Towards the identification of the allosteric Phe-binding site in phenylalanine hydroxylase

The enzyme phenylalanine hydroxylase (PAH) is defective in the inherited disorder phenylketonuria. PAH, a tetrameric enzyme, is highly regulated and displays positive cooperativity for its substrate, Phe. Whether Phe binds to an allosteric site is a matter of debate, despite several studies worldwide. To address this issue, we generated a dimeric model for Phe–PAH interactions, by performing molecular docking combined with molecular dynamics simulations on human and rat wild-type sequences and also on a human G46S mutant. Our results suggest that the allosteric Phe-binding site lies at the dimeric interface between the regulatory and the catalytic domains of two adjacent subunits. The structural and dynamical features of the site were characterized in depth and described. Interestingly, our findings provide evidence for lower allosteric Phe-binding ability of the G46S mutant than the human wild-type enzyme. This also explains the disease-causing nature of this mutant.     

Transferring sediment containing intact seed banks: a method for studying plant community ecology

The experimental study of the ecology of natural plant communities is necessary to demonstrate the effects of environmental factors on plant growth. It allows one to make predictions of the likely effects of environmental changes on plant communities. Manipulating an entire ecosystem is complicated, and is rarely attempted. An alternative method is applied here for the submerged plant communities of the seasonally-flooded oligohaline marshes of the Camargue. It consists of collecting undisturbed sediment samples with their contained intact seed bank, and submitting them to different salinities. The study of total biomass and of the biomass of the more frequent species was carried out using parametric tests. The precision of the results depended on the frequency of the species in the replicates. When the frequency was low, non-parametric statistics were necessary. The method seems to be particularly suitable for the study of communities of annual species in aquatic environments.

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Résumé L'étude expérimentale de l'écologie des communautés naturelles de plantes est nécessaire pour démontrer les relations de cause à effet entre les facteurs environnementaux et l'abondance des plantes. Elle l'est également pour faire des prédictions réalistes sur les effets de modifications envisagées de l'environnement sur des communautés de plantes. La manipulation de l'écosystème complet est complexe, ce qui rend son utilisation rare. Une méthode alternative a été utilisée pour l'étude de la composition spécifique des communautés de plantes submergées des marais temporaires de Camargue. Elle consiste à prélever des échantillons non perturbés de sédiment, avec leur stock de semences intact, et à les soumettre à des conditions de salinité. L'étude de la biomasse totale et de la biomasse des espèces les plus fréquentes est faite au moyen de test paramétriques. La précision attendue des résultats dépend de la fréquence de l'espèce dans les réplicats. Lorsque la fréquence n'est pas élevée l'emploi de statistiques non paramétriques est indispensable. La méthode se révéle particulièrement bien adaptée à l'étude des communautés d'annuelles en milieu aquatique.

     

Brain Intraventricular Injection of Amyloid-β in Zebrafish Embryo Impairs Cognition and Increases Tau Phosphorylation,Effects Reversed by Lithium

Alzheimer’s disease (AD) is a devastating neurodegenerative disorder with no effective treatment and commonly diagnosed only on late stages. Amyloid-β (Aβ) accumulation and exacerbated tau phosphorylation are molecular hallmarks of AD implicated in cognitive deficits and synaptic and neuronal loss. The Aβ and tau connection is beginning to be elucidated and attributed to interaction with different components of common signaling pathways. Recent evidences suggest that non-fibrillary Aβ forms bind to membrane receptors and modulate GSK-3β activity, which in turn phosphorylates the microtubule-associated tau protein leading to axonal disruption and toxic accumulation. Available AD animal models, ranging from rodent to invertebrates, significantly contributed to our current knowledge, but complementary platforms for mechanistic and candidate drug screenings remain critical for the identification of early stage biomarkers and potential disease-modifying therapies. Here we show that Aβ1–42 injection in the hindbrain ventricle of 24 hpf zebrafish embryos results in specific cognitive deficits and increased tau phosphorylation in GSK-3β target residues at 5dpf larvae. These effects are reversed by lithium incubation and not accompanied by apoptotic markers. We believe this may represent a straightforward platform useful to identification of cellular and molecular mechanisms of early stage AD-like symptoms and the effects of neuroactive molecules in pharmacological screenings.     

Species limits in butterflies (Lepidoptera: Nymphalidae): reconciling classical taxonomy with the multispecies coalescent

Species delimitation is at the core of biological sciences. During the last decade, molecular‐based approaches have advanced the field by providing additional sources of evidence to classical, morphology‐based taxonomy. However, taxonomy has not yet fully embraced molecular species delimitation beyond threshold‐based, single‐gene approaches, and taxonomic knowledge is not commonly integrated into multilocus species delimitation models. Here we aim to bridge empirical data (taxonomic and genetic) with recently developed coalescent‐based species delimitation approaches. We use the multispecies coalescent model as implemented in two Bayesian methods (dissect/stacey and bp&p ) to infer species hypotheses. In both cases, we account for phylogenetic uncertainty (by not using any guide tree) and taxonomic uncertainty (by measuring the impact of using a priori taxonomic assignments to specimens). We focus on an entire Neotropical tribe of butterflies, the Haeterini (Nymphalidae: Satyrinae). We contrast divergent taxonomic opinion – splitting, lumping and misclassifying species – in the light of different phenotypic classifications proposed to date. Our results provide a solid background for the recognition of 22 species. The synergistic approach presented here overcomes limitations in both traditional taxonomy (e.g. by recognizing cryptic species) and molecular‐based methods (e.g. by recognizing structured populations, and not raising them to species). Our framework provides a step forward towards standardization and increasing reproducibility of species delimitations.