Search PubMed⌕ Search

Biomedical subjects

F Rodier

Publications and source records attributed to F Rodier.

At least 19 recordsLinked to original sources

Microarray analysis of gene expression mirrors the biology of an ovarian cancer model.

We have previously described an ovarian cancer model based on four independent spontaneously immortalized epithelial ovarian cancer cell lines (TOV-21G, TOV-81D, TOV-112D and OV-90) from patients who were never exposed to chemotherapy or radiation therapy. These cell lines are particularly interesting since they retain characteristics of the original epithelial ovarian cancers (EOC) from which they were derived. Here we report the characterization of this model system using high-density DNA microarrays in order to assess gene expression. Expression profiles were generated from total RNAs extracted from the four EOC cell lines. For comparison, expression profiling is also provided for a primary culture of normal ovarian surface epithelium (NOV-31) and a fresh EOC sample (TOV-578G). Comparison of expression profiles revealed patterns of expression that distinguish NOV-31 from that of all tumor derived samples. The expression pattern of TOV-81D, an EOC cell line that was derived from a patient with indolent disease, most closely resembles NOV-31 while profiles of samples derived from patients with more aggressive disease (TOV-21G, OV-90, TOV-112D and TOV-578G) showed more divergent patterns of expression. The microarray analysis (http://genome.mcgill.ca) results confirm the usefulness of an ovarian cancer model based on the characterization of these EOC cell lines.

Blotting, Northern↗

Polyomavirus large T-antigen protects mouse cells from Fas-, TNF-alpha- and taxol-induced apoptosis.

Polyomavirus large T-antigen (PyLT-Ag), a nucleophosphoprotein essential for regulating viral gene expression, modulates the cell cycle by binding to the Rb tumor suppressor gene product. PyLT-Ag/Rb binding is essential for in vitro immortalization. However, the effect of PyLT-Ag on apoptosis has not been extensively studied. We have previously reported that FasR agonist antibodies (FasR(Ab)) treatment of Sertoli cells derived from transgenic mice expressing PyLT-Ag induces the growth arrest of these cells without concomitant apoptosis. Here we show that stable expression of PyLT-Ag in murine Sertoli TM4 and hybridoma NSO cell lines confers protection from FasR(Ab)-induced apoptosis. The protection was maintained up to 48 h when cells were grown continuously in the presence of FasR(Ab). Removal of the death stimulus after 24 h exposure was sufficient to allow full recovery of the PyLT-Ag expressing cells. The protective effect conferred by PyLT-Ag was associated with a delay in the sequential activation of caspase-8 and -3 after FasR(Ab) treatment. PyLT-Ag co-precipitated following immunoprecipitation of caspase-8 or FADD, both components of the DISC. Based on these results we suggest that PyLT-Ag directly impedes the recruitment or activation of caspase-8 by the FasR. PyLT-Ag expression in TM4 cells was also associated with protection from TNF-alpha- and taxol-induced apoptosis. In contrast, PyLT-Ag expression was not sufficient to confer protection from captothecin-induced apoptosis. Taken together, these results indicate that PyLT-Ag can be a potent inhibitor of Fas(R)(Ab)-, TNF-alpha- and taxol-induced apoptosis.

Adaptor Proteins, Signal Transducing↗

1.6 A structure of semisynthetic ribonuclease crystallized from aqueous ethanol. Comparison with crystals from salt solutions and with ribonuclease A from aqueous alcohol solutions.

The non-covalent combination of residues 1-118 of RNase A with a synthetic 14-residue peptide containing residues 111-124 of the molecule forms a highly active semisynthetic enzyme, RNase 1-118:111-124. With this enzyme, the roles played by the six C-terminal residues in generating the catalytic efficiency and substrate specificity of RNase can be studied using chemically synthesized analogs. The structure of RNase 1-118:111-124 from 43% aqueous ethanol has been determined using molecular-replacement methods and refined to a crystallographic R-factor of 0.166 for all observed reflections in the range 7.0-1.6 A (Protein Data Bank file ISSC). The structure is compared with the 2.0 A structure of RNase A from 43% aqueous 2-methyl-2-propanol and with the 1.8 A structure of the semisynthetic enzyme obtained from crystals grown in concentrated salt solution. The structure of RNase 1-118:111-124 from aqueous ethanol is virtually identical to that of RNase A from aqueous 2-methyl-2-propanol. Half of the crystallographically bound water molecules are not coincident, however. The structure is somewhat less similar to that of RNase 1-118:111-124 from salt solutions, with a major difference being the positioning of active-site residue His119.

Journal Article↗

Thermodynamics of the temperature-induced unfolding of globular proteins.

The heat capacity, enthalpy, entropy, and Gibbs energy changes for the temperature-induced unfolding of 11 globular proteins of known three-dimensional structure have been obtained by microcalorimetric measurements. Their experimental values are compared to those we calculate from the change in solvent-accessible surface area between the native proteins and the extended polypeptide chain. We use proportionality coefficients for the transfer (hydration) of aliphatic, aromatic, and polar groups from gas phase to aqueous solution, we estimate vibrational effects, and we discuss the temperature dependence of each constituent of the thermodynamic functions. At 25 degrees C, stabilization of the native state of a globular protein is largely due to two favorable terms: the entropy of non-polar group hydration and the enthalpy of interactions within the protein. They compensate the unfavorable entropy change associated with these interactions (conformational entropy) and with vibrational effects. Due to the large heat capacity of nonpolar group hydration, its stabilizing contribution decreases quickly at higher temperatures, and the two unfavorable entropy terms take over, leading to temperature-induced unfolding.

Calorimetry↗

Protein-protein interaction at crystal contacts.

Packing contacts are crystal artifacts, yet they make use of the same forces that govern specific recognition in protein-protein complexes and oligomeric proteins. They provide examples of a nonspecific protein-protein interaction which can be compared to biologically relevant ones. We evaluate the number and size of pairwise interfaces in 152 crystal forms where the asymmetric unit contains a monomeric protein. In those crystal forms that have no element of 2-fold symmetry, we find that molecules form 8 to 10 pairwise interfaces. The total area of the surface buried on each molecule is large, up to 4400 A2. Pairwise interfaces bury 200-1200 A2, like interfaces generated at random in a computer simulation, and less than interfaces in protease-inhibitor or antigen-antibody complexes, which bury 1500 A2 or more. Thus, specific contacts occurring in such complexes extend over a larger surface than nonspecific ones. In crystal forms with 2-fold symmetry, pairwise interfaces are fewer and larger on average than in the absence of 2-fold symmetry. Some bury 1500-2500 A2, like interfaces in oligomeric proteins, and create "crystal oligomers" which may have formed in the solution before crystallizing.

Adenylate Kinase↗

Packing forces in ribonuclease crystals.

Packing in Ribonuclease A and Ribonuclease S crystals have been compared in order to determine the possible role of the precipitant on lattice contacts. Both proteins have similar tertiary structures, but they crystallize in different space groups depending on the precipitating agent. It is found that packing differs either by the number of nearest neighbours or by the size of surface areas buried in individual contacts. Ammonium sulfate seems to promote hydrophobic interactions with interfaces similar to those found in oligomeric proteins. Organic precipitants favour electrostatic interactions.

Amino Acids↗

Chromosome localization-dependent compositional bias of point mutations in Alu repetitive sequences.

The Alu repetitive sequence family originated from a common ancestor. Its members, apparently free from functional constraints, are interspersed throughout primate genomes. We have found that base substitutions occurring during the evolution of primates caused a decrease in the average G + C content of those members of the family that are located in an A + T-rich region of the genome. The family members that are located in a G + C-rich genomic region have not changed their, already high, G + C content. This suggests that the regional differences in G + C content, which are responsible for chromosomal banding, are caused by an accumulation of mutations that, although selectively neutral in the majority, show different compositional bias in different regions of the vertebrate chromosome.

Animals↗

Allosteric transition of aspartokinase I-homoserine dehydrogenase I studied by time-resolved fluorescence.

The allosteric transition of threonine-sensitive aspartokinase I-homoserine dehydrogenase I from Escherichia coli has been studied by time-resolved fluorescence spectroscopy. Fluorescence decay can be resolved into 2 distinct classes of tryptophan emitters: a fast component, with a lifetime of about 1.5 ns; and a slow component, with a lifetime of about 4.5 ns. The fluorescence properties of the slow component are modified by the allosteric transition. In the T-form of the enzyme stabilized by threonine, the lifetime of the slow component is longer, with a red-shifted spectrum; its accessibility to quenching by acrylamide becomes slightly higher without any decrease of fluorescence anisotropy. These results indicate a change in polarity of the slow component environment. The quaternary structure change associated with the allosteric transition probably involves global movements of structural domains without leading to any local mobility on the nanosecond time-scale. We suggest that the slow component corresponds to the unique tryptophan of the buried kinase domain.

Acrylamide↗

Two distinct compositional classes of vertebrate gene-bearing DNA stretches, their structures and possible evolutionary origin.

Genomes of vertebrates are built of long, compositionally uniform DNA regions differing in guanine and cytidine (G + C) content. Examination of G + C distribution and CpG dinucleotide frequency in the longest stretches of vertebrate DNA base sequences available show that the long-range structural features are correlated with the structure of genes. Two classes of DNA stretches are conspicuous: (i) the stretches having low G + C content and low CpG doublet frequency and (ii) stretches rich in G + C containing CpG-rich islands. Both classes show other compositional islands containing exons. These structural features result from evolutionary pressures acting on the DNA or RNA level, as well as from mutations and repair differently biased in different genomic compartments. The analysis presented provides a rationale for a discussion of evolution of the long-range structural characteristics of DNA.

Animals↗

The mosaic genome of warm-blooded vertebrates.

Most of the nuclear genome of warm-blooded vertebrates is a mosaic of very long (much greater than 200 kilobases) DNA segments, the isochores; these isochores are fairly homogeneous in base composition and belong to a small number of major classes distinguished by differences in guanine-cytosine (GC) content. The families of DNA molecules derived from such classes can be separated and used to study the genome distribution of any sequence which can be probed. This approach has revealed (i) that the distribution of genes, integrated viral sequences, and interspersed repeats is highly nonuniform in the genome, and (ii) that the base composition and ratio of CpG to GpC in both coding and noncoding sequences, as well as codon usage, mainly depend on the GC content of the isochores harboring the sequences. The compositional compartmentalization of the genome of warm-blooded vertebrates is discussed with respect to its evolutionary origin, its causes, and its effects on chromosome structure and function.

Animals↗

Localization of the initiation of translation in messenger RNAs of prokaryotes by learning techniques.

Learning processes are applied to the recognition of protein coding regions in prokaryotes. Non-contradictory, statistical and logical rules are deduced from a set of known examples of coding sequences. These rules enable to build characteristic patterns on the m-RNA upstream of the initiating codon. These rules are applied with success to recognize more than 180 coding sequences and to detect and/or eliminate hypothetical reading frames or unknown genes.

Bacteria↗

Search for promoter sites of prokaryotic DNA using learning techniques.

Using learning techniques previously described in this journal, we have built an expert system able to point to the start DNA point of a sequence and therefore to recognize a promoter. However, to build this system, we have focused on the TATA box and its environment. We have used this expert system to look for new promoters and also to construct new promoters. The results obtained are discussed.

Base Sequence↗

[Localization of initiating codons in RNA prokaryotes messengers by learning technics].

Learning processes are applied to the recognition of protein coding regions in prokaryotes. Non-contradictory, statistical rules are deduced from a set of known examples of coding regions. These rules allow us to build characteristic patterns on the m-RNA upstream the initiating codon. These rules are applied to recognize more than 180 coding sequences.

Cell Physiological Phenomena↗

Key for protein coding sequences identification: computer analysis of codon strategy.

The signal qualifying an AUG or GUG as an initiator in mRNAs processed by E. coli ribosomes is not found to be a systematic, literal homology sequence. In contrast, stability analysis reveals that initiators always occur within nucleic acid domains of low stability, for which a high A/U content is observed. Since no aminoacid selection pressure can be detected at N-termini of the proteins, the A/U enrichment results from a biased usage of the code degeneracy. A computer analysis is presented which allows easy detection of the codon strategy. N-terminal codons carry rather systematically A or U in third position, which suggests a mechanism for translation initiation and helps to detect protein coding sequences in sequenced DNA.

Amino Acid Sequence↗

[Analysis of the stability and local cooperativity of DNA: proposal of a molecular mechanism for the initiation of the transcription of gene A3 of bacteriophage T7 by the RNA polymerase from E. coli].

RNA polymerase (RNAP) complexed to the A3 promoter of bacteriophage T7 is known to unwind a DNA segment located downstream of the Pribnow box. This finding can be accounted for if it is assumed that the subunit sigma of RNAP unstabilizes three GC base pairs located just upstream of the transcription start. As a consequence, the rate of promoter utilisation might be related to the relative stability of the DNA between the "Pribnow box" and the transcription start.

Base Composition↗

[Analysis of the stability and local cooperativity of DNA : elements permitting the recognition of promoters by DNA-dependent RNA polymerase].

Analysis of the local stability of promoters processed by E. Coli RNA polymerase shows that they bear a characteristic stability profile: two segments of low stability are located around --35 and --8 bases ahead of the transcription start and are generally bordered by more stable segments. This key profile may act as a recognition signal for both attracting and positioning the RNA polymerase in the promoter site.

Base Sequence↗

[Use of the degeneracy of the genetic code by selective pressure to cut up genes of procaryote genomes].

The DNA sequences of three bacteriophages are analysed in order to localise those parts coding for a protein. A weak stability on the DNA molecule allows us to characterize the beginning and the end of genes. A survey of the codons used shows that the cause for this weak stability is the systematic use of A-T bases in third position, which is made possible by the degeneracy of the genetic code.

Bacteriophage phi X 174↗

[Spectral properties of porcine plasminogen: study of the acidic transition (author's transl)].

The acidic transition of porcine plasminogen, prepared by affinity chromatography, was studied by non-destructive methods. These methods are based on the analysis of the behaviour of the tryptophyls under various conditions. The perturbation of the absorption and emission spectra by pH or temperature and the dynamic quenching of the intrinsic fluorescence are used to obtain information on structural changes which affect the environment of these residues. It is shown that by decreasing pH the fluorescence emission spectra are shifted toward the long wavelengths, with a broadening of the fluorescence band. The same effect can be obtained at constant pH by heating the protein solution. In order to analyze these phenomena, it is assumed that the fluorescence intensities at 355 nm and 328 nm reflect the proportion of the tryptophans which are exposed to the solvent, and buried, respectively. The plot of the ratio of the fluorescence intensities at these wavelengths versus pH or temperature leads to a titration curve showing an unmasking of tryptophans. The proportion of exposed tryptophans is measured by the dynamic fluorescence quenching technique and the data analyzed according to Lehrer. The plot of the fraction of exposed tryptophyls versus pH also shows the unmasking of these chromophores. Thermal perturbation of a solution of plaminogen at neutral pH induces a difference absorption spectrum whose amplitudes at the maxima are proportional to the number of exposed aromatic residues. The comparison with a solution of fully denatured plasminogen in 6 M guanidium chloride, where all the tryptophyls are exposed, shows that the percentage of exposure is equal to 59%. This number is significantly higher than the percentage found by the fluorescence quenching technique (20%), indicating that some tryptophyls are located in crevices, exposed to the solvent but not to the iodide. At acidic pH the absorption difference spectra induced by thermal perturbation are not classical, since they show an inversion and a new band between 300 nm and 305 nm. This band is mentioned in the literature as a minor band of tryptophan which appears when this chromophore is located in an asymmetric environment. On plotting the maximum amplitude of these spectra obtained at acidic pH versus temperature, we obtain a curve indicating that two types of antagonistic interactions are involved in the perturbation of the chromophores spectra. The spectrophotometric titration of plasminogen gives classical absorption difference spectra. By plotting the maximum amplitude at 292 nm versus pH, we obtain a titration curve with an apparent pK of 2.9 units. This pK is acidic which respect to the pK value of a normal carboxyl. This low value can be due to a positively charged group in the neighbourhood of a carboxyl, which interacts with one or more chromophores. When the carboxyl becomes protonated, this positively charged group is free and available to perturb the environment of some chromophores...

Animals↗