Publications

In 2002 a new dinosaur tracksite was discovered in calcareous laminites of early Late Kimmeridgian age along the future course of the “Transjurane” highway in Courtedoux, Canton Jura, Northern Switzerland. The site has an extraordinary scientific potential, as the laminites, which have been deposited in an intertidal to supratidal environment, contain at least 6 track-bearing levels in a total thickness of about 1 m. The laminites are being systematically excavated by the “Section de paleontologie” over an area of approximately 1500 m2. So far the main track level has been uncovered over an area of about 650 m2, which reveals 2 trackways of theropods and 17 trackways of sauropods. The sauropod tracks are the smallest known in the Kimmeridgian so far, and the trackways belong to the ichnogenus Parabrontopodus, which has been revealed for the first time in Switzerland. The tracksite belongs to the “Middle Kimmeridgian megatracksite” sensu Meyer (2000), and represents the most important dinosaur tracksite in Switzerland, perhaps with the potential for development into one of the world's largest sauropod tracksites. It will be protected in situ underneath an especially constructed highway-bridge, thus offering opportunities for future research and the development of an interpretative center for education and tourism.

A new semionotid fish, Lepidotes buddhabutrensis n. sp., is described from the continental Late Jurassic–Early Cretaceous Phu Kradung Formation, Phu Nam Jun, Kalasin Province. L. buddhabutrensis is characterized notably by the pattern of its cheek bones, by its short preorbital region, and by its numerous and well-developed premaxillary teeth. L. buddhabutrensis is provisionally placed in the genus Lepidotes; it shares, however, derived characters with other semionotids, such as Araripelepi- dotes and Pliodetes.

Sediment-dwelling protists are among the most abundant meiobenthic organisms, ubiquitous in all types of aquatic ecosystems. Yet, because their isolation and identification are difficult, their diversity remains largely unknown. In the present work, we applied molecular methods to examine the diversity of freshwater Foraminifera, a group of granuloreticulosan protists largely neglected until now. By using specific PCR primers, we detected the presence of Foraminifera in all sediment samples examined. Phylogenetic analysis of amplified SSU rDNA sequences revealed two distinct groups of freshwater foraminiferans. All obtained sequences branched within monothalamous (single-chambered), marine Foraminifera, suggesting a repeated colonization of freshwater environments. The results of our study challenge the traditional view of Foraminifera as essentially marine organisms, and provide a conceptual framework for charting the molecular diversity of freshwater granuloreticulosan protists.

The allelic variability at six Y-chromosome-specific polymorphisms (YAP, DYS19, DYS389-I, DYS390, DYS391, and DYS392) was used to generate male-specific haplotypes in 333 males representing 12 population samples from the region around the Mediterranean sea. Extreme interindividual variation was observed, as more than 160 distinct Y-chromosome variants could be defined as six-locus haplotypes. Concomitant with this high variability, low levels of population genetic structure were observed. In particular, a "core" of populations directly facing the north and the east of the Mediterranean basin, from the Middle East to the Italian Peninsula, was found to be genetically undifferentiated. This observation, supported by a reanalysis of Y-specific binary polymorphisms in the same populations, suggests that at least part of the male-specific gene pools of these populations has either a very recent common origin (that could be related with the Neolithic demic diffusion hypothesis), and/or that gene flow has played a significant role in shaping the patterns of genetic variability in this region. In agreement with both hypotheses, we found that the spatial distribution of DYS392 alleles revealed a marked differentiation between the East and the West of the Mediterranean area. Through the analysis of microsatellite variation, the time to the most recent common ancestor (TMRCA) of the YAP(+) sublineage 4 has been estimated. The estimations, based on two different data sets, turn out to be quite recent (7,000-11,000 YBP), suggesting that this lineage may have been first introduced into Southern Europe through Neolithic migrations from the Middle East.

During limb development, coordinated expression of several Hoxd genes is required in presumptive digits. We searched for the underlying control sequences upstream from the cluster and found Lunapark (Lnp), a gene which shares limb and CNS expression specificities with both Hoxd genes and Evx2, another gene located nearby. We used a targeted enhancer-trap approach to identify a DNA segment capable of directing reporter gene expression in both digits and CNS, following Lnp, Evx2, and Hoxd-specific patterns. This DNA region showed an unusual interspecies conservation, including with its pufferfish counterpart. It contains a cluster of global enhancers capable of controlling transcription of several genes unrelated in structure or function, thus defining large regulatory domains. These domains were interrupted in the Ulnaless mutation, a balanced inversion that modified the topography of the locus. We discuss the heuristic value of these results in term of locus specific versus gene-specific regulation.

Improving the performance of non-viral gene-delivery vehicles that consist of synthetic compounds and nucleic acids is a key to successful gene therapy. Supplementing synthetic vehicles with various biological functions by using natural or artificial peptides is a promising approach with which to achieve this goal. One of the obstacles hindering this effort is that some of the potentially useful peptides, especially those with many basic amino acid residues, interfere with the formation of the complex owing to strong electrostatic interactions with the nucleic acid. In this review, we describe our recent work in examining the potential of these peptides in gene delivery, using a recombinant lambda phage particle as the model for the gene-delivery complex. Lambda phage encapsulates large duplex DNA in a rigid polyplex-like shell with a diameter of 55 nm, and can display various peptides on this capsid, independently of particle formation. By examining the expression of marker genes encapsulated in the phage capsid, we have demonstrated that the protein transduction domain of HIV Tat protein and the nuclear localization signal derived from SV40 T antigen can remarkably facilitate the delivery of these marker genes across the two major barriers, the cell membrane and the nuclear membrane, respectively. Our results indicate that these basic peptides can constitute effective components of synthetic gene-transfer complexes, as long as sufficient copies are displayed on the outer surface of the complex.

Mice carrying transgenes targeted upstream the HoxD cluster display abnormal digits, with alterations resembling those obtained with loss of functions of Hoxd genes. Because the HoxD cluster remained entirely untouched by the insertional events, we investigated whether these phenotypes were induced by regulatory modifications at a distance. We report here that these targeted relocations behaved as hypomorphic alleles of the distantly located gene Hoxd13 and showed that posterior Hoxd genes located in cis with the integration site were down-regulated. Genetic analyses suggested that this down-regulation resulted from the titration of the activity of a remote located enhancer sequence. These results indicate that the transcriptional efficiency of Hoxd genes in digits could be modulated by the presence of other, unrelated, promoters, within the regulatory landscape of this enhancer. Modifications in these latter transcription units may thus impact upon digit morphology, through misregulation of Hoxd genes, thus illustrating the "buffering effect" that such a global regulatory element can exert upon a short genomic interval.

Vannella simplex (Gymnamoebia, Vannellidae) is one of the most common amoebae species, recorded from a variety of regions. It was originally described as a freshwater species, but has also been reported from shallow-water regions of the Baltic Sea. In the present work, we investigated the morphology and biology of three V. simplex isolates, originating from geographically distant regions. Among them is one brackish water strain, isolated from artificial cyanobacterial mats, which were originally sampled in Nivå Bay (Baltic Sea, The Sound). The strain is cyst-forming and can thrive at salinity ranges from 0-50 ppt. Phylogenetic relationships were investigated by sequencing partial SSU rDNA of the cultured V. simplex isolates. Additional sequences were obtained from four environmental DNA extractions of sediment samples collected from different localities in Switzerland. Analysis of all obtained sequences revealed a monophyletic group. Based on the analysis and comparison of morphological, ecological and molecular data sets we compiled a distribution map of V. simplex and propose an emendation of this species.

The mouse Fxy gene was translocated into the highly recombining pseudoautosomal region comparatively recently in evolutionary terms. This event resulted in a rapid increase of GC content. We investigated the consequences of the translocation further by sequencing exons and introns of Fxy in various rodent species. We found that the DNA fragment newly located in a highly recombining context has acquired every property of a GC-rich isochore, namely increased GC content (especially at the third codon positions of exons), shorter introns and high density of minisatellites. These results strongly suggest that recombination is the primary determinant of the isochore organization of mammalian genomes.