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R Gautier

Publications and source records attributed to R Gautier.

At least 19 recordsLinked to original sources
PubMed2006

SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace.

SABBAC is an on-line service devoted to protein backbone reconstruction from alpha-carbon trace. It is based on the assembly of fragments taken from a library of reduced size, selected from the encoding of the protein trace in a hidden Markov model-derived structural alphabet. The assembly of the fragments is achieved by a greedy algorithm, using an energy-based scoring. Alpha-carbon coordinates remain unaffected. SABBAC simply positions the missing backbone atoms, no further refinement is performed. From our tests, SABBAC performs equal or better than other similar on-line approach and is robust to deviations on the alpha-carbon coordinates. It can be accessed at http://bioserv.rpbs.jussieu.fr/SABBAC.html.

Carbon↗
PubMed2004

SCit: web tools for protein side chain conformation analysis.

SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit.

Amino Acids↗
PubMed2004

A hidden markov model derived structural alphabet for proteins.

Understanding and predicting protein structures depends on the complexity and the accuracy of the models used to represent them. We have set up a hidden Markov model that discretizes protein backbone conformation as series of overlapping fragments (states) of four residues length. This approach learns simultaneously the geometry of the states and their connections. We obtain, using a statistical criterion, an optimal systematic decomposition of the conformational variability of the protein peptidic chain in 27 states with strong connection logic. This result is stable over different protein sets. Our model fits well the previous knowledge related to protein architecture organisation and seems able to grab some subtle details of protein organisation, such as helix sub-level organisation schemes. Taking into account the dependence between the states results in a description of local protein structure of low complexity. On an average, the model makes use of only 8.3 states among 27 to describe each position of a protein structure. Although we use short fragments, the learning process on entire protein conformations captures the logic of the assembly on a larger scale. Using such a model, the structure of proteins can be reconstructed with an average accuracy close to 1.1A root-mean-square deviation and for a complexity of only 3. Finally, we also observe that sequence specificity increases with the number of states of the structural alphabet. Such models can constitute a very relevant approach to the analysis of protein architecture in particular for protein structure prediction.

Algorithms↗
PubMed2003

Critical assessment of side-chain conformational space sampling procedures designed for quantifying the effect of side-chain environment.

We introduce a family of procedures designed to sample side-chain conformational space at particular locations in protein structures. These procedures (CRSP) use intensive cycles of random assignment of side-chain conformations followed by minimization to determine all the conformations that a group of side-chains can adopt simultaneously. First, we consider a procedure evolving in the dihedral space (dCRSP). Our results suggest that it can accurately map low-energy conformations adopted by clusters of side-chains of a protein. dCRSP is relatively insensitive to various important parameters, and it is sufficiently accurate to capture efficiently the constraint induced by the environment on the conformations a particular side-chain can adopt. Our results show that dCRSP, compared with molecular dynamics (MD), can overcome the problem of the limited set of conformations reached in a reasonable amount of simulations. Next, we introduce procedures (vCRSP) in which valence angles are relaxed, and we assess how efficiently they quantify the conformational entropy of side-chains in the protein native state. For simple peptides, entropies obtained with vCRSP are fully compatible with those obtained with a Monte Carlo procedure. For side-chains in a protein environment, however, vCRSP appears of limited use. Finally, we consider a two-step procedure that combines dCRSP and vCRSP. Our tests suggest that it is able to overcome the limitations of vCRSP. We also note that dCRSP provides a reasonable initial approximation. This family of procedures offers promise in quantifying the contribution of conformational entropy to the energetics of protein structures.

Algorithms↗
PubMed2003

Structural trends and the electronic structure of the rare-earth oxomolybdates RMo(5)O(8) (R = La, Ce, Pr, Nd, Sm, Eu and Gd) containing chains of bioctahedral Mo(10) clusters.

The crystal structures of the rare-earth members of the series RMo(5)O(8) (R = Ce to Eu) have been investigated and compared with those of the La and Gd members previously published in order to understand the influences of the size and the charge of the cation on the different Mo-Mo bonds. The RMo(5)O(8) compounds crystallize in the monoclinic space group P2(1)/c. Their crystal structure is characterized by bioctahedral Mo(10) clusters forming extended chains. The results of our single-crystal studies show that the modification of charge predominantly affects the Mo-Mo bonds between the Mo(10) clusters and, to a lesser extent, the intra-cluster distances, while the cationic size induces only small variations. Theoretical investigations confirm this statement and allow the understanding of the bonding mode in these compounds.

Journal Article↗
PubMed2002

New mercury vanadium phosphate hydrate Hg(4)(-)(x)()O(1-)(y)()((VO)(PO(4))(2).H(2)O with unprecedented tetrahedral oxo-cluster [Hg( approximately )(4)O( approximately )(5)].

The new mercury vanadium phosphate hydrate Hg(4)(-)(x)()O(1)(-)(y)()(VO)(PO(4))(2).H(2)O has been synthesized under hydrothermal conditions. X-ray investigations led to orthorhombic symmetry, space group P2(1)2(1)2(1) (No. 19), a = 6.3632(2) A, b = 12.4155(5) A, c = 14.2292(6) A, Z = 4. The crystal structure was solved and refined from single-crystal diffractometer data to residuals R[F(2) > 2sigmaF(2)] = 0.039, R(w)(F(2)) = 0.055. The VPO framework consists of infinite one-dimensional [VO(PO(4))(2)]( infinity ) chains with corner-connected VO(6) octahedra and PO(4) tetrahedra. The chains run along the [100] direction and are held together by the unprecedented tetrahedral cationic units [Hg(4)(-)(x)()O(1)(-)(y)()](4+). Presence of Hg-Hg bonding contacts is proved from theoretical calculations.

Journal Article↗
PubMed2002

Synthesis, structural trends, and physical and electronic properties of the reduced molybdenum oxides R(4)Mo(4)O(11) (R = Nd-Tm and Y) containing infinite chains of trans-edge-shared octahedral clusters.

The new compounds R(4)Mo(4)O(11) (R = Y, Nd, Sm-Tm) have been synthesized as crystalline powders by solid-state reaction in a sealed molybdenum crucible at 1400 degrees C. Single crystals suitable for X-ray structure determinations and resistivity measurements were also prepared. The R(4)Mo(4)O(11) compounds crystallize in the orthorhombic space group Pbam with four formulas per unit cell. The crystal structure of these compounds is based on infinite chains of trans-edge-shared molybdenum octahedra, which are widely separated by the rare-earth cations that are in monocapped trigonal prismatic coordination of oxygen atoms. Consequently, adjacent metallic chains do not share oxygen atoms and the shortest interchain Mo-Mo distance is greater than 7 A. Within the infinite chains, a strong pairing between the apical Mo atoms occurs, leading to a pattern of alternating short and long distances between these atoms. Resistivity measurements on single crystals show that the R(4)Mo(4)O(11) compounds are small band gap semiconductors, and magnetic susceptibility studies are in agreement with the presence of R(3+) ions. In addition, antiferromagnetic orderings have also been observed for the R(4)Mo(4)O(11) compounds with R = Gd-Tm below 5 K. Theoretical calculations confirm the stabilization of the structure by the distortion and agree with the resistivity and magnetic measurements.

Journal Article↗
PubMed2001

MTi(0.7)Mo(0.3)Mo(5)O(10) (M = SR, Eu), first evidence of mono- and bicapped bioctahedral Mo(11) and Mo(12) clusters: synthesis, crystal structures, and physical properties.

The novel quaternary reduced molybdenum oxides MTi(0.7)Mo(0.3)Mo(5)O(10) (M = Sr, Eu) have been synthesized by solid-state reaction at 1400 degrees C for 48 h in sealed molybdenum crucibles. Their crystal structures were determined on single crystals by X-ray diffraction. Both compounds crystallize in the orthorhombic space group Pbca with 8 formula units per cell and the following lattice parameters: a(Sr) = 9.1085 (7), b(Sr) = 11.418 (1), and c(Sr) = 15.092 (3) A; a(Eu) = 9.1069 (7), b(Eu) = 11.421 (2), and c(Eu) = 15.075 (1) A. The Mo network is dominated by bioctahedral Mo(10) clusters, which coexist randomly with Mo(11) and Mo(12) clusters (monocapped and bicapped Mo(10) clusters). The Mo-Mo distances within the clusters range from 2.62 to 2.92 A and the Mo-O distances from 1.99 to 2.17 A as usually observed in the reduced molybdenum oxides. The Sr(2+) and Eu(2+) ions occupy large cavities, which result from the fusion of two cubooctahedra and thus are surrounded by 11 oxygen atoms. The M-O distances range from 2.50 to 3.23 A for the Sr compound and from 2.49 to 3.24 A for the Eu analogue. Single-crystal resistivity measurements indicate that both materials are poor metals with transitions to semiconducting states below 50 and 40 K and room temperature resistivity values of 9 x 10(-3) and 5 x 10(-3) Omega.cm for the Sr and Eu compounds, respectively. The magnetic susceptibility data indicate paramagnetic behavior due to the Eu(2+) moment at high temperatures for the Eu compound and do not reveal the existence of localized moments on the Mo and Ti sublattice in the Sr compound. An XPS study clearly suggests that the isolated Ti ions are tetravalent. Theoretical considerations preclude the existence of heterometallic Mo-Ti clusters.

Journal Article↗
PubMed2001

Gaussian process: an efficient technique to solve quantitative structure-property relationship problems.

We introduce the Gaussian process (GP) model for the empirical modelling of the log P values of 44 1,2-dithiole-3-one molecules. A brief theoretical description of the method is given. Descriptive and predictive abilities of GP are evaluated and compared to multilinear regression results. Special attention is devoted to the automatic relevance determination (ARD) to reduce input variable numbers, which avoid the use of principal component analysis. The present approach was found to be an efficient method and a good alternative to more complicated using artificial neural network systems.

Models, Chemical↗
PubMed2000

Tracing the progeny of the aortic hemangioblast in the avian embryo.

A population of hematopoietic progenitors becomes committed within the embryo proper in the floor of the aorta (P-Sp/AGM in the mouse). In birds, this first aspect of intraembryonic hematopoiesis is prominent during embryonic day 3 (E3) as endothelium-associated "intra-aortic clusters." Between E6 and E8, diffuse hematopoiesis then occurs as "para-aortic foci" located in the dorsal mesentery ventral to the aorta. These foci are not associated with endothelium. Whether these two hematopoietic cell populations arise from distinct or common progenitors is not known. We could recently trace back the origin of intra-aortic clusters in the avian embryo by labeling aortic endothelial cells (EC) in vivo with acetylated low-density lipoproteins. This approach established the derivation of early intraembryonic hemopoietic cells from the endothelium, but did not indicate how long during ontogeny such a relationship may exist, since the progeny of EC labeled at E2 could be traced for 1-2 days at most. Here we report that, when E2 aortic ECs were infected prior to the formation of intra-aortic clusters with a nonreplicative LacZ-bearing retroviral vector, numerous cells were labeled in the para-aortic foci at E6. In contrast, when the retroviral vector was inoculated at E4 rather than E2, that is, after the disappearance of intra-aortic clusters, no cells in the para-aortic foci were labeled. Taken together, our results demonstrate that ECs from the aortic floor seed the two aspects of aorta-associated hemopoiesis and that these ECs with hemangioblastic potential are present only transiently in the aorta.

Animals↗
PubMed2000

Avian reticuloendotheliosis virus strain A and spleen necrosis virus do not infect human cells.

Spleen necrosis virus (SNV) and Reticuloendotheliosis virus strain A (REV-A) belong to the family of reticuloendotheliosis viruses and are 90% sequence related. SNV-derived retroviral vectors produced by the REV-A-based D17.2G packaging cell line were shown to infect human cells (H.-M. Koo, A. M. C. Brown, Y. Ron, and J. P. Dougherty, J. Virol. 65:4769-4776, 1991), while similar vectors produced by another SNV-based packaging cell line, DSH134G, are not infectious in human cells (reviewed by R. Dornburg, Gene Ther. 2:301-310, 1995). Here we describe a careful reevaluation of the infectivity of vectors produced from the most commonly used REV-A- or SNV-based packaging cells obtained from various sources with, among them, one batch of D17.2G packaging cells obtained from the American Type Culture Collection. None of these packaging cells produced vectors able to infect human cells. Thus, contrary to previously published data, we conclude that REV-based vectors are not infectious in human cells.

Cell Separation↗
PubMed1999

[Affiliation between endothelial and intra-embryonic hematopoietic stem cells].

We have investigated the developmental relationship of the hemopoietic and endothelial lineages in the floor of the chicken aorta, a site of hemopoietic progenitor emergence in the embryo proper. We show that, prior to the onset of hemopoiesis, the aortic endothelium uniformly expresses the endothelium-specific membrane receptor VEGF-R2. The onset of hemopoiesis can be precisely determined by detecting the common leukocyte antigen CD45. VEGF-R2 and CD45 are expressed in complementary fashion, namely the hemopoietic clusters in the floor of the aorta are CD45+/VEGF-R2-, while the rest of the aortic endothelium is CD45-/VEGF-R2+. To determine if the hemopoietic clusters are derived from EC, we tagged the E2 endothelial tree with a non-replicative retroviral vector and low density lipoproteins. Twenty four-48 hours later, labelled cells in the vascular tree were found to be either endothelial or hemopoietic but exceptionally both. Another 1-2 days later, groups of labelled cells appear in the dorsal mesentery within the hemopoietic "paraortic foci". Since no CD45+ cells were inserted among endothelial cells at the time of vascular labelling, hemopoietic clusters and foci must be concluded to derive from precursors with an endothelial phenotype.

Animals↗
PubMed1998

Blood-borne seeding by hematopoietic and endothelial precursors from the allantois.

Until now the allantois has not been considered as a hematopoietic organ. Here we report experimental evidence demonstrating the in situ emergence of both hematopoietic and endothelial precursors in the avian allantoic bud. When the prevascularized allantoic bud from a quail embryo was grafted in the coelom of a chicken host, hematopoietic and endothelial cells later were found in the bone marrow of the host. Because the graft was located at a distance from the limb bud, these cells could reach the bone marrow only by the circulatory pathway. This blood-borne seeding may be accomplished by distinct hematopoietic and endothelial precursors, or by hemangioblasts, the postulated common precursors of these two lineages; we consider the latter interpretation more likely. We also show by reverse transcription-PCR that the allantois region expresses very early the GATA genes involved in hematopoiesis and some beta-globin chain genes.

Allantois↗
PubMed1998

Intraaortic hemopoietic cells are derived from endothelial cells during ontogeny.

We have investigated the developmental relationship of the hemopoietic and endothelial lineages in the floor of the chicken aorta, a site of hemopoietic progenitor emergence in the embryo proper. We show that, prior to the onset of hemopoiesis, the aortic endothelium uniformly expresses the endothelium-specific membrane receptor VEGF-R2. The onset of hemopoiesis can be determined by detecting the common leukocyte antigen CD45. VEGF-R2 and CD45 are expressed in complementary fashion, namely the hemopoietic cluster-bearing floor of the aorta is CD45(+)/VEGF-R2(-), while the rest of the aortic endothelium is CD45(-)/VEGF-R2(+). To determine if the hemopoietic clusters are derived from endothelial cells, we tagged the E2 endothelial tree from the inside with low-density lipoproteins (LDL) coupled to DiI. 24 hours later, hemopoietic clusters were labelled by LDL. Since no CD45(+) cells were inserted among endothelial cells at the time of vascular labelling, hemopoietic clusters must be concluded to derive from precursors with an endothelial phenotype.

Animals↗
PubMed1996

Generation of small fusion genes carrying phleomycin resistance and Drosophila alcohol dehydrogenase reporter properties: their application in retroviral vectors.

We have used the Drosophila ADH cDNA to engineer new fusion genes carrying both reporter activity and bleomycin/phleomycin resistance (Sh ble). Cassettes of ADH::Sh ble, Sh ble::ADH, or ADH::Sh ble::ADH with or without polyadenylation signals were constructed. Placed under the control of the strong CMV promoter, these constructs induced intense ADH substrate staining and phleomycin resistance, whatever the position of the ADH gene, in avian or mammalian cell lines. SW-based nonreplicative retroviral vectors were constructed and introduced into the appropriate packaging cell line. Titers up to 10(6) ADH forming units/ml of viral supernatant were obtained except for the ADH::Sh ble::ADH construct, which reached 10(5) ADH forming units. These retroviral vectors were inoculated to the E3 chick embryo via the coelom. Three days later, cells from different organs were put in culture for 24 h and stained to detect ADH activity. A large number of positive cells were found in cultures from all organs. The new fusion genes described here are, to our knowledge, the smallest (1.1 kb) published to date that carry both reporter and drug resistance properties. These genes represent the basis of a new retroviral vector model with three distinct properties in two genetic units; their advantage is to reduce the size and increase the efficiency of the vector.

Alcohol Dehydrogenase↗
PubMed1994

Avian myeloblastic cell lines transformed by two nuclear oncoproteins, P135gag-myb-ets and p61/63myc: a model of retinoic acid-induced differentiation not abrogated by v-erbA.

We previously demonstrated that the retroviral construct MHE226 transducing both the P135gag-myb-ets and p61/63myc nuclear proteins induces solid hemopoietic tumors in early chicken embryos. In the present paper, we report the characterization of two MHE226-transformed cell lines established from such hemopoietic tumors retrieved from the heart of a 13-day embryo. Cytological analysis indicated a myeloblastic phenotype. These MHE226 cell lines were positive for the MEP17 monoclonal antibody but were negative for the myeloblast-specific 51/2 monoclonal antibody. MHE226 cell lines displayed a doubling time of about 20-24 h and were maintained for at least 1 year. Contrary to E26 myeloblastic cell lines, MHE226 cell lines were independent of chicken myelomonocytic growth factor and could be maintained in serum-free medium. MHE226 cell lines could be induced to differentiate toward the monocytic lineage by retinoic acid. Retinoic acid inhibited proliferation of MHE226 cell lines as early as day 1. After 3 days, MHE226 cells displayed cytological, enzymatic (alpha-naphthyl acetate esterase and chloroacetate esterase), and functional (phagocytosis) characteristics of monocytic cells. The retinoic acid-induced differentiation of MHE226 cells could not be inhibited by v-erbA. Thus, MHE226-transformed cell lines represent a novel model of cell transformation by two nuclear oncoproteins. Furthermore, they provide a model to study molecular mechanisms implicated in the monocytic differentiation program.

Animals↗
PubMed1993

Patterns of integration and expression of retroviral, non-replicative vectors in avian embryos: embryo developmental stage and virus subgroup envelope modulate tissue-tropism.

We previously demonstrated that Avian Leukemia Viruses (ALV) carrying the v-myc gene specifically induce two types of tumors, cardiomyocytic tumors when the virus is injected before embryonic day 3 (E3), skin tumors when the virus is injected at E3 or E5. Aiming to elucidate the mechanisms which determine this time-dependent change in target, we infected chick and quail embryos at E3 and E5 with replication-deficient, lacZ gene-carrying, ALV-based viruses produced by a packaging cell line. Three constructs driven by 3 different Long Terminal Repeats (LTRs) were tested and yielded similar results. When the constructs were inoculated at E3 and the lacZ gene product revealed 5 days later, around 70% of the embryos carried lacZ+ clones in the heart, around 50% had positive clones in the skin anywhere on the body, while a few embryos displayed clones in internal organs (liver, stomach, lungs). Immunocytological identification of the heart cell type(s) expressing the virus revealed that the only cells infected were cardiomyocytes. When the constructs were inoculated at E5, no lacZ+ clones appeared in the heart but all were located in the cephalic skin. In order to examine the relationship between viral integration and expression, DNA of different organs or tissues from lacZ stained embryos was analyzed by PCR. A tight correlation between integration and expression in the heart and in the skin was revealed in most cases. In contrast, a significant PCR signal was often detected in the liver or the stomach despite weak or absent expression as revealed by lacZ+ clones. We then investigated the influence of envelope glycoprotein subgroups on the tropism of these constructs. The lacZ vector driven by RAV-2 LTRs was packaged as subgroups A, B or E viral particles. The A subgroup, used in the part of the study described above, infects both chick and quail while the B and E subgroups are specific for chick or quail respectively. These B and E subgroups induced lacZ+ clones in the heart (after E3 injection) while no clones or only a few were detected in the skin either after E3 or E5 injection. The following conclusions can be drawn: 1) cardiomyocytes are at E3 the major target for integration and expression of ALV-derived viruses in vivo; 2) targets change rapidly with embryonic age; and 3) tissue-specific infections depend on the envelope subgroup, thus presumably on the presence of the cognate receptor.(ABSTRACT TRUNCATED AT 400 WORDS)

Alpharetrovirus↗