Animal Toxins: How is Complexity Represented in Databases?

Peptide toxins synthesized by venomous animals have been extensively studied in the last decades. To be useful to the scientific community, this knowledge has been stored, annotated and made easy to retrieve by several databases. The aim of this article is to present what type of information users can access from each database. ArachnoServer and ConoServer focus on spider toxins and cone snail toxins, respectively. UniProtKB, a generalist protein knowledgebase, has an animal toxin-dedicated annotation program that includes toxins from all venomous animals. Finally, the ATDB metadatabase compiles data and annotations from other databases and provides toxin ontology.

Bioinformatic study of selection in animal genomes

Les gènes orthologues divergent sur plusieurs aspects durant l'évolution. Après une revue de la littérature cherchant à montrer de la divergence entre les orthologues de l'humain et de la souris, j'ai souligné les différentes causes de cette divergence. En comparant les gènes qui divergent en fonction, je n'ai pas trouvé de lien avec la divergence des séquences, pour cette raison je me suis penché sur l'étude de l'expression. Notamment, j'ai étudié le niveau, la spécificité ainsi que la présence/absence d'expression des orthologues humain-souris liés aux maladies Mendéliennes. Malgré les similarités trouvées entre l'humain et la souris, j'ai détecté une différence d'expression spécifique à une des deux espèces liée a un phénotype précis (gène essentiel/non-essentiel). Cela m'a permis de conclure que la différence sur le plan phénotypique entre l'humain et la souris est mieux expliquée par les patrons d'expression plutôt que le niveau d'expression ou la sélection. J'ai été également intéressé par l'évolution des séquences d'ADN codantes pour des protéines, en particulier sur le rôle de la sélection. J'ai commencé par une étude sur la fiabilité de détection de la sélection positive en comparant des séquences divergentes. J'ai trouvé, en utilisant le model de branche-site que la sélection peut être détectée sur des séquences qui ont divergé il y a plus de 500 millions d'années. J'ai analysé le biais de GC entres les séquences sans trouver une influence sur l'estimation de la sélection positive. Finalement, Je crois que ce travail est une première étape dans l'établissement d'un lien entre la sélection et les patrons d'expression des gènes chez les vertébrés.

Rapid cohort generation and analysis of disease spectrum of large animal model of cone dystrophy.

Large animal models are an important resource for the understanding of human disease and for evaluating the applicability of new therapies to human patients. For many diseases, such as cone dystrophy, research effort is hampered by the lack of such models. Lentiviral transgenesis is a methodology broadly applicable to animals from many different species. When conjugated to the expression of a dominant mutant protein, this technology offers an attractive approach to generate new large animal models in a heterogeneous background. We adopted this strategy to mimic the phenotype diversity encounter in humans and generate a cohort of pigs for cone dystrophy by expressing a dominant mutant allele of the guanylate cyclase 2D (GUCY2D) gene. Sixty percent of the piglets were transgenic, with mutant GUCY2D mRNA detected in the retina of all animals tested. Functional impairment of vision was observed among the transgenic pigs at 3 months of age, with a follow-up at 1 year indicating a subsequent slower progression of phenotype. Abnormal retina morphology, notably among the cone photoreceptor cell population, was observed exclusively amongst the transgenic animals. Of particular note, these transgenic animals were characterized by a range in the severity of the phenotype, reflecting the human clinical situation. We demonstrate that a transgenic approach using lentiviral vectors offers a powerful tool for large animal model development. Not only is the efficiency of transgenesis higher than conventional transgenic methodology but this technique also produces a heterogeneous cohort of transgenic animals that mimics the genetic variation encountered in human patients.

Assessment of a sheep animal model to optimize photodynamic therapy in the oesophagus

Background and Objectives: Precursor lesions of oesophagus adenocarcinoma constitute a clinical dilemma. Photodynamic therapy (PDT) is an effective treatment for this indication, but it is difficult to optimise without an appropriate animal model. For this reason, we assessed the sheep model for PDT in the oesophagus with the photosensitiser meta-(tetra-hydroxyphenyl) chlorin (mTHPC). Materials and Methods: Twelve sheep underwent intravenous mTHPC injection, blood sampling and fluorescence measurements. mTHPC's pharmacokinetics was measured in vivo and in plasma by fluorescence spectroscopy. Biopsies of sheep oesophagus were compared to corresponding human tissue, and the mTHPC's biodistribution was studied under fluorescence microscopy. Finally, the sheep oesophageal mucosa was irradiated, 4 days after mTHPC's injection. Results: Histologically, the sheep and human oesophagus were closely comparable, with the exception of additional fatty tissue in the sheep oesophagus. mTHPC's pharmacokinetics in sheep and human plasmas were similar, with a maximum of concentration in the sheep 10 hours after i.v. injection. mTHPC's pharmacokinetics in vivo reached its maximum after 30-50 hours, then decreased to background levels, as in humans under similar conditions. Two days after injection, mTHPC was mainly distributed in the lamina propria, followed by a penetration into the epithelium. The sheep and human tissue sensitivity to mTHPC PDT was similar. Conclusion: In conclusion, this model showed many similarities with humans as to mTHPC's plasma and tissue pharmacokinetics, and for tissue PDT response, making it suitable to optimise oesophagus PDT. Lasers Surg. Med. 41:643-652,2009. (C) 2009Wiley-Liss,Inc.

Detritivorous crustaceans become herbivores on jasmonate-deficient plants.

The jasmonate signal pathway is known to control defenses against herbivores, such as leaf eaters (folivores). Does the reach of the pathway extend to defense against other types of animal? Among the arthropods attracted to seed baits placed below flowering Arabidopsis thaliana plants are 2 largely nocturnal isopod crustaceans generally considered as detritivores: Porcellio scaber and Armadillidium vulgare. Parallel laboratory experiments identified the isopods as being capable of predation on intact plants. Isopod feeding was strongly facilitated in jasmonate-deficient Arabidopsis and rice plants. The feeding activity of isopods revealed potentially detritivore-sensitive, jasmonate-protected Achilles' heels in these architecturally different plants (petioles and inflorescence stems in Arabidopsis, and lower stem and mesocotyl in rice). The work addresses the question of what stops 2 detritivores from attacking living plants and provides evidence that it is, in part, the jasmonate signal pathway. Furthermore, senescent leaves from an Arabidopsis jasmonate mutant were consumed more rapidly than senescent wild-type leaves, suggesting that past activity of the jasmonate signal pathway in leaves may slow carbon recycling through detritivory.

The congenital soidum diarrhea and Spint2: from the molecules to the disease

La diarrhée congénitale de sodium est une maladie génétique très rare. Les enfants touchés par cette maladie présentent une diarrhée aqueuse sévère accompagnée d'une perte fécale de sodium et bicarbonates causant une déshydratation hyponatrémique et une acidose métabolique. Des analyses génétiques ont identifié des mutations du gène Spint2 comme cause de cette maladie. Le gène Spint2 code pour un inhibiteur de sérine protéase transmembranaire exprimé dans divers épithéliums tels que ceux du tube digestif ou des tubules rénaux. Le rôle physiologique de Spint2 n'est pas connu. De plus, aucun partenaire physiologique de Spint2 n'a été identifié et le mécanisme d'inhibition par Spint2 nous est peu connu. Le but de ce projet est donc d'obtenir de plus amples informations concernant la fonction et le rôle de Spint2 dans le contexte de la diarrhée congénitale de sodium, cela afin de mieux comprendre la physiopathologie des diarrhées et peut-être d'identifier de nouvelles cibles thérapeutiques. Un test fonctionnel dans les ovocytes de Xenopus a identifié les sérine protéases transmembranaires CAPI et Tmprssl3 comme potentielles cibles de Spint2 dans la mesure où ces deux protéases n'étaient plus bloquées par le mutant de Spint2 Y163C qui est associé avec la diarrhée congénitale de sodium. Des expériences fonctionnelles et biochimiques plus poussées suggèrent que l'inhibition de Tmprssl3 par Spint2 est le résultat d'une interaction complexe entre ces deux protéines. Les effets des sérine protéases transmembranaires sur l'échangeur Na+-H+ NHE3, qui pourrait être impliqué dans la pathogenèse de la diarrhée congénitale de sodium ont aussi été testés. Un clivage spécifique de NHE3 par la sérine protéase transmembranaire Tmprss3 a été observé lors d'expériences biochimiques. Malheureusement, la pertinence physiologique de ces résultats n'a pas pu être évaluée in vivo, étant donné que le modèle de souris knockout conditionnel de Spint2 que nous avons créé ne montrait une réduction de l'expression de Spint2 que de 50% et aucun phénotype. En résumé, ce travail met en évidence deux nouveaux partenaires possibles de Spint2, ainsi qu'une potentielle régulation de NHE3 par des sérine protéases transmembranaires. Des expériences supplémentaires faites dans des modèles animaux et lignées cellulaires sont requises pour évaluer la pertinence physiologique de ces données et pour obtenir de plus amples informations au sujet de Spint2 et de la diarrhée congénitale de sodium. - The congenital sodium diarrhea is a very rare genetic disease. Children affected by this condition suffer from a severe diarrhea characterized by watery stools with a high fecal loss of sodium and bicarbonates, resulting in hyponatremic dehydration and metabolic acidosis. Genetic analyses have identified mutations in the Spint2 gene as a cause of this disease. The spint2 gene encodes a transmembrane serine protease inhibitor expressed in various epithelial tissues including the gastro-intestinal tract and renal tubules. The physiological role of Spint2 is completely unknown. In addition, physiological partners of Spint2 are still to be identified and the mechanism of inhibition by Spint2 remains elusive. Therefore, the aim of this project was to get insights about the function and the role of Spint2 in the context of the congenital sodium diarrhea in order to better understand the pathophysiology of diarrheas and maybe identify new therapeutic targets. A functional assay in Xenopus oocytes identified the membrane-bound serine proteases CAPI and Tmprssl3 as potential targets of Spint2 because both proteases were no longer inhibited by the mutant Spint2 Y163C that has been associated with the congenital diarrhea. Further functional and biochemical experiments suggested that the inhibition of Tmprssl3 by Spint2 occurs though a complex interaction between both proteins. The effects of membrane-bound serine proteases on the Na+-H+ exchanger NHE3, which has been proposed to be involved in the pathogenesis of the congenital sodium diarrhea, were also tested. A specific cleavage of NHE3 by the membrane-bound serine protease Tmprss3 was observed in biochemical experiments. Unfortunately, the physiological relevance of these results could not be assessed in vivo since the conditional Spint2 knockout mouse model that we generated showed a reduction in Spint2 expression of only 50% and displayed no phenotype. Briefly, this work provides two new potential partners of Spint2 and emphasizes a putative regulation of NHE3 by membrane-bound serine proteases. Further work done in animal models and cell lines is required to assess the physiological relevance of these results and to obtain additional data about Spint2 and the congenital diarrhea.

Animal Toxins: How is Complexity Represented in Databases?

Peptide toxins synthesized by venomous animals have been extensively studied in the last decades. To be useful to the scientific community, this knowledge has been stored, annotated and made easy to retrieve by several databases. The aim of this article is to present what type of information users can access from each database. ArachnoServer and ConoServer focus on spider toxins and cone snail toxins, respectively. UniProtKB, a generalist protein knowledgebase, has an animal toxin-dedicated annotation program that includes toxins from all venomous animals. Finally, the ATDB metadatabase compiles data and annotations from other databases and provides toxin ontology.

Deciphering genetic disease in the genomic era: the model of GnRH deficiency.

Isolated gonadotropin-releasing hormone (GnRH) deficiency is a treatable albeit rare form of reproductive failure that has revealed physiological mechanisms controlling human reproduction, but despite substantial progress in discovering pathogenic single-gene defects, most of the genetic basis of GnRH deficiency remains uncharted. Although unbiased genetic investigations of affected families have identified mutations in previously unsuspected genes as causes of this disease in some cases, their application has been severely limited because of the negative effect of GnRH deficiency on fertility; moreover, relatively few of the many candidate genes nominated because of biological plausibility from in vitro or animal model experiments were subsequently validated in patients. With the advent of exciting technological platforms for sequencing, homozygosity mapping, and detection of structural variation at the whole-genome level, human investigations are again assuming the leading role for gene discovery. Using human GnRH deficiency as a paradigm and presenting original data from the screening of numerous candidate genes, we discuss the emerging model of patient-focused clinical genetic research and its complementarities with basic approaches in the near future.

MHC-genotype of progeny influenced by parental infection.

In a previous series of in vitro fertilization experiments with mice we found non-random combination of major histocompatibility complex (MHC) haplotypes in the very early embryos. Our results suggested that two selection mechanisms were operating: (i) the eggs selected specific sperm; and (ii) the second meiotic division in the eggs was influenced by the type of sperm that entered the egg. Furthermore, the proportion of MHC-heterozygous embryos varied over time, suggesting that non-random fertilization was dependent on an external factor that changed over time. As a higher frequency of heterozygous individuals correlated with an uncontrolled epidemic by MHV (mouse hepatitis virus), we suggested that MHV-infection might have influenced the outcome of fertilization. Here, we present an experiment that tests this hypothesis. We infected randomly chosen mice with MHV and sham-infected control mice five days before pairing. We recovered the two-cell embryos from the oviduct, cultured them until the blastocyst stage, and determined the genotype of each resulting blastocyst by polymerase chain reaction. We found the pattern that we expected from our previous experiments: virus-infected mice produced more MHC-heterozygous embryos than sham-infected ones. This suggests that parents are able to promote specific combinations of MHC-haplotypes during fertilization according to the presence or absence of a viral infection.

Social evolution: the smell of cheating.

Coercion is a powerful means to enforce altruism and promote social cohesion in animal groups, but it requires the reliable identification of selfish individuals. Experiments in a desert ant provide the first direct proof that a single cuticular hydrocarbon elicits the policing of reproductive workers by other colony members.

Melanic color-dependent anti-predator behavior strategies in barn owl nestlings

The arms race between predators and prey has led to morphological and behavioral adaptations. Different antipredator strategies can coexist within a population if each strategy is the result of a trade-off with competing demands. Antipredator behavior can be associated with morphological traits, like color patterns, either because in the context of sexual selection, coloration signals the ability to avoid predators or because coloration is a naturally selected trait useful in avoiding predators. Because in the barn owl (Tyto alba), heritable eumelanic plumage coloration is associated with the glucocorticoid-dependent response to stress, we tested whether antipredator behavior is also related to this trait. Compared with small-spotted nestlings, individuals displaying larger black spots hissed more intensely in the presence of humans, feigned death longer, had a lower breathing rate under stress, and were more docile when handled. Cross-fostering experiments showed that the covariation between the spot size and the duration of feigning death was inherited from the biological mother, whereas covariation between spot size and docility was inherited from the biological father. Our results confirm that melanin-based coloration is associated with suites of behavioral traits, which are under both genetic and environmental influence. Coloration can thus evolve as a direct or indirect response to predation, but it can also be a signal of antipredator strategies to potential mates.

Excitotoxicity-induced endocytosis confers drug targeting in cerebral ischemia.

OBJECTIVE: Targeting neuroprotectants specifically to the cells that need them is a major goal in biomedical research. Many peptidic protectants contain an active sequence linked to a carrier such as the transactivator of transcription (TAT) transduction sequence, and here we test the hypothesis that TAT-linked peptides are selectively endocytosed into neurons stressed by excitotoxicity and focal cerebral ischemia. METHODS: In vivo experiments involved intracerebroventricular injection of TAT peptides or conventional tracers (peroxidase, fluorescein isothiocyanate-dextran) in young rats exposed to occlusion of the middle cerebral artery at postnatal day 12. Cellular mechanisms of uptake were analyzed in dissociated cortical neuronal cultures. RESULTS: In both models, all tracers were taken up selectively into stressed neurons by endocytosis. In the in vivo model, this was neuron specific and limited to the ischemic area, where the neurons displayed enhanced immunolabeling for early endosomal antigen-1 and clathrin. The highly efficient uptake of TAT peptides occurred by the same selective mechanism as for conventional tracers. All tracers were targeted to the nucleus and cytoplasm of neurons that appeared viable, although ultimately destined to die. In dissociated cortical neuronal cultures, an excitotoxic dose of N-methyl-D-aspartate induced a similar endocytosis. It was 100 times more efficient with TAT peptides than with dextran, because the former bound to heparan sulfate proteoglycans at the cell surface, but it depended on dynamin and clathrin in both cases. INTERPRETATION: Excitotoxicity-induced endocytosis is the main entry route for protective TAT peptides and targets selectively the neurons that need to be protected.