Publications

In hydra, the endodermal epithelial cells carry out the digestive function together with the gland cells that produce zymogens and express the evolutionarily conserved gene Kazal1. To assess the hydra Kazal1 function, we silenced gene expression through double-stranded RNA feeding. A progressive Kazal1 silencing affected homeostatic conditions as evidenced by the low budding rate and the induced animal death. Concomitantly, a dramatic disorganization followed by a massive death of gland cells was observed, whereas the cytoplasm of digestive cells became highly vacuolated. The presence of mitochondria and late endosomes within those vacuoles assigned them as autophagosomes. The enhanced Kazal1 expression in regenerating tips was strongly diminished in Kazal1(-) hydra, and the amputation stress led to an immediate disorganization of the gland cells, vacuolization of the digestive cells and death after prolonged silencing. This first cellular phenotype resulting from a gene knock-down in cnidarians suggests that the Kazal1 serine-protease-inhibitor activity is required to prevent excessive autophagy in intact hydra and to exert a cytoprotective function to survive the amputation stress. Interestingly, these functions parallel the pancreatic autophagy phenotype observed upon mutation within the Kazal domain of the SPINK1 and SPINK3 genes in human and mice, respectively.

Microarray technology is generating huge amounts of data about the expression level of thousands of genes, or even whole genomes, across different experimental conditions. To extract biological knowledge, and to fully understand such datasets, it is essential to include external biological information about genes and gene products to the analysis of expression data. However, most of the current approaches to analyze microarray datasets are mainly focused on the analysis of experimental data, and external biological information is incorporated as a posterior process.

The Drosophila protein SU(VAR)3-7 is essential for fly viability, chromosome structure, and heterochromatin formation. We report that searches in silico and in vitro for homologues of SU(VAR)3-7 were successful within, but not outside, the Drosophila genus. Protein sequence homology between the distant sibling species Drosophila melanogaster and Drosophila virilis is low, except for the general organization of the protein and three conserved motives: seven widely spaced zinc fingers in the N-terminal half and the BESS and BoxA motives in the C-terminal half of the protein. We have undertaken a fine functional dissection of SU(VAR)3-7 in vivo using transgenes encoding truncations of the protein. BESS mediates interaction of SU(VAR)3-7 with itself, and BoxA is required for specific heterochromatin association. Both are necessary for the silencing properties of SU(VAR)3-7. The seven zinc fingers, widely spaced over the N-terminal half of SU(VAR)3-7, are required for binding to polytene chromosomes. One finger is necessary and sufficient to determine the appropriate chromatin association of the C-terminal half of the protein. Conferring a function to each of the conserved motives allows us to better understand the mode of action of SU(VAR)3-7 in triggering heterochromatin formation and subsequent genomic silencing.

Specific targeting of the protein complexes formed by the Polycomb group of proteins is critically required to maintain the inactive state of a group of developmentally regulated genes. Although the role of DNA binding proteins in this process has been well established, it is still not understood how these proteins target the Polycomb complexes specifically to their response elements. Here we show that the grainyhead gene, which encodes a DNA binding protein, interacts with one such Polycomb response element of the bithorax complex. Grainyhead binds to this element in vitro. Moreover, grainyhead interacts genetically with pleiohomeotic in a transgene-based, pairing-dependent silencing assay. Grainyhead also interacts with Pleiohomeotic in vitro, which facilitates the binding of both proteins to their respective target DNAs. Such interactions between two DNA binding proteins could provide the basis for the cooperative assembly of a nucleoprotein complex formed in vitro. Based on these results and the available data, we propose that the role of DNA binding proteins in Polycomb group-dependent silencing could be described by a model very similar to that of an enhanceosome, wherein the unique arrangement of protein-protein interaction modules exposed by the cooperatively interacting DNA binding proteins provides targeting specificity.

Hoxd genes are essential for limb growth and patterning. They are activated following a complex transcriptional regulation, leading to expression domains that are collinear in both space and time. To understand the mechanism(s) underlying collinearity, we produced and analyzed a set of mouse strains containing systematic deletions and duplications within the HoxD cluster. We show that two waves of transcriptional activation, controlled by different mechanisms, generate the observed developmental expression patterns. The first wave is time-dependent, involves the action of opposite regulatory modules, and is essential for the growth and polarity of the limb up to the forearm. The second phase involves a different regulation and is required for the morphogenesis of digits. We propose that these two phases reflect the different phylogenetic histories of proximal versus distal limb structures and discuss the biological relevance of these collinear patterns, particularly for the origin of the anterior-to-posterior limb polarity.

The general-time-reversible (GTR) model is one of the most popular models of nucleotide substitution because it constitutes a good trade-off between mathematical tractability and biological reality. However, when it is applied for inferring evolutionary distances and/or instantaneous rate matrices, the GTR model seems more prone to inapplicability than more restrictive time-reversible models. Although it has been previously noted that the causes for intractability are caused by the impossibility of computing the logarithm of a matrix characterised by negative eigenvalues, the issue has not been investigated further.

Isolated teeth of five hybodont taxa (Hybodus sp., Parvodus sp., Lonchidion khoratensis nov. sp., Isanodus paladeji nov. gen., nov. sp., Heteroptychodus steinmanni) are described from the freshwater Sao Khua Formation of Thailand (Lower Cretaceous). This Early Cretaceous fauna appears less endemic, with some European affinities, than the hybodont fauna found in Thailand in the more recent Aptian/Albian Khok Kruat Formation. Teeth of Isanodus paladeji (Lonchidiidae) and Heteroptychodus steinmanni (Ptychodontidae) share an unusual ornamentation pattern suggesting that the origin of the family Ptychodontidae is nested among Asian Lonchidiidae.

The majority of extant families of larger Foraminifera are hosts for cndosymbiotic diatoms, among them also Nummulitidae, which are the largest calcareous foraminiferans. Nummulitidae occur in reef environments and extend their depth distribution down to the base of the photic zone. They reach their highest diversity and abundance in the western Pacific. Some information about the diversity of nummulitid diatom symbionts has been gained by investigating morphological and ultrastructural…

The General Time Reversible (GTR) model of nucleotide substitution is at the core of many distance-based and character-based phylogeny inference methods. The procedure described by Waddell and Steel (1997), for estimating distances and instantaneous substitution rate matrices, R, under the GTR model, is known to be inapplicable under some conditions, ie, it leads to the inapplicability of the GTR model. Here, we simulate the evolution of DNA sequences along 12 trees characterized by different combinations of tree length, (non-)homogeneity of the substitution rate matrix R, and sequence length. We then evaluate both the frequency of the GTR model inapplicability for estimating distances and the accuracy of inferred alignments. Our results indicate that, inapplicability of the Waddel and Steel's procedure can be considered a real practical issue, and illustrate that the probability of this inapplicability is a function of substitution rates and sequence length.We also discuss the implications of our results on the current implementations of maximum likelihood and Bayesian methods.