Lateglacial and Holocene vegetation history in the mountain range of central Pyrenees

We present the pollen analysis of a new sedimentary sequence taken at La Pouretère ( 1720 m), in the mountain vegetation zone of the Marcadau valley (central Pyrenees). The Lateglacial and Holocene chronology is supported by six 14C-dating results. The complementary analysis of some vegetal macroremains, stomata, pollen-clusters and the use of pollen influx allows us to elucidate the dynamic of mountain species such as Pinus and specially Abies but also to infer the unusual part played by Betula at the beginning of the Postglacial period.     

Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae

We have screened the genome of Saccharomyces cerevisiae for fragments that confer a growth-retardation phenotype when overexpressed in a multicopy plasmid with a tetracycline-regulatable (Tet-off) promoter. We selected 714 such fragments with a mean size of 700 base-pairs out of around 84,000 clones tested. These include 493 in-frame open reading frame fragments corresponding to 454 distinct genes (of which 91 are of unknown function), and 162 out-of-frame, antisense and intergenic genomic fragments, representing the largest collection of toxic inserts published so far in yeast.     

TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences

Background  

In the emerging field of environmental genomics, direct cloning and sequencing of genomic fragments from complex microbial communities has proven to be a valuable source of new enzymes, expanding the knowledge of basic biological processes. The central problem of this so called metagenome-approach is that the cloned fragments often lack suitable phylogenetic marker genes, rendering the identification of clones that are likely to originate from the same genome difficult or impossible. In such cases, the analysis of intrinsic DNA-signatures like tetranucleotide frequencies can provide valuable hints on fragment affiliation. With this application in mind, the TETRA web-service and the TETRA stand-alone program have been developed, both of which automate the task of comparative tetranucleotide frequency analysis.     

Study of protein conformation and orientation in silkworm and spider silk fibers using Raman microspectroscopy

Raman microspectroscopy has been used for the first time to determine quantitatively the orientation of the beta-sheets in silk monofilaments from Bombyx mori and Samia cynthia ricini silkworms, and from the spider Nephila edulis. It is shown that, for systems with uniaxial symmetry such as silk, it is possible to determine the order parameters P2 and P4 of the orientation distribution function from intensity ratios of polarized Raman spectra. The equations allowing the calculation of P2 and P4 using polarized Raman microspectroscopy for a vibration with a cylindrical Raman tensor were first derived and then applied to the amide I band that is mostly due to the C=O stretching vibration of the peptide groups. The shape of the Raman tensor for the amide I vibration of the beta-sheets was determined from an isotropic film of Bombyx mori silk treated with methanol. For both the Bombyx mori and Samia cynthia ricini fibroin fibers, the values of P2 and P4 obtained are equal to -0.36 +/- 0.03 and 0.19 +/- 0.02, respectively, even though the two types of silkworm fibroins strongly differ in their primary sequences. For the Nephila edulis dragline silk, values of P2 and P4 of -0.32 +/- 0.02 and 0.13 +/- 0.02 were obtained, respectively. These results clearly indicate that the carbonyl groups are highly oriented perpendicular to the fiber axis and that the beta-sheets are oriented parallel to the fiber axis, in agreement with previous X-ray and NMR results. The most probable distribution of orientation was also calculated from the values of P2 and P4 using the information entropy theory. For the three types of silk, the beta-sheets are highly oriented parallel to the fiber axis. The orientation distributions of the beta-sheets are nearly Gaussian functions with a width of 32 degrees and 40 degrees for the silkworm fibroins and the spider dragline silk, respectively. In addition to these results, the comparison of the Raman spectra recorded for the different silk samples and the polarization dependence of several bands has allowed to clarify some important band assignments.     

Versatile and efficient formation of colloids of biopolymer-based polyelectrolyte complexes

The formation of colloids based on polyelectrolyte complexes (PECs) of biopolymers was investigated through the complexation between two charged polysaccharides, chitosan as polycation, and dextran sulfate as polyanion. The slow dropwise addition of components, generally used for the formation of PECs, allowed to elaborate both cationic or anionic particles with an excess of chitosan or dextran sulfate, respectively. The PEC particles featured a core/shell structure, the hydrophobic core resulting from the segregation of complexed segments whereas excess component in the outer shell ensured the colloidal stabilization against further coagulation. Considering the host/guest concept for the formation of PECs, the influence of the molecular weight of components on particles sizes could be well explained by the chain length ratios of the two polymers. As an irreversible flocculation occurred with a dropwise approach for both cationic and anionic PEC particles when the mixing ratio was close to unity, a more versatile, and simpler to setup, method was designed: the one-shot addition of one solution to the other. Because process of addition is faster than the flocculation, cationic or anionic particles could be elaborated irrespective of the order of addition of the reactant. Characterization of these particles by quasielastic light scattering, electrophoresis, and scanning electron microscopy revealed very similar properties to those obtained by a slow dropwise approach. Critical coagulation concentrations of 0.12 and 0.09 M (with sodium chloride) for cationic and anionic particles evidenced a mostly electrostatic stabilization.     

Tailoring of bioresorbable polymers for elaboration of sugar-functionalized nanoparticles

Maleic copolymers with different contents of galactose moieties and dodecyl chains were synthesized and used as both a stabilizer and a surface coating for the preparation of poly(epsilon-caprolactone) nanoparticles by the emulsification-diffusion technique. The size of the nanoparticles was controlled by varying the initial concentration of the modified maleic copolymers. As the concentration of the latter increased, the particle size decreased, indicating that the copolymers serve as a stabilizer. Moreover, surface modification of nanoparticles was confirmed by xi-potential measurements. Nanoparticles were also shown to be recognized by a galactose-specific lectin, demonstrating the presence of galactose units on the particle surface. This approach offers opportunities for the production of novel targeted drug delivery systems.     

Floxed allele for conditional inactivation of the GABAB(1) gene

GABA(B) receptors are the G-protein-coupled receptors for the neurotransmitter GABA. GABA(B) receptors are broadly expressed in the nervous system. Their complete absence in mice causes premature lethality or--when mice are viable--epilepsy, impaired memory, hyperalgesia, hypothermia, and hyperactivity. A spatially and temporally restricted loss of GABA(B) function would allow addressing how the absence of GABA(B) receptors leads to these diverse phenotypes. To permit a conditional gene inactivation, we flanked critical exons of the GABA(B(1)) gene with lox511 sites. GABA(B(1)) (lox511/lox511) mice exhibit normal levels of GABA(B(1)) protein, are fertile, and do not display any behavioral phenotype. We crossed GABA(B(1)) (lox511/lox511) with Cre-deleter mice to produce mice with an unrestricted GABA(B) receptor elimination. These GABA(B(1)) (-/-) mice no longer synthesize GABA(B(1)) protein and exhibit the expected behavioral abnormalities. The conditional GABA(B(1)) allele described here is therefore suitable for generating mice with a site- and time-specific loss of GABA(B) function.     

Definition and characterization of a "trypsinosome" from specific peptide characteristics by nano-HPLC-MS/MS and in silico analysis of complex protein mixtures

Although HPLC-ESI-MS/MS is rapidly becoming an indispensable tool for the analysis of peptides in complex mixtures, the sequence coverage it affords is often quite poor. Low protein expression resulting in peptide signal intensities that fall below the limit of detection of the MS system in combination with differences in peptide ionization efficiency plays a significant role in this. A second important factor stems from differences in physicochemical properties of each peptide and how these properties relate to chromatographic retention and ultimate detection. To identify and understand those properties, we compared data from experimentally identified peptides with data from peptides predicted by in silico digest of all corresponding proteins in the experimental set. Three different complex protein mixtures extracted were used to define a training set to evaluate the amino acid retention coefficients based on linear regression analysis. The retention coefficients were also compared with other previous hydrophobic and retention scale. From this, we have constructed an empirical model that can be readily used to predict peptides that are likely to be observed on our HPLC-ESI-MS/MS system based on their physicochemical properties. Finally, we demonstrated that in silico prediction of peptides and their retention coefficients can be used to generate an inclusion list for a targeted mass spectrometric identification of low abundance proteins in complex protein samples. This approach is based on experimentally derived data to calibrate the method and therefore may theoretically be applied to any HPLC-MS/MS system on which data are being generated.