Computing biological functions using BioΨ, a formal description of biological processes based on elementary bricks of actions

Motivation: In the available databases, biological processes are described from molecular and cellular points of view, but these descriptions are represented with text annotations that make it difficult to handle them for computation. Consequently, there is an obvious need for formal descriptions of biological processes

Methodology and bioinformatics tools to design synthetic biological systems for new human health diagnosis

La biologie synthétique est une discipline en pleine expansion visant à concevoir et construire des systèmes biologiques possédant des fonctions qui n'existent pas dans la nature. Elle se fonde sur des principes d'ingénierie pour rationnaliser la conception de tels systèmes. Le projet CompuBioTic a pour objectif le développement d'un nouveau type de diagnostic du cancer colorectal, se fondant sur une approche de biologie synthétique. Un choix stratégique a été fait et consiste à vouloir développer un système non vivant, ne nécessitant pas de cellule hôte et fondé sur l'utilisation de réseaux protéiques plutôt que génétiques. Très peu de méthodologies et d'outils ont été développés pour faciliter la conception de ce type de système. Cette thèse propose une méthodologie en trois points : conception, simulation et validation expérimentale ainsi que deux outils bioinformatiques, développés pour aider à la conception de réseaux biochimiques synthétiques. Tout d'abord, CompuBioTicDB est une base de données qui regroupe et annote des dispositifs fonctionnels et des molécules réalisant des processus (protéines et petites molécules) pouvant être exploités dans un contexte de biologie synthétique. Deuxièmement, BioNetCAD est un outil permettant de concevoir un réseau biochimique composé de molécules réelles à partir d'un réseau abstrait. BioNetCAD facilite également la simulation spatio-temporelle du système conçu grâce à un lien vers le logiciel HSim. Des portes logiques moléculaires et un dispositif de détection du glucose ont ainsi été conçus, modélisés et validés expérimentalement. Les principes d'un système pour le diagnostic du cancer colorectal sont également proposés.Synthetic biology is a growing discipline which aims to design and construct biological systems with functions that do not exist in nature. It is based on engineering principles to rationalize the design such systems. The CompuBioTic project aims at the development of a new system for the diagnosis of the colorectal cancer, based on a synthetic biology approach. A strategic choice has been done and consists in wanting to develop a non-living system, which does not require a host cell and which is based on the use of protein rather than genetic networks. Very few methodologies and tools have been developed to facilitate the design of such systems. This thesis proposes a methodology in three steps: design, simulation and experimental validation, as well as two bioinformatics tools, developed to assist the design of synthetic biochemical networks. Firstly, CompuBioTicDB is a database that registers and annotates functional devices and molecules carrying processes (proteins and small molecules) that can be exploited in a context of synthetic biology. Secondly, BioNetCAD is a tool for designing a biochemical network composed of real molecules from an abstract network. BioNetCAD also facilitates spatiotemporal simulation of the designed system with a link to the HSim software. Molecular logic gates and a device for detecting glucose have been designed, modeled and then validated experimentally. The principles of a system for the diagnosis of colorectal cancer are also proposed

Méthodologie et outils bioinformatiques d'aide à la conception de systèmes biologiques synthétiques pour de nouveaux diagnostics en santé humaine

La biologie synthétique est une discipline en pleine expansion visant à concevoir et construire des systèmes biologiques possédant des fonctions qui n'existent pas dans la nature. Elle se fonde sur des principes d'ingénierie pour rationnaliser la conception de tels systèmes. Le projet CompuBioTic a pour objectif le développement d'un nouveau type de diagnostic du cancer colorectal, se fondant sur une approche de biologie synthétique. Un choix stratégique a été fait et consiste à vouloir développer un système non vivant, ne nécessitant pas de cellule hôte et fondé sur l'utilisation de réseaux protéiques plutôt que génétiques. Très peu de méthodologies et d'outils ont été développés pour faciliter la conception de ce type de système. Cette thèse propose une méthodologie en trois points : conception, simulation et validation expérimentale ainsi que deux outils bioinformatiques, développés pour aider à la conception de réseaux biochimiques synthétiques. Tout d'abord, CompuBioTicDB est une base de données qui regroupe et annote des dispositifs fonctionnels et des molécules réalisant des processus (protéines et petites molécules) pouvant être exploités dans un contexte de biologie synthétique. Deuxièmement, BioNetCAD est un outil permettant de concevoir un réseau biochimique composé de molécules réelles à partir d'un réseau abstrait. BioNetCAD facilite également la simulation spatio-temporelle du système conçu grâce à un lien vers le logiciel HSim. Des portes logiques moléculaires et un dispositif de détection du glucose ont ainsi été conçus, modélisés et validés expérimentalement. Les principes d'un système pour le diagnostic du cancer colorectal sont également proposés.Synthetic biology is a growing discipline which aims to design and construct biological systems with functions that do not exist in nature. It is based on engineering principles to rationalize the design such systems. The CompuBioTic project aims at the development of a new system for the diagnosis of the colorectal cancer, based on a synthetic biology approach. A strategic choice has been done and consists in wanting to develop a non-living system, which does not require a host cell and which is based on the use of protein rather than genetic networks. Very few methodologies and tools have been developed to facilitate the design of such systems. This thesis proposes a methodology in three steps: design, simulation and experimental validation, as well as two bioinformatics tools, developed to assist the design of synthetic biochemical networks. Firstly, CompuBioTicDB is a database that registers and annotates functional devices and molecules carrying processes (proteins and small molecules) that can be exploited in a context of synthetic biology. Secondly, BioNetCAD is a tool for designing a biochemical network composed of real molecules from an abstract network. BioNetCAD also facilitates spatiotemporal simulation of the designed system with a link to the HSim software. Molecular logic gates and a device for detecting glucose have been designed, modeled and then validated experimentally. The principles of a system for the diagnosis of colorectal cancer are also proposed.MONTPELLIER-BU Sciences (341722106) / SudocSudocFranceF

Comparative Genomics of Glossina palpalis gambiensis and G. morsitans morsitans to Reveal Gene Orthologs Involved in Infection by Trypanosoma brucei gambiense

International audienceBlood-feeding Glossina palpalis gambiense (Gpg) fly transmits the single-celled eukaryotic parasite Trypanosoma brucei gambiense (Tbg), the second Glossina fly African trypanosome pair being Glossina morsitans/T.brucei rhodesiense. Whatever the T. brucei subspecies, whereas the onset of their developmental program in the zoo-anthropophilic blood feeding flies does unfold in the fly midgut, its completion is taking place in the fly salivary gland where does emerge a low size metacyclic trypomastigote population displaying features that account for its establishment in mammals-human individuals included. Considering that the two Glossina-T. brucei pairs introduced above share similarity with respect to the developmental program of this African parasite, we were curious to map on the Glossina morsitans morsitans (Gmm), the Differentially Expressed Genes (DEGs) we listed in a previous study. Briefly, using the gut samples collected at days 3, 10, and 20 from Gpg that were fed or not at day 0 on Tbg-hosting mice, these DGE lists were obtained from RNA seq-based approaches. Here, post the mapping on the quality controlled DEGs on the Gmm genome, the identified ortholog genes were further annotated, the resulting datasets being compared. Around 50% of the Gpg DEGs were shown to have orthologs in the Gmm genome. Under one of the three Glossina midgut sampling conditions, the number of DEGs was even higher when mapping on the Gmm genome than initially recorded. Many Gmm genes annotated as "Hypothetical" were mapped and annotated on many distinct databases allowing some of them to be properly identified. We identify Glossina fly candidate genes encoding (a) a broad panel of proteases as well as (b) chitin-binding proteins, (c) antimicrobial peptide production-Pro3 protein, transferrin, mucin, atttacin, cecropin, etc-to further select in functional studies, the objectives being to probe and validated fly genome manipulation that prevents the onset of the developmental program of one or the other T. brucei spp. stumpy form sampled by one of the other bloodfeeding Glossina subspecies

Regulatory Divergence between Parental Alleles Determines Gene Expression Patterns in Hybrids

International audienceBoth hybridization and allopolyploidization generate novel phenotypes by conciliating divergent genomes and regulatory networks in the same cellular context. To understand the rewiring of gene expression in hybrids, the total expression of 21,025 genes and the allele-specific expression of over 11,000 genes were quantified in interspecific hybrids and their parental species, Coffea canephora and Coffea eugenioides using RNA-seq technology. Between parental species, cis-and trans-regulatory divergences affected around 32% and 35% of analyzed genes, respectively, with nearly 17% of them showing both. The relative importance of trans-regulatory divergences between both species could be related to their low genetic divergence and perennial habit. In hybrids, among divergently expressed genes between parental species and hybrids, 77% was expressed like one parent (expression level dominance), including 65% like C. eugenioides. Gene expression was shown to result from the expression of both alleles affected by intertwined parental trans-regulatory factors. A strong impact of C. eugenioides trans-regulatory factors on the upregulation of C. canephora alleles was revealed. The gene expression patterns appeared determined by complex combinations of cis-and trans-regulatory divergences. In particular, the observed biased expression level dominance seemed to be derived from the asymmetric effects of trans-regulatory parental factors on regulation of alleles. More generally, this study illustrates the effects of divergent trans-regulatory parental factors on the gene expression pattern in hybrids. The characteristics of the transcriptional response to hybridization appear to be determined by the compatibility of gene regulatory networks and therefore depend on genetic divergences between the parental species and their evolutionary history

New insights into replication origin characteristics in metazoans

International audienc

Transcriptomic profiles of consistent risk-taking behaviour across time and contexts in European sea bass

Bolder individuals have greater access to food sources and reproductive partners but are also at increased risk of predation. Boldness is believed to be consistent across time and contexts, but few studies have investigated the stability of this trait across variable environments, such as varying stress loads or long periods of time. Moreover, the underlying molecular components of boldness are poorly studied. Here, we report that boldness of 1154 European sea bass, evaluated using group risk-taking tests, is consistent over seven months and for individuals subjected to multiple environments, including a chronically stressful environment. Differences in risk-taking behaviour were further supported by differences observed in the responses to a novel environment test: shy individuals displayed more group dispersion, more thigmotaxic behaviour and lower activity levels. Transcriptomic analyses performed on extreme phenotypes revealed that bold individuals display greater expression for genes involved in social and exploration behaviours, and memory in the pituitary, and genes involved in immunity and responses to stimuli in the head kidney. This study demonstrates that personality traits come with an underpinning molecular signature, especially in organs involved in the endocrine and immune systems. As such, our results help to depict state–behaviour feedback mechanisms, previously proposed as key in shaping animal personality

FliZ is a global regulatory protein affecting the expression of flagellar and virulence genes in individual Xenorhabdus nematophila bacterial cells

Heterogeneity in the expression of various bacterial genes has been shown to result in the presence of individuals with different phenotypes within clonal bacterial populations. The genes specifying motility and flagellar functions are coordinately regulated and form a complex regulon, the flagellar regulon. Complex interplay has recently been demonstrated in the regulation of flagellar and virulence gene expression in many bacterial pathogens. We show here that FliZ, a DNA-binding protein, plays a key role in the insect pathogen, Xenorhabdus nematophila, affecting not only hemolysin production and virulence in insects, but efficient swimming motility. RNA-Seq analysis identified FliZ as a global regulatory protein controlling the expression of 278 Xenorhabdus genes either directly or indirectly. FliZ is required for the efficient expression of all flagellar genes, probably through its positive feedback loop, which controls expression of the flhDC operon, the master regulator of the flagellar circuit. FliZ also up- or downregulates the expression of numerous genes encoding non-flagellar proteins potentially involved in key steps of the Xenorhabdus lifecycle. Single-cell analysis revealed the bimodal expression of six identified markers of the FliZ regulon during exponential growth of the bacterial population. In addition, a combination of fluorescence-activated cell sorting and RT-qPCR quantification showed that this bimodality generated a mixed population of cells either expressing ("ON state") or not expressing ("OFF state") FliZ-dependent genes. Moreover, studies of a bacterial population exposed to a graded series of FliZ concentrations showed that FliZ functioned as a rheostat, controlling the rate of transition between the "OFF" and "ON" states in individuals. FliZ thus plays a key role in cell fate decisions, by transiently creating individuals with different potentials for motility and host interactions

In vivo investigation of Lcr35® anti-candidiasis properties in Caenorhabditis elegans reveals the involvement of highly conserved immune pathways

International audienceLactic acid bacteria, including the microorganisms formerly designated as Lactobacillus, are the major representatives of Live Biotherapeutic Microorganisms (LBM) when used for therapeutic purposes. However, in most cases, the mechanisms of action remain unknown. The antifungal potential of LBM has already been demonstrated using preclinical models (cell cultures, laboratory animals). Understanding their mechanisms of action is strategic for the development of new therapeutics for humans. Here, Caenorhabditis elegans was used as an in vivo model to analyze pro-longevity, anti-aging and anti-candidiasis effects of the LBM Lacticaseibacillus rhamnosus (formerly Lactobacillus rhamnosus) Lcr35®. A high-throughput transcriptomic analysis revealed a specific response of C. elegans depending on whether it is in the presence of the LBM L. rhamnosus Lcr35 (structural response), the yeast Candida albicans (metabolic response) or both (structural and metabolic responses) in a preventive and a curative conditions. Studies on C. elegans mutants demonstrated that the p38 MAPK (sek-1, skn-1) and the insulin-like (daf-2, daf-16) signaling pathways were involved in the extended lifespan provided by L. rhamnosus Lcr35® strain whereas the JNK pathway was not involved (jnk-1). In addition, the anti C. albicans effect of the bacterium requires the daf-16 and sek-1 genes while it is independent of daf-2 and skn-1. Moreover, the anti-aging effect of Lcr35®, linked to the extension of longevity, is not due to protection against oxidative stress (H2O2). Taken together, these results formally show the involvement of the p38 MAP kinase and insulin- like signaling pathways for the longevity extension and anti-Candida albicans properties of Lcr35 with, however, differences in the genes involved. Overall, these findings provide new insight for understanding the mechanisms of action of a probiotic strain with antimicrobial potential