly accumulated at the graft interface of the incompatible scion/rootstock combination. We then used correlation analysis and generalized linear models to identify potential metabolite markers of grafting success measured one year after grafting. Here we present the first attempt to quantitatively predict graft compatibility and identify marker metabolites (especially asparagine, trans-resveratrol, trans-piceatannol and α-viniferin) 33 days after grafting, which was found to be particularly informative for homo-graft combinations.

Maize metabolome and proteome responses to controlled cold stress partly mimic early-sowing effects in the field and differ from those of Arabidopsis

In Northern Europe, sowing maize one-month earlier than current agricultural practices may lead to moderate chilling damage. However, studies of the metabolic responses to low, non-freezing, temperatures remain scarce. Here, genetically-diverse maize hybrids (Zea mays, dent inbred lines crossed with a flint inbred line) were cultivated in a growth chamber at optimal temperature and then three decreasing temperatures for 2 days each, as well as in the field. Leaf metabolomic and proteomic profiles were determined. In the growth chamber, 50% of metabolites and 18% of proteins changed between 20 and 16°C. These maize responses, partly differing from those of Arabidopsis to short-term chilling, were mapped on genome-wide metabolic maps. Several metabolites and proteins showed similar variation for all temperature decreases: seven MS-based metabolite signatures and two proteins involved in photosynthesis decreased continuously. Several increasing metabolites or proteins in the growth-chamber chilling conditions showed similar trends in the early-sowing field experiment, including trans-aconitate, three hydroxycinnamate derivatives, a benzoxazinoid, a sucrose synthase, lethal leaf-spot 1 protein, an allene oxide synthase, several glutathione transferases and peroxidases. Hybrid groups based on field biomass were used to search for the metabolite or protein responses differentiating them in growth-chamber conditions, which could be of interest for breeding.

Overproduction of ascorbic acid impairs pollen fertility in tomato

Ascorbate is a major antioxidant buffer in plants. Several approaches have been used to increase the ascorbate content of fruits and vegetables. Here, we combined forward genetics with mapping-by-sequencing approaches using an ethyl methanesulfonate (EMS)-mutagenized Micro-Tom population to identify putative regulators underlying a high-ascorbate phenotype in tomato fruits. Among the ascorbate-enriched mutants, the family with the highest fruit ascorbate level (P17C5, up to 5-fold wild-type level) had strongly impaired flower development and produced seedless fruit. Genetic characterization was performed by outcrossing P17C5 with cv. M82. We identified the mutation responsible for the ascorbate-enriched trait in a cis-acting upstream open reading frame (uORF) involved in the downstream regulation of GDP-l-galactose phosphorylase (GGP). Using a specific CRISPR strategy, we generated uORF-GGP1 mutants and confirmed the ascorbate-enriched phenotype. We further investigated the impact of the ascorbate-enriched trait in tomato plants by phenotyping the original P17C5 EMS mutant, the population of outcrossed P17C5 × M82 plants, and the CRISPR-mutated line. These studies revealed that high ascorbate content is linked to impaired floral organ architecture, particularly anther and pollen development, leading to male sterility. RNA-seq analysis suggested that uORF-GGP1 acts as a regulator of ascorbate synthesis that maintains redox homeostasis to allow appropriate plant development.

Polyphenol Profiles of Just Pruned Grapevine Canes from Wild Vitis Accessions and Vitis vinifera Cultivars

Grapevine canes are an abundant byproduct of the wine industry. The stilbene contents of Vitis vinifera cultivars have been largely studied, but little is known about the stilbene contents of wild Vitis accessions. Moreover, there have only been few studies on the quantification of other phenolic compounds in just pruned grapevine canes. In our study, we investigated the polyphenol profile of 51 genotypes belonging to 15 Vitis spp. A total of 36 polyphenols (20 stilbenes, 6 flavanols, 7 flavonols, and 3 phenolic acids) were analyzed by high-performance liquid chromatography coupled with a triple quadrupole mass spectrometer. Our results suggest that some wild Vitis accessions could be of interest in terms of the concentration of bioactive polyphenols and that flavanols contribute significantly to the antioxidant activity of grapevine cane extracts. To the best of our knowledge, this is the most exhaustive study of the polyphenolic composition of grapevine canes of wild Vitis spp.

Biomass composition explains fruit relative growth rate and discriminates climacteric from non-climacteric species

Fleshy fruits are very varied, whether in terms of their composition, physiology, or rate and duration of growth. To understand the mechanisms that link metabolism to phenotypes, which would help the targeting of breeding strategies, we compared eight fleshy fruit species during development and ripening. Three herbaceous (eggplant, pepper, and cucumber), three tree (apple, peach, and clementine) and two vine (kiwifruit and grape) species were selected for their diversity. Fruit fresh weight and biomass composition, including the major soluble and insoluble components, were determined throughout fruit development and ripening. Best-fitting models of fruit weight were used to estimate relative growth rate (RGR), which was significantly correlated with several biomass components, especially protein content (R=84), stearate (R=0.72), palmitate (R=0.72), and lignocerate (R=0.68). The strong link between biomass composition and RGR was further evidenced by generalized linear models that predicted RGR with R-values exceeding 0.9. Comparison of the fruit also showed that climacteric fruit (apple, peach, kiwifruit) contained more non-cellulosic cell-wall glucose and fucose, and more starch, than non-climacteric fruit. The rate of starch net accumulation was also higher in climacteric fruit. These results suggest that the way biomass is constructed has a major influence on performance, especially growth rate.

Proton-NMR Metabolomics of Rainbow Trout Fed a Plant-Based Diet Supplemented with Graded Levels of a Protein-Rich Yeast Fraction Reveal Several Metabolic Processes Involved in Growth

BACKGROUND

Plant raw materials are commonly used in aquafeeds, as marine resources are unsustainable. However, full plant-based diets lead to poorer fish growth performance.

OBJECTIVE

We aimed to understand the metabolic effects of a yeast fraction as a protein supplement in a plant-based diet and to integrate such effects with phenotypic traits as a new approach to assess the interest of this raw material.

METHODS

Juvenile (49 g) rainbow trout (Oncorhynchus mykiss) were fed graded levels of a yeast protein-rich fraction (5% YST05, 10% YST10, 15% YST15) in a plant-based diet (PB) for 84 d. Final body weight, feed conversion ratio, and hepatosomatic and viscerosomatic indexes were measured. Plasma, liver, and muscle 1H-NMR fingerprints were analyzed with principal component analyses, and their metabolite patterns were clustered according to the yeast level to identify concomitant metabolic effects. A regression modeling approach was used to predict tissue metabolite changes from plasma fingerprints.

RESULTS

In tissues, the patterns of metabolite changes followed either linear trends with the gradual inclusion of a yeast fraction (2 patterns out of 6 in muscle, 1 in liver) or quadratic trends (4 patterns in muscle, 5 in liver). Muscle aspartate and glucose (395 and 138% maximum increase in relative content compared with PB, respectively) revealing modification in energy metabolism, as well as modification of liver betaine (163% maximum increase) and muscle histidine (57% maximum decrease) related functions, indicates that the yeast fraction could improve growth in several ways. The highest correlation between measured and predicted metabolite intensities in a tissue based on plasma fingerprints was observed for betaine in liver (r = 0.80).

CONCLUSIONS

These findings herald a new approach to assess the plurality of metabolic effects induced by diets and establish the optimal level of raw materials. They open the way for using plasma as a noninvasive matrix in trout nutrition studies.

Metabolomics to Exploit the Primed Immune System of Tomato Fruit

Tomato is a major crop suffering substantial yield losses from diseases, as fruit decay at a postharvest level can claim up to 50% of the total production worldwide. Due to the environmental risks of fungicides, there is an increasing interest in exploiting plant immunity through priming, which is an adaptive strategy that improves plant defensive capacity by stimulating induced mechanisms. Broad-spectrum defence priming can be triggered by the compound ß-aminobutyric acid (BABA). In tomato plants, BABA induces resistance against various fungal and bacterial pathogens and different methods of application result in durable protection. Here, we demonstrate that the treatment of tomato plants with BABA resulted in a durable induced resistance in tomato fruit against Botrytis cinerea, Phytophthora infestans and Pseudomonas syringae. Targeted and untargeted metabolomics were used to investigate the metabolic regulations that underpin the priming of tomato fruit against pathogenic microbes that present different infection strategies. Metabolomic analyses revealed major changes after BABA treatment and after inoculation. Remarkably, primed responses seemed specific to the type of infection, rather than showing a common fingerprint of BABA-induced priming. Furthermore, top-down modelling from the detected metabolic markers allowed for the accurate prediction of the measured resistance to fruit pathogens and demonstrated that soluble sugars are essential to predict resistance to fruit pathogens. Altogether, our results demonstrate that metabolomics is particularly insightful for a better understanding of defence priming in fruit. Further experiments are underway in order to identify key metabolites that mediate broad-spectrum BABA-induced priming in tomato fruit.

Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs)

Recent advancements in the use of microbial cells for scalable production of industrial enzymes encourage exploring new environments for efficient microbial cell factories (MCFs). Here, through a comparison study, ten newly sequenced Bacillus species, isolated from the Rabigh Harbor Lagoon on the Red Sea shoreline, were evaluated for their potential use as MCFs. Phylogenetic analysis of 40 representative genomes with phylogenetic relevance, including the ten Red Sea species, showed that the Red Sea species come from several colonization events and are not the result of a single colonization followed by speciation. Moreover, clustering reactions in reconstruct metabolic networks of these Bacillus species revealed that three metabolic clades do not fit the phylogenetic tree, a sign of convergent evolution of the metabolism of these species in response to special environmental adaptation. We further showed Red Sea strains Bacillus paralicheniformis (Bac48) and B. halosaccharovorans (Bac94) had twice as much secreted proteins than the model strain B. subtilis 168. Also, Bac94 was enriched with genes associated with the Tat and Sec protein secretion system and Bac48 has a hybrid PKS/NRPS cluster that is part of a horizontally transferred genomic region. These properties collectively hint towards the potential use of Red Sea Bacillus as efficient protein secreting microbial hosts, and that this characteristic of these strains may be a consequence of the unique ecological features of the isolation environment.

Regulation of Pyridine Nucleotide Metabolism During Tomato Fruit Development Through Transcript and Protein Profiling

Central metabolism is the engine of plant biomass, supplying fruit growth with building blocks, energy, and biochemical cofactors. Among metabolic cornerstones, nicotinamide adenine dinucleotide (NAD) is particularly pivotal for electron transfer through reduction-oxidation (redox) reactions, thus participating in a myriad of biochemical processes. Besides redox functions, NAD is now assumed to act as an integral regulator of signaling cascades involved in growth and environmental responses. However, the regulation of NAD metabolism and signaling during fruit development remains poorly studied and understood. Here, we benefit from RNAseq and proteomic data obtained from nine growth stages of tomato fruit (var. Moneymaker) to dissect mRNA and protein profiles that link to NAD metabolism, including de novo biosynthesis, recycling, utilization, and putative transport. As expected for a cofactor synthesis pathway, protein profiles failed to detect enzymes involved in NAD synthesis or utilization, except for nicotinic acid phosphoribosyltransferase (NaPT) and nicotinamidase (NIC), which suggested that most NAD metabolic enzymes were poorly represented quantitatively. Further investigations on transcript data unveiled differential expression patterns during fruit development. Interestingly, among specific NAD metabolism-related genes, early de novo biosynthetic genes were transcriptionally induced in very young fruits, in association with NAD kinase, while later stages of fruit growth rather showed an accumulation of transcripts involved in later stages of de novo synthesis and in NAD recycling, which agreed with augmented NAD(P) levels. In addition, a more global overview of 119 mRNA and 78 protein significant markers for NAD(P)-dependent enzymes revealed differential patterns during tomato growth that evidenced clear regulations of primary metabolism, notably with respect to mitochondrial functions. Overall, we propose that NAD metabolism and signaling are very dynamic in the developing tomato fruit and that its differential regulation is certainly critical to fuel central metabolism linking to growth mechanisms.

Modeling Protein Destiny in Developing Fruit

Protein synthesis and degradation are essential processes that regulate cell status. Because labeling in bulky organs, such as fruits, is difficult, we developed a modeling approach to study protein turnover at the global scale in developing tomato (Solanum lycopersicum) fruit. Quantitative data were collected for transcripts and proteins during fruit development. Clustering analysis showed smaller changes in protein abundance compared to mRNA abundance. Furthermore, protein and transcript abundance were poorly correlated, and the coefficient of correlation decreased during fruit development and ripening, with transcript levels decreasing more than protein levels. A mathematical model with one ordinary differential equation was used to estimate translation (kt ) and degradation (kd ) rate constants for almost 2,400 detected transcript-protein pairs and was satisfactorily fitted for >1,000 pairs. The model predicted median values of ∼2 min for the translation of a protein, and a protein lifetime of ∼11 d. The constants were validated and inspected for biological relevance. Proteins involved in protein synthesis had higher kt and kd values, indicating that the protein machinery is particularly flexible. Our model also predicts that protein concentration is more strongly affected by the rate of translation than that of degradation.

Reconstruction of 24 Penicillium genome-scale metabolic models shows diversity based on their secondary metabolism

Modeling of metabolism at the genome-scale has proved to be an efficient method for explaining the phenotypic traits observed in living organisms. Further, it can be used as a means of predicting the effect of genetic modifications for example, development of microbial cell factories. With the increasing amount of genome sequencing data available, there exists a need to accurately and efficiently generate such genome-scale metabolic models (GEMs) of nonmodel organisms, for which data is sparse. In this study, we present an automatic reconstruction approach applied to 24 Penicillium species, which have potential for production of pharmaceutical secondary metabolites or use in the manufacturing of food products, such as cheeses. The models were based on the MetaCyc database and a previously published Penicillium GEM and gave rise to comprehensive genome-scale metabolic descriptions. The models proved that while central carbon metabolism is highly conserved, secondary metabolic pathways represent the main diversity among species. The automatic reconstruction approach presented in this study can be applied to generate GEMs of other understudied organisms, and the developed GEMs are a useful resource for the study of Penicillium metabolism, for example, for the scope of developing novel cell factories.

A targeted 3D EM and correlative microscopy method using SEM array tomography

Using electron microscopy to localize rare cellular events or structures in complex tissue is challenging. Correlative light and electron microscopy procedures have been developed to link fluorescent protein expression with ultrastructural resolution. Here, we present an optimized scanning electron microscopy (SEM) workflow for volumetric array tomography for asymmetric samples and model organisms (Caenorhabditis elegans, Drosophila melanogaster, Danio rerio). We modified a diamond knife to simplify serial section array acquisition with minimal artifacts. After array acquisition, the arrays were transferred to a glass coverslip or silicon wafer support. Using light microscopy, the arrays were screened rapidly for initial recognition of global anatomical features (organs or body traits). Then, using SEM, an in-depth study of the cells and/or organs of interest was performed. Our manual and automatic data acquisition strategies make 3D data acquisition and correlation simpler and more precise than alternative methods. This method can be used to address questions in cell and developmental biology that require the efficient identification of a labeled cell or organelle.

Nature-Based Tourism Elicits a Phenotypic Shift in the Coping Abilities of Fish

Nature-based tourism is gaining extensive popularity, increasing the intensity and frequency of human-wildlife contacts. As a consequence, behavioral and physiological alterations were observed in most exposed animals. However, while the majority of these studies investigated the effects of punctual exposure to tourists, the consequences of constant exposition to humans in the wild remains overlooked. This is an important gap considering the exponential interest for recreational outdoor activities. To infer long-term effects of intensive tourism, we capitalized on Odontostilbe pequira, a short-lived sedentary Tetra fish who spends its life close to humans, on which it feeds on dead skin. Hence, those fish are constantly exposed to tourists throughout their lifecycle. Here we provide an integrated picture of the whole phenomenon by investigating, for the first time, the expression of genes involved in stress response and neurogenesis, as well as behavioral and hormonal responses of animals consistently exposed to tourists. Gene expression of the mineralocorticoid (and cortisol) receptor (mr) and the neurogenic differentiation factor (NeuroD) were significantly higher in fish sampled in the touristic zone compared to those sampled in the control zone. Additionally, after a simulated stress in artificial and controlled conditions, those fish previously exposed to visitors produced more cortisol and presented increased behavioral signs of stress compared to their non-exposed conspecifics. Overall, nature-based tourism appeared to shift selection pressures, favoring a sensitive phenotype that does not thrive under natural conditions. The ecological implications of this change in coping style remain, nevertheless, an open question.

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

Increasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce Meneco, a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. Meneco reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks Meneco was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of Meneco we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then Meneco was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that Meneco is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to suggest relevant reactions that explain the metabolic capacity of a biological system.

The Concise Guide to PHARMACOLOGY 2013/14: overview

The Concise Guide to PHARMACOLOGY 2013/14 provides concise overviews of the key properties of over 2000 human drug targets with their pharmacology, plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties from the IUPHAR database. The full contents can be found at http://onlinelibrary.wiley.com/doi/10.1111/bph.12444/full. This compilation of the major pharmacological targets is divided into seven areas of focus: G protein-coupled receptors, ligand-gated ion channels, ion channels, catalytic receptors, nuclear hormone receptors, transporters and enzymes. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. A new landscape format has easy to use tables comparing related targets. It is a condensed version of material contemporary to late 2013, which is presented in greater detail and constantly updated on the website www.guidetopharmacology.org, superseding data presented in previous Guides to Receptors & Channels. It is produced in conjunction with NC-IUPHAR and provides the official IUPHAR classification and nomenclature for human drug targets, where appropriate. It consolidates information previously curated and displayed separately in IUPHAR-DB and GRAC and provides a permanent, citable, point-in-time record that will survive database updates.

The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond

Brown algae (stramenopiles) are key players in intertidal ecosystems, and represent a source of biomass with several industrial applications. Ectocarpus siliculosus is a model to study the biology of these organisms. Its genome has been sequenced and a number of post-genomic tools have been implemented. Based on this knowledge, we report the reconstruction and analysis of a genome-scale metabolic network for E. siliculosus, EctoGEM (http://ectogem.irisa.fr). This atlas of metabolic pathways consists of 1866 reactions and 2020 metabolites, and its construction was performed by means of an integrative computational approach for identifying metabolic pathways, gap filling and manual refinement. The capability of the network to produce biomass was validated by flux balance analysis. EctoGEM enabled the reannotation of 56 genes within the E. siliculosus genome, and shed light on the evolution of metabolic processes. For example, E. siliculosus has the potential to produce phenylalanine and tyrosine from prephenate and arogenate, but does not possess a phenylalanine hydroxylase, as is found in other stramenopiles. It also possesses the complete eukaryote molybdenum co-factor biosynthesis pathway, as well as a second molybdopterin synthase that was most likely acquired via horizontal gene transfer from cyanobacteria by a common ancestor of stramenopiles. EctoGEM represents an evolving community resource to gain deeper understanding of the biology of brown algae and the diversification of physiological processes. The integrative computational method applied for its reconstruction will be valuable to set up similar approaches for other organisms distant from biological benchmark models.

Effects of a saturated layer and recirculation on nitrogen treatment performances of a single stage Vertical Flow Constructed Wetland (VFCW)

Upgrades to enhance nitrogen removal were tested in a 2 year old pilot vertical flow constructed wetland in spring and summer periods. The effects of a saturated layer and of recirculation were tested in particular. Two pilots (L = 2 m, W = 1.25 m, H = 1.2 m), filled with expanded schist (Mayennite(®)), were designed with hydraulic saturated layers of 20 and 40 cm at the bottom. Each pilot was fed with raw domestic wastewater under field conditions according to a hydraulic load of 15-38 cm d(-1) (i.e. 158-401 g COD (chemical oxygen demand) m(-2) d(-1)) and to recirculation rates ranging from 0% up to 150%. The initial load during the first 2 years of operation resulted in an incomplete mineralized accumulated sludge leading to total suspended solids (TSS), COD and biochemical oxygen demand (BOD5) release. A 40 cm hydraulic saturated layer enabled an increase of 5-10% total nitrogen (TN) removal compared to a 20 cm saturated layer. Recirculation allowed the dilution of raw wastewater and enhanced nitrification in a single stage. A design of 1.8 m² pe(-1) (48 cm d(-1), 191 g COD m(-2) d(-1)) with a 40 cm saturated layer and 100% recirculation enabled the French standard D4 (35 mg TSS L(-1), 125 mg COD L(-1), 25 mg BOD5 L(-1)), nitrogen concentrations below 20 mg TKN (total Kjeldahl nitrogen) L(-1) and 50 mg TN L(-1), to be met.

Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment

Brown algae belong to a phylogenetic lineage distantly related to land plants and animals. They are almost exclusively found in the intertidal zone, a harsh and frequently changing environment where organisms are submitted to marine and terrestrial constraints. In relation with their unique evolutionary history and their habitat, they feature several peculiarities, including at the level of their primary and secondary metabolism. The establishment of Ectocarpus siliculosus as a model organism for brown algae has represented a framework in which several omics techniques have been developed, in particular, to study the response of these organisms to abiotic stresses. With the recent publication of medium to high throughput profiling data, it is now possible to envision integrating observations at the cellular scale to apply systems biology approaches. As a first step, we propose a protocol focusing on integrating heterogeneous knowledge gained on brown algal metabolism. The resulting abstraction of the system will then help understanding how brown algae cope with changes in abiotic parameters within their unique habitat, and to decipher some of the mechanisms underlying their (1) acclimation and (2) adaptation, respectively consequences of (1) the behavior or (2) the topology of the system resulting from the integrative approach.

Investigation of the role of sigma1-receptors in inositol 1,4,5-trisphosphate dependent calcium signaling in hepatocytes

In hepatocytes, as in other cell types, Ca(2+) signaling is subject to complex regulations, which result largely from the intrinsic characteristics of the different inositol 1,4,5-trisphosphate receptor (InsP(3)R) isoforms and from their interactions with other proteins. Although sigma1 receptors (Sig-1Rs) are widely expressed in the liver, their involvement in hepatic Ca(2+) signaling remains unknown. We here report that in this cell type Sig-1R interact with type 1 isoforms of the InsP(3) receptors (InsP(3)R-1). These results obtained by immunoprecipitation experiments are confirmed by the observation that Sig-1R proteins and InsP(3)R-1 colocalize in hepatocytes. However, Sig-1R ligands have no effect on InsP(3)-induced Ca(2+) release in hepatocytes. This can be explained by the rather low expression level expression of InsP(3)R-1. In contrast, we find that Sig-1R ligands can inhibit agonist-induced Ca(2+) signaling via an inhibitory effect on InsP(3) synthesis. We show that this inhibition is due to the stimulation of PKC activity by Sig-1R, resulting in the well-known down-regulation of the signaling pathway responsible for the transduction of the extracellular stimulus into InsP(3) synthesis. The PKC sensitive to Sig-1R activity belongs to the family of conventional PKC, but the precise molecular mechanism of this regulation remains to be elucidated.

Model of cap-dependent translation initiation in sea urchin: a step towards the eukaryotic translation regulation network

The large and rapid increase in the rate of protein synthesis following fertilization of the sea urchin egg has long been a paradigm of translational control, an important component of the regulation of gene expression in cells. This translational up-regulation is linked to physiological changes that occur upon fertilization and is necessary for entry into first cell division cycle. Accumulated knowledge on cap-dependent initiation of translation makes it suited and timely to start integrating the data into a system view of biological functions. Using a programming environment for system biology coupled with model validation (named Biocham), we have built an integrative model for cap-dependent initiation of translation. The model is described by abstract rules. It contains 51 reactions involved in 74 molecular complexes. The model proved to be coherent with existing knowledge by using queries based on computational tree logic (CTL) as well as Boolean simulations. The model could simulate the change in translation occurring at fertilization in the sea urchin model. It could also be coupled with an existing model designed for cell-cycle control. Therefore, the cap-dependent translation initiation model can be considered a first step towards the eukaryotic translation regulation network.

Cutaneous events during treatment of chronic inflammatory joint disorders with anti-tumour necrosis factor alpha: a cross-sectional study

BACKGROUND

Anti-tumour necrosis factors (anti-TNF) are more and more used, but the rate of skin adverse events is not known.

OBJECTIVE

The aim was to assess the number of skin infections and other dermatoses in patients treated with anti-TNFalpha.

PATIENTS AND METHODS

One hundred eighty-seven patients suffering from rheumatoid arthritis or ankylosing spondylitis underwent a dermatological exam. Patients with anti-TNF were compared with those without this treatment in a prospective transversal study.

RESULTS

Among them, 59 patients were treated with anti-TNFalpha and steroids were prescribed in 100 cases. There was no difference in the prevalence of skin infections or eczema or tumours. Skin drug reactions were observed in six patients. Infections by dermatophytes appear very frequent, approaching 70% in both groups.

CONCLUSIONS

This study shows that skin infections (or other skin diseases) are not more frequent in these patients. No differences were observed in infections (bacterial fungal, parasital or viral), tumours, psoriasis or the manifestations of atopic dermatitis. Nonetheless, a long-term survey might be interesting, especially about skin tumours.

Effects of the prostaglandins PGF2alpha and PGE2 on calcium signaling in rat hepatocyte doublets

Coordination of intercellular Ca2+ signals is important for certain hepatic functions including biliary flow and glucose output. Prostaglandins, such as PGF2alpha and PGE2, may modify these hepatocyte functions by inducing Ca2+ increase, but very little is known about the organization of the Ca2+ signals induced by these agonists. We studied Ca2+ signals induced by PGF2alpha and PGE2 in fura-2 AM-loaded hepatocyte doublets. Even though both prostaglandins induced Ca2+ oscillations, neither PGF2alpha nor PGE2 induced coordinated Ca2+ oscillations in hepatocyte doublets. Gap junction permeability (GJP), assessed by fluorescence recovery after photobleaching, showed that this absence of coordination was not related to a defect in GJP. Inositol (1,4,5)trisphosphate [Ins(1,4,5)P3] assays and the increase in Ins(1,4,5)P3 receptor sensitivity to Ins(1,4,5)P3 observed in response to thimerosal suggested that the absence of coordination was a consequence of the very small quantity of Ins(1,4,5)P3 formed by these prostaglandins. Furthermore, when PGE2 and PGF2alpha were added just before norepinephrine, they favored the coordination of Ca2+ signals induced by norepinephrine. However, GJP between hepatocyte doublets was strongly inhibited by prolonged (>or=2 h) treatment with PGF2alpha, thereby preventing the coordination of Ca2+ oscillations induced by norepinephrine in these cells. Thus, depending on the time window, prostaglandins, specially PGF2alpha, may enhance or diminish the propagation of Ca2+ signals. They may therefore contribute to the fine tuning of Ca2+ wave-dependent functions, such as nerve stimulation, hormonal regulation of liver metabolism, or bile secretion, in both normal and pathogenic conditions.

Identification of three distinct regions of allelic deletions on the short arm of chromosome 8 in hepatocellular carcinoma

The chromosome 8p is associated with a large number of allelic imbalances in epithelial tumors including hepatocellular carcinoma (HCC). However, no tumor suppressor gene has been identified so far in this particular region of the genome. To further clarify the pattern of allelic deletions on chromosome 8p in HCC, we have undertaken high-density polymorphic marker analysis of 109 paired normal and primary tumor samples using 40 microsatellites positioned every 2 cm in average throughout 8p. We found that 60% of the tumors exhibited loss of heterozygosity (LOH) at one or more loci at 8p with three distinct minimal deleted areas: a 13 cm region in the distal part of 8p21, a 9 cm area in the more proximal portion of 8p22 and a 5 cm area in 8p23. These data strongly suggest the presence of at least three novel tumor suppressor loci on 8p in hepatocellular carcinoma.

The proapoptotic effect of hepatitis B virus HBx protein correlates with its transactivation activity in stably transfected cell lines

The role of hepatitis B virus HBx protein in the carcinogenesis associated with chronic viral infection remains ill-defined. Indeed, pleiotropic effects have been ascribed to HBx: in addition to its well-documented ability to indirectly stimulate transcription, the protein has been reported to affect cell growth, signal transduction, DNA repair and apoptosis. In this work, we generated Chang (CCL-13)-derived cell lines constitutively expressing wild type or mutant HBx, as a model of HBx-host cell interaction closer to the chronic infection setting, than the classically used transient expression systems. We document the potentiation by HBx of the apoptotic cell death pathway in the recipient cells. This effect is unlikely to rely on p53 activity since the protein is functionally inactivated in CCL-13. In addition, antioxidants and cyclosporin A failed to reduce the apoptotic response back to the normal level, suggesting that production of reactive oxygen species and calcineurin activation are not directly involved in the proapoptotic effect of HBx. In contrast, our data show that transactivation and stimulation of apoptosis are tightly linked HBx activities. Finally, expression of transactivation-active protein did not result in detectable change in the pattern of MAP kinases phosphorylation nor did it affect the ability of the host cell to repair in vitro irradiated plasmid DNA.

Metabolic evolution in alpha-amylases from Drosophila virilis and D. repleta, two species with different ecological niches

alpha-Amylases from Drosophila virilis and D. repleta were partially purified by ion exchange chromatography. The two amylases share common characteristics for pH and cations effects, although with slight differences. D. virilis has optimal activity at pH 6.6 and D. repleta at pH 7.2. Calcium, sodium, and potassium cations activate amylolytic activity in both species but Ba2+ has an activation effect in D. repleta only. In contrast, there are major differences in thermal offbility and kinetics among amylases of the two species. D. virilis amylase is much more stable at high temperature and the optimal temperatures are very different between the two species, respectively, 45 degrees C and 30 degrees C for D. virilis and D. repleta. alpha-Amylase activity using different substrates is greater on starch than on glycogen in both species and still higher on amylose for D. virilis, the nonfungus feeder species. alpha-Amylase of D. repleta, the mycophagous species, has a better affinity to amylopectin and glycogen. Such differences in substrate specificity suggest adaptation to different resources in these species living in different habitats. Metabolic evolution seems to have occurred through a "tradeoff" between kinetic effectiveness and the nature of substrate, with a higher Vmax on amylose for D. virilis and a lower K(m) on glycogen for D. repleta.

Interaction of the UV-damaged DNA-binding protein with hepatitis B virus X protein is conserved among mammalian hepadnaviruses and restricted to transactivation-proficient X-insertion mutants

We carried out a comparative analysis of several proposed host protein partners of the human hepatitis B virus X protein (HBx) using both the GAL4- and the LexA-based yeast two-hybrid system. We showed that the interaction of HBx with the UV-damaged DNA-binding protein (UVDDB) is positive in both yeast systems, detectable in cotransfected human cells, conserved by rodent hepadnavirus X proteins (known to transactivate in human cells), and tightly correlated with the transactivation proficiency of X-insertion mutants. Taken together, our results strongly suggest that UVDDB is involved in X-mediated transactivation.

RalGDS functions in Ras- and cAMP-mediated growth stimulation

Thyroid-stimulating hormone stimulates proliferation through both the cAMP-dependent protein kinase and Ras but not through Raf-1 and mitogen-activated and extracellular signal-related kinase kinase. We now report that thyroid-stimulating hormone represses mitogen-activated protein kinase activity and that microinjection of an effector domain mutant Ha-Ras protein, Ras(12V,37G), defective in Raf-1 binding and mitogen-activated protein kinase activation, stimulates DNA synthesis in quiescent and thyroid-stimulating hormone-treated thyrocytes. A yeast two-hybrid screen identified RalGDS as a Ras(12V,37G) binding protein and therefore a potential effector of Ras in these cells. Associations between Ras and RalGDS were observed in extracts prepared from thyroid cells. Microinjection of a mutant RalA(28N) protein thought to sequester RalGDS family members reduced DNA synthesis stimulated by Ras as well as cAMP-mediated DNA synthesis in two cell lines which respond to cAMP with mitogenesis. These results support the idea that RalGDS may be an effector of Ras in cAMP-mediated growth stimulation.

Efficient production of biologically active human recombinant proteins in human lymphoblastoid cells from integrative and episomal expression vectors

The ability of human lymphoblastoid cells to secrete large amounts of biologically active human hematopoietic growth factors from adenovirus-based expression vectors was investigated. The gene for human erythropoietin (EPO) was inserted into integrative (pTS39) and episomal (pTS53) vectors. Cell clones, originating from pTS39 or pTS53-transfected and stably selected cells, secreted recombinant human EPO (re-hEPO) at similar levels. The highest production, 60 mu/10(6) cells per 24 h, was obtained from a subclone of pTS39-transfected cells, grown in nonselective medium. The re-hEPO was shown to be biologically active in vivo by incorporation of 59Fe into red blood cells of polycythemic mice and in vitro by the proliferative response of the EPO-dependent cell line UT7. The purified protein of 36 kDa in SDS-PAGE slightly differed from re-hEPO from CHO cells. pTS39 vector was integrated at 15-30 copies per genome, whereas the pTS53 vector replicated at 10 copies per cell. Genes encoding human interleukin-3 (IL-3) and granulocyte-macrophage colony-stimulating factor (GM-CSF) were also expressed in the integrative system as biologically active growth factors, demonstrating that our host-vector system allows the expression of any little gene or cDNA and efficient secretion of the re-protein produced.

Production and characterization of human monoclonal antibodies against core protein p25 and transmembrane glycoprotein gp41 of HIV-1

With a view to obtaining human monoclonal antibodies against HIV-1 antigens we used the Epstein-Barr virus immortalization technique to induce lymphoblastoid cell lines from peripheral blood lymphocytes of 10 people who were seropositive for HIV-1 and had no clinical symptoms. A number of polyclonal lines were obtained which synthesized antibodies against most of the major proteins and glycoproteins of HIV-1. Three stable clones were characterized for class, secretion characteristics and specificity. Two of these clones produce antibodies which react with gp41, and the third reacts with p25. One of the anti-gp41 antibodies was found to have neutralizing activity.