Sociogenetics of fire ants

RÉSUMÉ GRAND PUBLIC La complexité des sociétés d'insectes (telles que les abeilles, les termites ou les fourmis) a depuis longtemps fasciné l'Homme. Depuis le débfit du XIXème siècle, de nombreux travaux observationnels, comportementaux et théoriques leur on été consacrés afin de mieux les décrire et comprendre. L'avènement de la biologie moléculaire à la fin du XXèrne siècle a offert de nouveaux outils scientifiques pour identifier et étudier les gènes et molécules impliqués dans le développement et le comportement des êtres vivants. Alors que la majorité de ces études s'est focalisée sur des organismes de laboratoire tel que la mouche ou les nématodes, l'utilisation de ces outils est restée marginale jusqu'à présent dans l'étude des sociétés d'insectes. Lors de ma thèse, j'ai développé des outils moléculaires permettant de déterminer le niveau d'activité de zo,ooo gènes chez la fourmi de feu, Solenopsis invicta, ainsi qu'une base de données et un portail en ligne regroupant les informations relatives à l'étude génétique des fourmis: Fourmidable. J'ai ensuite utilisé ces outils dans le cadre d'une étude comportementale chez la fourmis S. invicta. Dans les sociétés d'insectes, une hiérarchie peut déterminer le statut reproducteur des individus. Suite à la mort d'un dominant, les subordonnés entrent en compétition en vue d'améliorer leur statut. Un tel phénomène se produit au sein des colonies de S. invicta contenant une unique reine mère, des milliers d'ouvrières et des centaines de reines vierges ailées. A la mort de la reine mère, un grand nombre de reines vierges tentent de la remplacer en arrachant leurs ailes et en activant leurs organes reproducteurs plutôt que de partir en vol nuptial. Ces tentatives sont le plus souvent arrêtées par les ouvrières qui exécutent la plupart de ces reines sur la base de signaux olfactifs produits lors de l'activation des organes reproducteurs. Afin de mieux comprendre les mécanismes moléculaires impliqués, j'ai étudié l'activité de gènes au sein des reines au début de ce processus. J'ai ainsi déterminé que des gènes impliqués dans communication olfactive, le développement des organes reproducteurs et la métabolisation de l'hormone juvénile sont activês à ce moment là. La vitesse à laquelle les reines perdent leurs ailes ainsi que les niveaux d'expression de gènes sont ensuite liés à leur probabilité de survie. ABSTRACT : Honeybees, termites and ants occupy the "pinnacle of social evolution" with societies of a complexity that rivals our own. Humans have long been fascinated by social insects, but studying them has been mostly limited to observational and behavioral experiments. The advent of molecular biology first made it possible to investigate the molecular-genetic basis of development in model systems such as the fruit fly Drosophila melarcogaster or the roundworm Caenorhabditis elegans and subsequently their behavior. Molecular and genomic tools are now becoming available for the study of social insects as well. To permit genomic research on the fire ant, Solenopsis invicta, we developed a cDNA microarray that can simultaneously determine the expression levels of approximately 1oooo genes. These genes were assembled and bioinformatically annotated using custom pipelines. The obtained data formed the cornerstones for Fourmidable, a web portal centralizing sequence, gene annotation and gene expression data as well as laboratory protocols for research on ants. In many animals living in groups the reproductive status of individuals is determined by their social status. In species with social hierarchies, the death of dominant individuals typically upheaves the social hierarchy and provides an opportunity for subordinate individuals to improve their social status. Such a phenomenon occurs in the monogyne form of S. invicta, where colonies typically contain a single wingless reproductive queen, thousands of workers and hundreds of winged non-reproductive virgin queens. Upon the death of the mother queen, many virgin queens shed their wings and initiate reproductive development instead of departing on a mating flight. Workers progressively execute almost all of them over the following weeks. The workers base their collective decision on pheromonal cues associated with the onset of reproductive development of the virgin queens which occurs after orphaning. We used the aforementioned tools to determine that genes putatively involved in processes including olfactory signaling, reproductive development and Juvenile Hormone metabolism are differentially expressed at the onset of competition. Additionally, we found that queens that initiate reproductive development faster and, to a certain extent, shed their wings faster after orphaning are more likely to become replacement queens. These results provide candidate genes that are putatively linked to competition outcome. To determine the extent to which specific genes affect different aspects of life in ant colonies, functional tests such as gene activation and silencing will still be required. We conclude by discussing some of the challenges and opportunities for molecular-genetic research on ants. RÉSUMÉ Les sociétés d'abeilles, de termites et de fourmis sont d'une complexité proche de celle de la nôtre et ont depuis longtemps fasciné l'Homme. Cependant, leur étude était jusqu'à présent limitée aux observations et expériences comportementales. L'avènement de la biologie moléculaire a d'abord rendu possible l'étude moléculaire et génétique du développement d'organismes modèles tels que la mouche Drosophila melanogaster ou le nématode Caenorhabditis elegans, puis dans un second temps de leur comportement. De telles études deviennent désormais possibles pour les insectes sociaux. Nous avons développé une puce à ADN permettant de déterminer simultanément les niveaux d'expression de 1oooo gènes de la fourmi de feu, Solenopsís invicta. Ces gènes ont été séquencés puis assemblés et annotés à l'aide de pipelines que nous avons développés. En se basant sur les informations obtenues, nous avons créé un portail web, Fourmidable. Ce portail vise à centraliser toutes les informations de séquence, d'annotation et d'expression de gènes, ainsi que les protocoles de laboratoire utilisés pour la recherche sur les fourmis. Par la suite, nous avons utilisé les outils développés pour étudier un aspect particulier de S. invicta. Chez les animaux grégaires, une hiérarchie sociale peut déterminer le statut reproducteur des individus. Suite à la mort d'un individu dominant, les individus subordonnés peuvent entrer en compétition en vue d'améliorer leur statut. Un tel phénomène se produit au sein des colonies monogynes de S. invicta, qui contiennent habituellement une unique reine mère, des milliers d'ouvrières et des centaines de reines vierges ailées. Suite à la mort de la reine mère, dominante, un grand nombre de reines vierges, subordonnées, perdent leurs ailes et activent leurs organes reproducteurs au lieu de partir en vol nuptial. Au cours des semaines suivantes, les ouvrières exécutent la plupart de ces reines sur la base de signaux olfactifs produits lors de l'activation des organes reproducteurs. Afin de mieux comprendre les mécanismes moléculaires impliqués, nous avons étudié l'expression de gènes au début de cette compétition. Nous avons identifié 297 gènes différemment exprimés, dont l'annotation indique qu'ils seraient impliqués dans des processus biologiques dont la communication olfactive, le développement des organes reproducteurs et la métabolisation de l'hormone juvénile. Par la suite, nous avons déterminé que la vitesse à laquelle les reines perdent leurs ailes en début de compétition ainsi que les niveaux d'expression de gènes sont corrélés à la probabilité de survie des reines. Nous concluons en discutant des opportunités offertes par la recherche génétique sur les fourmis ainsi que les défis qu'elle devra surmonter.

Viral inhibitor of apoptosis vFLIP/K13 protects endothelial cells against superoxide-induced cell death.

Human herpesvirus 8 (HHV-8) is the etiological agent of Kaposi's sarcoma (KS). HHV-8 encodes an antiapoptotic viral Fas-associated death domain-like interleukin-1beta-converting enzyme-inhibitory protein (vFLIP/K13). The antiapoptotic activity of vFLIP/K13 has been attributed to an inhibition of caspase 8 activation and more recently to its capability to induce the expression of antiapoptotic proteins via activation of NF-kappaB. Our study provides the first proteome-wide analysis of the effect of vFLIP/K13 on cellular-protein expression. Using comparative proteome analysis, we identified manganese superoxide dismutase (MnSOD), a mitochondrial antioxidant and an important antiapoptotic enzyme, as the protein most strongly upregulated by vFLIP/K13 in endothelial cells. MnSOD expression was also upregulated in endothelial cells upon infection with HHV-8. Microarray analysis confirmed that MnSOD is also upregulated at the RNA level, though the differential expression at the RNA level was much lower (5.6-fold) than at the protein level (25.1-fold). The induction of MnSOD expression was dependent on vFLIP/K13-mediated activation of NF-kappaB, occurred in a cell-intrinsic manner, and was correlated with decreased intracellular superoxide accumulation and increased resistance of endothelial cells to superoxide-induced death. The upregulation of MnSOD expression by vFLIP/K13 may support the survival of HHV-8-infected cells in the inflammatory microenvironment in KS.

Genomic roles of the HCF transcriptional regulator in "Drosophila"

Abstract : Transcriptional regulation is the result of a combination of positive and negative effectors, such as transcription factors, cofactors and chromatin modifiers. During my thesis project I studied chromatin association, and transcriptional and cell cycle regulatory functions of dHCF, the Drosophila homologue of the human protein HCF-1 (host cell factor-1). The human and Drosophila HCF proteins are synthesized as large polypeptides that are cleaved into two subunits (HCFN and HCFC), which remain associated with one another by non covalent interactions. Studies in mammalian cells over the past 20 years have been devoted to understanding the cellular functions of HCF-1 and have revealed that it is a key regulator of transcription and cell cycle regulation. In human cells, HCF-1 interacts with the histone methyltransferase Set1/Ash2 and MLL/Ash2 complexes and the histone deacetylase Sin3 complex, which are involved in transcriptional activation and repression, respectively. HCF-1 is also recruited to promoters to regulate G1 -to-S phase progression during the cell cycle by the activator transcription factors E2F1 and E2F3, and by the repressor transcription factor E2F4. HCF-1 protein structure and these interactions between HCP-1 and E2F transcriptional regulator proteins are also conserved in Drosophila. In this doctoral thesis, I use proliferating Drosophila SL2 cells to study both the genomic-binding sites of dHCF, using a combination of chromatin immunoprecipitation and ultra high throughput sequencing (ChIP-seq) analysis, and dHCF regulated genes, employing RNAi and microarray expression analysis. I show that dHCF is bound to over 7500 chromosomal sites in proliferating SL2 cells, and is located at +-200 bp relative to the transcriptional start sites of about 30% of Drosophila genes. There is also a direct relationship between dHCF promoter association and promoter- associated transcriptional activity. Thus, dHCF binding levels at promoters correlated directly with transcriptional activity. In contrast, expression studies showed that dHCF appears to be involved in both transcriptional activation and repression. Analysis of dHCF-binding sites identified nine dHCF-associated motifs, four of them linked dHCF to (i) two insulator proteins, GAGA and BEAF, (ii) the E-box motif, and (iii) a degenerated TATA-box. The dHCF-associated motifs allowed the organization of the dHCF-bound genes into five biological processes: differentiation, cell cycle and gene expression, regulation of endocytosis, and cellular localization. I further show that different mechanisms regulate dHCF association with chromatin. Despite that after dHCF cleavage the dHCFN and dHCFC subunits remain associated, the two subunits showed different affinities for chromatin and differential binding to a set of tested promoters, suggesting that dHCF could target specific promoters through each of the two subunits. Moreover, in addition to the interaction between dHCF and E2F transcription factors, the dHCF binding pattern is correlated with dE2F2 genomic 4 distribution. I show that dE2F factors are necessary for recruitment of dHCF to the promoter of a set of dHCF regulated genes. Therefore dHCF, as in mammals, is involved in regulation of G1 to S phase progression in collaboration with the dE2Fs transcription factors. In addition, gene expression arrays reveal that dHCF could indirectly regulate cell cycle progression by promoting expression of genes involved in gene expression and protein synthesis, and inhibiting expression of genes involved in cell-cell adhesion. Therefore, dHCF is an evolutionary conserved protein, which binds to many specific sites of the Drosophila genome via interaction with DNA of chromatin-binding proteins to regulate the expression of genes involved in many different cellular functions. Résumé : La regulation de la transcription est le résultat des effets positifs et négatifs des facteurs de transcription, cofacteurs et protéines effectrices qui modifient la chromatine. Pendant mon projet de thèse, j'ai étudié l'association a la chromatine, ainsi que la régulation de la transcription et du cycle cellulaire par dHCF, l'homologue chez la drosophile de la protéine humaine HCF-1 (host cell factor-1). Chez 1'humain et la V drosophile, les deux protéines HCF sont synthétisées sous la forme d'un long polypeptide, qui est ensuite coupé en deux sous-unités au centre de la protéine. Les deux sous-unités restent associées ensemble grâce a des interactions non-covalentes. Des études réalisées pendant les 20 dernières années ont permit d'établir que HCF-l et un facteur clé dans la régulation de la transcription et du cycle cellulaire. Dans les cellules humaines, HCF-1 active et réprime la transcription en interagissant avec des complexes de protéines qui activent la transcription en méthylant les histones (HMT), comme par Set1/Ash2 et MLL/Ash2, et d'autres complexes qui répriment la transcription et sont responsables de la déacétylation des histones (HDAC) comme la protéine Sin3. HCF-l est aussi recruté aux promoteurs par les activateurs de la transcription E2F l et E2F3a, et par le répresseur de la transcription E2F4 pour réguler la transition entre les phases G1 et S du cycle cellulaire. La structure de HCF-1 et les interactions entre HCF-l et les régulateurs de la transcription sont conservées chez la drosophile. Pendant ma these j'ai utilisé les cellules de la drosophile, SL2 en culture, pour étudier les endroits de liaisons de HCF-l à la chromatine, grâce a immunoprecipitation de la chromatine et du séquençage de l'ADN massif ainsi que les gènes régulés par dHCF 3 grâce a la technique de RNAi et des microarrays. Mes résultats on montré que dHCF se lie à environ 7565 endroits, et estimé a 1200 paire de bases autour des sites d'initiation de la transcription de 30% des gènes de la drosophile. J 'ai observe une relation entre dHCF et le niveau de la transcription. En effet, le niveau de liaison dHCF au promoteur corrèle avec l'activité de la transcription. Cependant, mes études d'expression ont montré que dHCF est implique dans le processus d'activation et mais aussi de répression de la transcription. L'analyse des séquences d'ADN liées par dHCF a révèle neuf motifs, quatre de ces motifs ont permis d'associer dl-ICF a deux protéines isolatrices GAGA et BEAF, au motif pour les E-boxes et a une TATA-box dégénérée. Les neuf motifs associes à dHCF ont permis d'associer les gènes lies par dHCF au promoteur a cinq processus biologiques: différentiation, cycle cellulaire, expression de gènes, régulation de l'endocytosis et la localisation cellulaire, J 'ai aussi montré qu'il y a plusieurs mécanismes qui régulent l'association de dHCF a la chromatine, malgré qu'après clivage, les deux sous-unites dHCFN and dHCFC, restent associées, elles montrent différentes affinités pour la chromatine et lient différemment un group de promoteurs, les résultats suggèrent que dHCF peut se lier aux promoteurs en utilisant chacune de ses sous-unitées. En plus de l'association de dHCF avec les facteurs de transcription dE2F s, la distribution de dHCF sur le génome corrèle avec celle du facteur de transcription dE2F2. J'ai aussi montré que les dE2Fs sont nécessaires pour le recrutement de dHCF aux promoteurs d'un sous-groupe de gènes régules par dHCF. Mes résultats ont aussi montré que chez la drosophile comme chez les humains, dl-ICF est implique dans la régulation de la progression de la phase G1 a la phase S du cycle cellulaire en collaboration avec dE2Fs. D'ailleurs, les arrays d'expression ont suggéré que dHCF pourrait réguler le cycle cellulaire de façon indirecte en activant l'expression de gènes impliqués dans l'expression génique et la synthèse de protéines, et en inhibant l'expression de gènes impliqués dans l'adhésion cellulaire. En conclusion, dHCF est une protéine, conservée dans l'évolution, qui se lie spécifiquement a beaucoup d'endroits du génome de Drosophile, grâce à l'interaction avec d'autres protéines, pour réguler l'expression des gènes impliqués dans plusieurs fonctions cellulaires.

p21 as a transcriptional co-repressor of S-phase and mitotic control genes.

It has been previously described that p21 functions not only as a CDK inhibitor but also as a transcriptional co-repressor in some systems. To investigate the roles of p21 in transcriptional control, we studied the gene expression changes in two human cell systems. Using a human leukemia cell line (K562) with inducible p21 expression and human primary keratinocytes with adenoviral-mediated p21 expression, we carried out microarray-based gene expression profiling. We found that p21 rapidly and strongly repressed the mRNA levels of a number of genes involved in cell cycle and mitosis. One of the most strongly down-regulated genes was CCNE2 (cyclin E2 gene). Mutational analysis in K562 cells showed that the N-terminal region of p21 is required for repression of gene expression of CCNE2 and other genes. Chromatin immunoprecipitation assays indicated that p21 was bound to human CCNE2 and other p21-repressed genes gene in the vicinity of the transcription start site. Moreover, p21 repressed human CCNE2 promoter-luciferase constructs in K562 cells. Bioinformatic analysis revealed that the CDE motif is present in most of the promoters of the p21-regulated genes. Altogether, the results suggest that p21 exerts a repressive effect on a relevant number of genes controlling S phase and mitosis. Thus, p21 activity as inhibitor of cell cycle progression would be mediated not only by the inhibition of CDKs but also by the transcriptional down-regulation of key genes.

The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal.

Quorum sensing, a cell-to-cell communication system based on small signal molecules, is employed by the human pathogen Pseudomonas aeruginosa to regulate virulence and biofilm development. Moreover, regulation by small trans-encoded RNAs has become a focal issue in studies of virulence gene expression of bacterial pathogens. In this study, we have identified the small RNA PhrS as an activator of PqsR synthesis, one of the key quorum-sensing regulators in P. aeruginosa. Genetic studies revealed a novel mode of regulation by a sRNA, whereby PhrS uses a base-pairing mechanism to activate a short upstream open reading frame to which the pqsR gene is translationally coupled. Expression of phrS requires the oxygen-responsive regulator ANR. Thus, PhrS is the first bacterial sRNA that provides a regulatory link between oxygen availability and quorum sensing, which may impact on oxygen-limited growth in P. aeruginosa biofilms.

Waddlia, Parachlamydia and Chlamydiaceae in bovine abortion.

The etiology remains unknown in many cases of bovine abortion in Switzerland. Bacteria of the Chlamydiales order are known abortive agents, therefore cases of bovine abortion from three representative regions of Switzerland were investigated in this study. Particularly Chlamydiaceae as well as the Chlamydia-like organisms Waddlia and Parachlamydia were of interest, especially because of their possible zoonotic potential. Placenta samples (n=343) were tested for these bacteria by different PCR-methods, immunohistochemistry and serology for Chlamydia abortus. Additionally an attempt for the isolation of Waddlia and Parachlamydia was made by co-cultivation in amoebae. In 67.3% of the 343 cases a necrotizing and/or purulent placentitis was found histologically. By real-time PCR, 0.9% (3/343) of the cases were positive for Waddlia, 13.4% (46/343) positive for Parachlamydia and 14.6% (50/343) positive or questionable positive for Chlamydiaceae. Of these samples, confirmation by immunohistochemistry was possible in 2/3 cases for Waddlia, 25/46 for Parachlamydia and 4/50 for Chlamydiaceae. Of the 50 cases positive or questionable positive for Chlamydiaceae, species-identification by ArrayTube Microarray or 16S rRNA PCR resulted in 41 cases positive for C. abortus whereas the presence of Chlamydia suis was confirmed in four and Chlamydia pecorum in one case. This study brought evidence for the importance of different members of Chlamydiales in different regions of Switzerland although Waddlia is not occurring in a high prevalence. On the other hand mixed infections with different Chlamydiales as well as with other abortigenic agents could be found.

The cooperative induction of hypoxia-inducible factor-1 alpha and STAT3 during hypoxia induced an impairment of tumor susceptibility to CTL-mediated cell lysis.

Hypoxia is an essential component of tumor microenvironment. In this study, we investigated the influence of hypoxia (1% PO(2)) on CTL-mediated tumor cell lysis. We demonstrate that exposure of target tumor cells to hypoxia has an inhibitory effect on the CTL clone (Heu171)-induced autologous target cell lysis. Such inhibition correlates with hypoxia-inducible factor-1alpha (HIF-1alpha) induction but is not associated with an alteration of CTL reactivity as revealed by granzyme B polarization or morphological change. Western blot analysis indicates that although hypoxia had no effect on p53 accumulation, it induced the phosphorylation of STAT3 in tumor cells by a mechanism at least in part involving vascular endothelial growth factor secretion. We additionally show that a simultaneous nuclear translocation of HIF-1alpha and phospho-STAT3 was observed. Interestingly, gene silencing of STAT3 by small interfering RNA resulted in HIF-1alpha inhibition and a significant restoration of target cell susceptibility to CTL-induced killing under hypoxic conditions by a mechanism involving at least in part down-regulation of AKT phosphorylation. Moreover, knockdown of HIF-1alpha resulted in the restoration of target cell lysis under hypoxic conditions. This was further supported by DNA microarray analysis where STAT3 inhibition resulted in a partly reversal of the hypoxia-induced gene expression profile. The present study demonstrates that the concomitant hypoxic induction of phospho-STAT3 and HIF-1alpha are functionally linked to the alteration of non-small cell lung carcinoma target susceptibility to CTL-mediated killing. Considering the eminent functions of STAT3 and HIF-1alpha in the tumor microenvironment, their targeting may represent novel strategies for immunotherapeutic intervention.

Malaria haplotype frequency estimation.

We present a Bayesian approach for estimating the relative frequencies of multi-single nucleotide polymorphism (SNP) haplotypes in populations of the malaria parasite Plasmodium falciparum by using microarray SNP data from human blood samples. Each sample comes from a malaria patient and contains one or several parasite clones that may genetically differ. Samples containing multiple parasite clones with different genetic markers pose a special challenge. The situation is comparable with a polyploid organism. The data from each blood sample indicates whether the parasites in the blood carry a mutant or a wildtype allele at various selected genomic positions. If both mutant and wildtype alleles are detected at a given position in a multiply infected sample, the data indicates the presence of both alleles, but the ratio is unknown. Thus, the data only partially reveals which specific combinations of genetic markers (i.e. haplotypes across the examined SNPs) occur in distinct parasite clones. In addition, SNP data may contain errors at non-negligible rates. We use a multinomial mixture model with partially missing observations to represent this data and a Markov chain Monte Carlo method to estimate the haplotype frequencies in a population. Our approach addresses both challenges, multiple infections and data errors.

Protein-binding microarrays: probing disease markers at the interface of proteomics and genomics.

DNA-binding proteins mediate a variety of crucial molecular functions, such as transcriptional regulation and chromosome maintenance, replication and repair, which in turn control cell division and differentiation. The roles of these proteins in disease are currently being investigated using microarray-based approaches. However, these assays can be difficult to adapt to routine diagnosis of complex diseases such as cancer. Here, we review promising alternative approaches involving protein-binding microarrays (PBMs) that probe the interaction of proteins from crude cell or tissue extracts with large collections of synthetic or natural DNA sequences. Recent studies have demonstrated the use of these novel PBM approaches to provide rapid and unbiased characterization of DNA-binding proteins as molecular markers of disease, for example cancer progression or infectious diseases.

The role of AUF1 in AU-rich interleukin-6 mRNA regulation

Abstract: The AU-rich elements (AREs) consisting of repeated AUUUA motifs confer rapid degradation to many cellular mRNAs when present in the 3' untranslated region (3'UTR). We have studied the instability of interleukin-6 mRNA by grafting its 3' untranslated region to a stable green fluorescent protein mRNA. Subsequent scanning mutagenesis identified two conserved elements, which taken together account for most of the instability. The first corresponds to a short non-canonical AU-rich element. The other comprises a sequence predicted to form astern-loop structure. Both elements need to be present in order to confer full instability (Paschoud et al. 2006). Destabilization of ARE-containing mRNAs is thought to involve ARE-binding proteins such as AUF1. We tested whether AUF1 binding to interleukin-6 mRNA correlates with decreased mRNA stability. Overexpression of myc-tagged p37AUFl and p42AUF1 as well as suppression of all four AUF1 isoforms by RNA interference stabilized the interleukin-6 mRNA. Furthermore, the interleukin-6 mRNA co-immunoprecipitated specifically with myc-tagged p37AUF1 and p42AUF1 in cell extracts. Both the stabilization and AUF1-binding required the non-canonical AU-rich sequence. These results indicate that AUF1 binds to the AU-rich element in vivo and promotes interleukin6 mRNA degradation. The combination of mRNA co-immunoprecipitation with microarray technology revealed that at least 500 cellular mRNAs associate with AUF1. Résumé: "La présence d'éléments riches en A et U (ARE), en particulier les motifs répétés d'AUUUA dans la région 3' non traduite, confère une dégradation rapide à beaucoup d'ARN cellulaires. Nous avons étudié l'instabilité de l'ARN codant pour l'interleukine 6 en greffant sa région 3' non traduite à un ARN stable codant pour la protéine fluorescente verte. La mutagenèse systématique des séquences non traduites a permis l'identification de deux éléments conservés qui confèrent l'instabilité à l'ARN. Le premier correspond à un élément AU-riche non canonique court. Le second comporte une structure en 'épingle à cheveux'. Tous les deux éléments doivent être présents afin de conférer une instabilité complète (Paschoud et al. 2006). On pense que des protéines telles que AUF1, pouvant se lier aux éléments ARE, sont impliquées dans la dégradation des ARN messagers. Nous avons examiné si la liaison de AUFl sur l'ARN de l'interleukine 6 corrèle avec une stabilité diminuée. La surexpression des protéines p37AUF1 et de p42AUF1 myc-étiquetées ainsi que la suppression de chacun des quatre isoformes de AUF1 par interférence d'ARN a stabilisé l'ARN messager d'interleukine 6. En outre, cet ARN co-immunoprécipite spécifiquement avec p37AUF1 et p42AUF1 dans des extraits cellulaires. La présence de l'élément AUriche non canonique est nécessaire pour la stabilisation de l'ARN et sa liaison avec AUFI. Ces résultats indiquent qu'AUF1 se lie à l'élément AU-riche in vivo et favorise la dégradation de l'ARN messager d'interleukine 6. La combinaison des techniques de coimmunoprécipitation des ARN messagers et des analyses par `microarray' indique qu'au moins 500 ARN cellulaires s'associent à AUF1.

Effects of fou8/fry1 mutation on sulfur metabolism: is decreased internal sulfate the trigger of sulfate starvation response?

The fou8 loss of function allele of adenosine bisphosphate phosphatase FIERY1 results in numerous phenotypes including the increased enzymatic oxygenation of fatty acids and increased jasmonate synthesis. Here we show that the mutation causes also profound alterations of sulfur metabolism. The fou8 mutants possess lower levels of sulfated secondary compounds, glucosinolates, and accumulate the desulfo-precursors similar to previously described mutants in adenosine 5'phosphosulfate kinase. Transcript levels of genes involved in sulfate assimilation differ in fou8 compared to wild type Col-0 plants and are similar to plants subjected to sulfate deficiency. Indeed, independent microarray analyses of various alleles of mutants in FIERY1 showed similar patterns of gene expression as in sulfate deficient plants. This was not caused by alterations in signalling, as the fou8 mutants contained significantly lower levels of sulfate and glutathione and, consequently, of total elemental sulfur. Analysis of mutants with altered levels of sulfate and glutathione confirmed the correlation of sulfate deficiency-like gene expression pattern with low internal sulfate but not low glutathione. The changes in sulfur metabolism in fou8 correlated with massive increases in 3'-phosphoadenosine 5'-phosphate levels. The analysis of fou8 thus revealed that sulfate starvation response is triggered by a decrease in internal sulfate as opposed to external sulfate availability and that the presence of desulfo-glucosinolates does not induce the glucosinolate synthesis network. However, as well as resolving these important questions on the regulation of sulfate assimilation in plants, fou8 has also opened an array of new questions on the links between jasmonate synthesis and sulfur metabolism.

Laser-induced forward transfer of liquids: Study of the droplet ejection process

Laser-induced forward transfer (LIFT) is a laser direct-write technique that offers the possibility of printing patterns with a high spatial resolution from a wide range of materials in a solid or liquid state, such as conductors, dielectrics, and biomolecules in solution. This versatility has made LIFT a very promising alternative to lithography-based processes for the rapid prototyping of biomolecule microarrays. Here, we study the transfer process through the LIFT of droplets of a solution suitable for microarray preparation. The laser pulse energy and beam size were systematically varied, and the effect on the transferred droplets was evaluated. Controlled transfers in which the deposited droplets displayed optimal features could be obtained by varying these parameters. In addition, the transferred droplet volume displayed a linear dependence on the laser pulse energy. This dependence allowed determining a threshold energy density value, independent of the laser focusing conditions, which acted as necessary conditions for the transfer to occur. The corresponding sufficient condition was given by a different total energy threshold for each laser beam dimension. The threshold energy density was found to be the dimensional parameter that determined the amount of the transferred liquid per laser pulse, and there was no substantial loss of material due to liquid vaporization during the transfer.

Evolution of mRNA expression levels of autosomal and sex-linked genes in amniotes

In addition to differences in protein-coding gene sequences, changes in expression resulting from mutations in regulatory sequences have long been hypothesized to be responsible for phenotypic differences between species. However, unlike comparison of genome sequences, few studies, generally restricted to pairwise comparisons of closely related mammalian species, have assessed between-species differences at the transcriptome level. They reported that gene expression evolves at different rates in various organs and in a pattern that is overall consistent with neutral models of evolution. In the first part of my thesis, I investigated the evolution of gene expression in therian mammals (i.e.7 placental and marsupials), based on microarray data from human, mouse and the gray short-tailed opossum (Monodelphis domestica). In addition to autosomal genes, a special focus was given to the evolution of X-linked genes. The therian X chromosome was recently shown to be younger than previously thought and to harbor a specific gene content (e.g., genes involved in brain or reproductive functions) that is thought to have been shaped by specific sex-related evolutionary forces. Sex chromosomes derive from ordinary autosomes and their differentiation led to the degeneration of the Y chromosome (in mammals) or W chromosome (in birds). Consequently, X- or Z-linked genes differ in gene dose between males and females such that the heterogametic sex has half the X/Z gene dose compared to the ancestral state. To cope with this dosage imbalance, mammals have been reported to have evolved mechanisms of dosage compensation.¦In the first project, I could first show that transcriptomes evolve at different rates in different organs. Out of the five tissues I investigated, the testis is the most rapidly evolving organ at the gene expression level while the brain has the most conserved transcriptome. Second, my analyses revealed that mammalian gene expression evolution is compatible with a neutral model, where the rates of change in gene expression levels is linked to the efficiency of purifying selection in a given lineage, which, in turn, is determined by the long-term effective population size in that lineage. Thus, the rate of DNA sequence evolution, which could be expected to determine the rate of regulatory sequence change, does not seem to be a major determinant of the rate of gene expression evolution. Thus, most gene expression changes seem to be (slightly) deleterious. Finally, X-linked genes seem to have experienced elevated rates of gene expression change during the early stage of X evolution. To further investigate the evolution of mammalian gene expression, we generated an extensive RNA-Seq gene expression dataset for nine mammalian species and a bird. The analyses of this dataset confirmed the patterns previously observed with microarrays and helped to significantly deepen our view on gene expression evolution.¦In a specific project based on these data, I sought to assess in detail patterns of evolution of dosage compensation in amniotes. My analyses revealed the absence of male to female dosage compensation in monotremes and its presence in marsupials and, in addition, confirmed patterns previously described for placental mammals and birds. I then assessed the global level of expression of X/Z chromosomes and contrasted this with its ancestral gene expression levels estimated from orthologous autosomal genes in species with non-homologous sex chromosomes. This analysis revealed a lack of up-regulation for placental mammals, the level of expression of X-linked genes being proportional to gene dose. Interestingly, the ancestral gene expression level was at least partially restored in marsupials as well as in the heterogametic sex of monotremes and birds. Finally, I investigated alternative mechanisms of dosage compensation and found that gene duplication did not seem to be a widespread mechanism to restore the ancestral gene dose. However, I could show that placental mammals have preferentially down-regulated autosomal genes interacting with X-linked genes which underwent gene expression decrease, and thus identified a novel alternative mechanism of dosage compensation.

Fourmidable: a database for ant genomics.

BACKGROUND: Fourmidable is an infrastructure to curate and share the emerging genetic, molecular, and functional genomic data and protocols for ants. DESCRIPTION: The Fourmidable assembly pipeline groups nucleotide sequences into clusters before independently assembling each cluster. Subsequently, assembled sequences are annotated via Interproscan and BLAST against general and insect-specific databases. Gene-specific information can be retrieved using gene identifiers, searching for similar sequences or browsing through inferred Gene Ontology annotations. The database will readily scale as ultra-high throughput sequence data and sequences from additional species become available. CONCLUSION: Fourmidable currently houses EST data from two ant species and microarray gene expression data for one of these. Fourmidable is publicly available at http://fourmidable.unil.ch.

eVOC: a controlled vocabulary for unifying gene expression data.

Expression data contribute significantly to the biological value of the sequenced human genome, providing extensive information about gene structure and the pattern of gene expression. ESTs, together with SAGE libraries and microarray experiment information, provide a broad and rich view of the transcriptome. However, it is difficult to perform large-scale expression mining of the data generated by these diverse experimental approaches. Not only is the data stored in disparate locations, but there is frequent ambiguity in the meaning of terms used to describe the source of the material used in the experiment. Untangling semantic differences between the data provided by different resources is therefore largely reliant on the domain knowledge of a human expert. We present here eVOC, a system which associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. We have curated and annotated 7016 cDNA libraries represented in dbEST, as well as 104 SAGE libraries,with expression information,and provide this as an integrated, public resource that allows the linking of transcripts and libraries with expression terms. Both the vocabularies and the vocabulary-annotated libraries can be retrieved from http://www.sanbi.ac.za/evoc/. Several groups are involved in developing this resource with the aim of unifying transcript expression information.