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Biomedical subjects

A Lefebvre

Publications and source records attributed to A Lefebvre.

At least 19 recordsLinked to original sources
PubMed2003

FORRepeats: detects repeats on entire chromosomes and between genomes.

MOTIVATION: As more and more whole genomes are available, there is a need for new methods to compare large sequences and transfer biological knowledge from annotated genomes to related new ones. BLAST is not suitable to compare multimegabase DNA sequences. MegaBLAST is designed to compare closely related large sequences. Some tools to detect repeats in large sequences have already been developed such as MUMmer or REPuter. They also have time or space restrictions. Moreover, in terms of applications, REPuter only computes repeats and MUMmer works better with related genomes. RESULTS: We present a heuristic method, named FORRepeats, which is based on a novel data structure called factor oracle. In the first step it detects exact repeats in large sequences. Then, in the second step, it computes approximate repeats and performs pairwise comparison. We compared its computational characteristics with BLAST and REPuter. Results demonstrate that it is fast and space economical. We show FORRepeats ability to perform intra-genomic comparison and to detect repeated DNA sequences in the complete genome of the model plant Arabidopsis thaliana.

Algorithms↗
PubMed2003

Interpretation of unexpected rocking curve asymmetry in LACBED patterns of semiconductors.

Transmission electron microscopy rocking curves diffracted from inclined planes in argon ion-thinned Si and III-V semiconductors display a significant asymmetry around the Bragg condition. Kinematical and dynamical calculations of the rocking curves show that such an asymmetry can be attributed to the dilation of coherent crystalline surface layers implanted with argon atoms. The surface layers are characterized with two parameters, their width h and the strain component epsilon (z) normal to the thin foil plane. The dark-field rocking curve asymmetry is shown, for sufficiently high values of h (> approximately 2 nm), to strongly depend on epsilon (z) which is directly related to the density of implanted argon atoms in the surface layers. Calculations also show that a significant rocking curve asymmetry is only observed for intermediate values of epsilon (z) of about a few percentage points.

Algorithms↗
PubMed2002

Moiré-like fringes in transmission electron microscopy images of coherently strained semiconductor islands.

Moiré-like fringes are observed in transmission electron microscopy images of coherently strained semiconductor islands. They are due to the misfit between the island and the underlying substrate and they can be used to determine the chemical composition of these islands by measuring the fringe spacing of the Moiré-like system. The results of a simple kinematical analysis are shown to be very similar to those of dynamical two-beam calculations. The interest of the kinematical analysis is that, contrary to the dynamical two-beam calculations, it makes it possible to understand how Moiré-like fringes are related to parallel Moiré fringes and how the fringe spacing is related to the strain field at the apex of the island, and then to the mean composition of the island.

Journal Article↗
PubMed2002

Cells under stress: a non-destructive evaluation of adhesion by ultrasounds.

The adhesion process plays a major role in the development of osteoblastic cells on various substrates used in orthopaedic applications such as metals, bioceramics, or glass. High frequency and low power ultrasounds seem to be an appropriate tool for an evaluation of interface mechanical properties. Is it a non-destructive method? We investigated osteoblastic cell cultures, maintained in their medium with high frequency, bulk longitudinal waves. The influence of both acoustical frequency and acoustical power on cell adhesion is evaluated by cell detachment ratio and re-adhesion ratio. We demonstrate the existence of a power threshold depending on the frequency, allowing optimal cellular detachment and re-adhesion. Finally, a qualitative study of the detachment phenomena is performed by use of scanning electron microscopy (SEM), Confocal Laser Scanning Microscopy and cytochemical labelling.

Acoustic Stimulation↗
PubMed2001

Low-energy measurement of the 7Be(p,gamma)8B cross section.

We have measured the cross section of the 7Be(p,gamma)8B reaction for E(c.m.) = 185.8, 134.7, and 111.7 keV using a radioactive 7Be target (132 mCi). Single and coincidence spectra of beta+ and alpha particles from 8B and 8Be* decay, respectively, were measured using a large acceptance spectrometer. The zero energy S factor inferred from these data is 18.5+/-2.4 eV b and a weighted mean value of 18.8+/-1.7 eV b (theoretical uncertainty included) is deduced when combining this value with our previous results at higher energies.

Journal Article↗
PubMed2001

LACBED measurement of the chemical composition of a thin In(x)Ga(1-x)As layer buried in a GaAs matrix.

Large angle convergent beam electron diffraction (LACBED) observations are used to determine the x indium content of a thin In(x)Ga(1-x)As quantum well buried in a GaAs matrix. The method consists in a quantitative analysis of the Bragg line intensities lying in the central disc of any LACBED pattern. This analysis makes it possible to determine the displacement vector R introduced, between the two parts of the GaAs matrix, by the deformation of the quantum well and consequently to determine the x indium content. This indium content is found to be consistent with the value expected from the molecular beam epitaxy growth conditions.

Journal Article↗
PubMed2000

Control of CYP11B2 gene expression through differential regulation of its promoter by atypical and conventional protein kinase C isoforms.

We reported previously that the protein kinase C (PKC) inhibitor GF109203X stimulated the hamster CYP11B2 promoter activity in transfected NCI-H295 cells. PKCalpha, -epsilon, and -zeta were detected in hamster adrenal zona glomerulosa and NCI-H295 cells, and PKCtheta in NCI-H295 cells. 12-O-Tetradecanoylphorbol-13-acetate (TPA) inhibited basal and stimulated cytochrome P450 aldosterone synthase mRNA expression by angiotensin (AII), dibutyryl cyclic adenosine 3':5'-monophosphate (Bt2cAMP), or KCl in NCI-H295 cells. Basal CYP11B2 promoter activity was inhibited in cells cotransfected with constitutively active (CA) PKCalpha, -epsilon, and -theta mutants, whereas it was increased with CA-PKCzeta. Dominant negative (DN) PKCalpha, -theta, -epsilon, and -zeta mutants stimulated the promoter activity. AII-, KCl-, and Bt2cAMP-stimulatory effects were abolished in cells cotransfected with CA-PKCalpha, -epsilon, or -theta. The effect of Bt2cAMP was abolished by CA-PKCzeta but AII and KCl were still able to enhance the promoter activity. DN-PKCalpha, -epsilon, -theta, or -zeta did not inhibit these effects. Gö6976 enhanced promoter activity, providing further evidence that PKCalpha was involved. Various CYP11B2 promoter constructs were used to identify the area associated with TPA and PKC inhibition. TPA and CA-PKCalpha, -epsilon, or -theta abolished the effects of AII, KCl, and Bt2cAMP on the activity of -102 and longer constructs. In summary, our findings suggest that the hamster CYP11B2 gene is under differential control by conventional (alpha) and atypical (zeta) PKC.

Animals↗
PubMed2000

Regulation of CYP11B2 gene expression by protein kinase C.

Bisindolylmaleimide, a protein kinase C (PKC) inhibitor, was shown to stimulate the hamster CYP11B2 promoter activity in transfected NCI-H295 cells. In this study we have found that TPA, an activator of PKC, also inhibited the hamster CYP11B2 promoter activity. DAG-dependent PKC alpha and PKC epsilon, and atypical PKC zeta were detected in hamster adrenal zona glomerulosa, whereas the isoforms alpha, epsilon, zeta and theta were found in NCI-H295 cells. CYP11B2 promoter activity was inhibited in cells co-transfected with constitutively active PKC alpha and epsilon mutants, whereas it was increased with the constitutively active PKC zeta mutant. Dominant negative PKC alpha, epsilon and zeta mutants stimulated the promoter activity. Gö6976, a specific inhibitor of classical PKCs, enhanced promoter activity, providing further evidence that PKC alpha, the only classical PKC revealed in hamster adrenal and NCI-H295 cells, was involved in the promoter inhibition.

Adrenal Glands↗
PubMed1999

[Health status and its effects on the work of national education nurses].

This study presents a pedagogical work carried out with a group of 13 school nurses of the Academy of Rennes, as part of a course in survey methodology. A descriptive survey aiming to achieve a better understanding of experienced health status of nurses, and of its repercussions on the execution of their missions, was implemented during the course, as a result of the demand and the expertise of the participants. Overall, nurses report to be in good health. However, one can not underestimate the existence of a group at risk (5% of the sample) that often suffers somatic troubles accompanied by sleep disorders and anxiety, as these risks concern primarily permanent staff nurses working in boarding establishments, with half of them falling into this category. A demand for regular monitoring of their health was clearly expressed through the study. This may be the object of a subsequent study by an academic team.

Absenteeism↗
PubMed1998

Transcriptional activity of the hamster CYP11B2 promoter in NCI-H295 cells stimulated by angiotensin II, potassium, forskolin and bisindolylmaleimide.

We studied the regulation of the hamster CYP11B2 gene in the NCI-H295 cell line, which is known to produce aldosterone in response to stimulation by angiotensin II (AII) and KCl. Ten deletion plasmids harboring the 5'-untranslated region of the CYP11B2 gene were used for chloramphenicol acetyltransferase (CAT) assays. Transient transfections showed progressively increasing basal promoter activity by constructs beyond the TATA box, with a peak occurring with the -167 bp construct which contains putative Adl, Ad2, Ad5 and the newly reported -143/-161 cis-element sequences. The promoter activity was lower with the construct containing the putative Ad3 cis-element and increased with longer constructs. This indicates the presence of both inhibitory and stimulatory cis-elements in this area of the gene. Expression of the reporter gene of all constructs was stimulated by AII and KCl, with the exception of the construct containing only the TATA box, which showed 6-fold and 10-fold increases occurring with the -167 bp deletion plasmid. The patterns of increase in CAT activity with AII and KCI treatment were similar, showing that these two regulators can stimulate hamster CYP11B2 promoter activity through common cis-elements. The calcium channel antagonist nifedipine blocked the stimulatory effects of KCl on CAT activity, showing the involvement of calcium channels in the regulation of CYP11B2 gene transcription by KCl. 12-O-Tetradecanoylphorbol 13-acetate, a known stimulator of the protein kinase C (PKC) signaling pathway, was without significant effect on CAT activity. Bisindolylmaleimide, a specific inhibitor of PKC, had a significant enhancing effect (3.4- to 6-fold), indicating that PKC may negatively regulate the expression of the hamster CYP11B2 gene in NCI-H295 cells. A mutation was induced in the sequence -143/-161 of the - 350 bp construct in order to determine its importance in the regulation of hamster CYP11B2 promoter activity. The stimulatory effects of AII, KCl, forskolin and bisindolylmaleimide on CAT activity were significantly less in the mutant than in the wild type. These results confirm that this cis-element is necessary in maintaining a high level of transcriptional activity in stimulated NCI-295H cells. In conclusion, using NCI-295H transfected cells, we have found that the 5'-untranslated region of the hamster CYP11B2 gene possesses transcriptional activity with stimulatory and also inhibitory cis-elements; CYP11B2 promoter activity can be stimulated by AII, KCl, forskolin, dibutyryl cAMP and bisindolylmaleimide. Our results suggest that this gene is positively regulated through the protein kinase A signaling pathway and through calcium channels, whereas PKC may have a negative regulatory effect upon the transcription of the CYP11B2 gene. Furthermore, we have shown that the cis-element -143/-161 in the 5'-untranslated region of the hamster CYP11B2 gene is important in maintaining a high level of promoter activity in stimulated NCI-295H cells.

Aldosterone↗
PubMed1997

Sensitivity of NMR internucleotide distances to B-DNA conformation: underlying mechanics.

Nuclear magnetic resonance (NMR) spectroscopy, combining correlated spectroscopy (COSY) coupling constant measurements with nuclear Overhauser effect spectroscopy (NOESY) interatomic distances, should make it possible to determine an averaged solution structure for DNA oligomers. However, even if such data could be obtained with high accuracy, it is not clear which structural parameters of DNA would be determined. Here, the relationships between measurable internucleotide distances and helical parameters are systematically studied through molecular modelling. Investigations are carried out using four representative sequences, (ACGT)n, (TCGA)n, (AGCT)n and (TGCA)n, composed of repeated tetranucleotides belonging to oligomers previously studied by NMR. Correlations between interatomic distances become evident and strong connections between distances and inter-base helical parameters are observed. Results imply that twist, roll, shift and slide values can be accurately determined from NMR data. Sequence independent mechanical coupling which link backbone and sugar conformations to helical twist are also described.

Base Sequence↗
PubMed1997

Characterization of the hamster CYP11B2 gene encoding adrenal cytochrome P450 aldosterone synthase.

A CYP11B2 gene encoding cytochrome P450 aldosterone synthase (P450aldo) was isolated from a hamster genomic library. The gene, which contained 9 exons, was composed of 9,045 bp, of which 3,722 bp were located in the 5' untranslated region (5' UTR). A TATA box sequence (gataaa) and other putative cis elements, previously named Ad1 to Ad6, were identified in the 5' UTR of the hamster gene comparable to the CYP11B2 gene of other animal species. Footprint analysis showed protection by nuclear protein extracts from hamster adrenal zona glomerulosa (ZG) in the regions containing the above mentioned cis elements. In addition, a new protected cis element, between -143 and -161 bp, was demonstrated, and gel-shift assays revealed that the sequence of this new cis element was specifically retarded by factors in the nuclear extracts of hamster adrenal ZG. We then examined the transcriptional activity of the 5' UTR of the CYP11B2 gene, using chloramphenicol acyltransferase (CAT) as the reporter gene. Ten deletion plasmids were constructed using a modified pCAT vector. Transient transfections of the chimeric reporter constructs into Y1 cells showed that the highest basal promoter activity was obtained with the construct containing up to -134 bp. Increasing the length of the regulatory region of CYP11B2 gene to -167 bp resulted in less than two-thirds of the maximal activity, indicating the probability of putative inhibitory cis elements in this area of the gene. Forskolin stimulated the expression of the reporter gene of deletion plasmids excepting the construct containing only the TATA box, and the highest activity also occurred with the -134 bp construct. TPA had no stimulatory effects on any of the constructs, and interestingly it slightly inhibited CAT activity. In contrast to TPA, staurosporine, an inhibitor of the PKC pathway, stimulated CAT activity. To conclude, the promoter region of the hamster CYP11B2 gene transfected in Y1 cells is responsive to forskolin, indicating that the gene is controlled by the PKA signaling pathway. Paradoxically, staurosporine, but not TPA, stimulates the promoter activity of the CYP11B2 gene, indicating that PKC might, at least in Y1 cells, act as a negative regulator on the aldosterone synthase promoter. Moreover, a new cis element was shown to exert a negative effect on basal as well as on stimulated activities of the hamster promoter CYP11B2 gene.

Animals↗
PubMed1996

Solution structure of the CpG containing d(CTTCGAAG)2 oligonucleotide: NMR data and energy calculations are compatible with a BI/BII equilibrium at CpG.

We report the analysis of the solution structure of the DNA duplex d(CTTCGAAG)2 compared to that of d(CATCGATG)2, the two oligonucleotides being related by the permutation of residues 2 and 7. An earlier study has demonstrated the malleability of CpG in the tetrad TCGA of d(CATCGATG)2 [Lefebvre et al. (1995) Biochemistry 34, 12019-12028]. Conformations of d(CTTCGAAG)2 were evaluated by (a) two-dimensional NMR, including proton and phosphorus experiments, (b) adiabatic mapping of the conformational space, (c) restrained molecular mechanics undertaken with sugar phase angle, epsilon-zeta difference angle, and NOE distances as input, and (d) back-calculation-refinement against NOE spectra at various mixing times. d(CTTCGAAG)2 like d(CATCGATG)2 exhibits a B-DNA conformation. However, significant differences are noted between the two oligonucleotides, extending up to the central CpG step, although this step resides in the same TCGA tetrad in both sequences. In structures obtained with refined NMR data, CpG adopts, for instance, a greater twist and a higher guanine phase within d(CTTCGAAG)2 compared to d(CATCGATG)2. In the former oligonucleotide, the structure of CpG resembles strikingly that found in the ACGT tetrad of the cAMP responsive element [Mauffret et al. (1992) J. Mol. Biol. 227, 852-875]. Moreover, two conformers with CpG either in the BII state (epsilon, zeta = g-, t) or in the BI state (epsilon, zeta = t, g-) are found equally stable for d(CTTCGAAG)2. The energy barrier from BI to BII comes to only 5.7 kcal/mol, and the path of the transition is very short. When calculations on d(CTTCGAAG)2 are performed taking the BI/BII equilibrium into account, the agreement with both the 1H and 31P data is found better than in the case with a single conformation taken alone. The BI/BII equilibrium may also occur in d(CATCGATG)2, but the amount of BII conformer is now found weaker compared to its analogue. The ability of the CpG phosphate groups to adopt the BII conformation could provide a satisfying explanation for the high mutation rates observed at these sites.

CpG Islands↗
PubMed1996

The hamster adrenal cytochrome P450C11 has equipotent 11beta-hydroxylase and 19-hydroxylase activities, but no aldosterone synthase activity.

We have isolated a hamster adrenal P45OC11 cDNA which shared 90 and 84% homology, respectively, with the nucleotide sequence and the amino acid sequence of the hamster adrenal P450aldo. Both P450C11 and P450aldo cDNA coding sequences were inserted in the plasmid pBluescript SK, transcribed and then translated using a rabbit reticulocyte system in the presence of [35S]methionine. The reaction products were immunoprecipitated with an anti-bovine P450C11 antibody for P450C11 and with an anti-hamster P450aldo for P450aldo. Immunoprecipitated proteins were analyzed by polyacrylamide gel electrophoresis. A single 35S-labeled protein band was detected for P450C11 and for P450aldo, respectively. P450C11 and P450aldo cDNAs were then both inserted into the expression vector pCMV5 containing a viral sequence specific for the attachment of ribosomes to mRNA. These constructions were transfected in COS-1 cells. 24 h after transfection, the presence of P450C11 and P450aldo mRNAs was determined by Northern blot analysis. In a time study experiment we found that P450C11 transformed the labeled-steroid into [14C]corticosterone, [14C]19-OH-deoxycorticosterone and [14C]18-OH-deoxycorticosterone in ratios of 1:1.11:0.07, after 2 h of incubation; no [14C]aldosterone could be detected. Cells transfected with plasmids harboring the P450aldo cDNA transformed [14C]deoxycorticosterone to [14C]corticosterone, [14C]aldosterone, [14C]18-OH-corticosterone, [14C]18-OH-deoxycorticosterone, [14C]19-OH-deoxycorticosterone and [14C]11-dehydrocorticosterone in ratios of 1:0.25:0.45:0.04:0.04:0.04 after 12 h of incubation. These results indicate that one P450 catalyzes the ultimate step of glucocorticoid formation and a separate P450 is involved in the final steps of aldosterone formation in hamster adrenals. The capacity of the hamster adrenal P450C11 to hydroxylate at positions 11beta and 19 in nearly equal ratio makes this animal an excellent model to study the mechanism of synthesis and inhibition of 19-OH-deoxycorticosterone, the precursor of 19-nor-deoxycorticosterone, a very potent mineralocorticoid involved in the development of essential hypertension.

Adrenal Glands↗
PubMed1996

Adrenocorticotropin regulates the level of the steroidogenic acute regulatory (StAR) protein mRNA in hamster adrenals.

In this study, we report the cloning of a StAR cDNA from a hamster adrenal cDNA library. The library was screened using a PCR fragment specific for the hamster adrenal StAR cDNA. Several clones of different lengths were obtained and one of these was sequenced. Northern blotting analysis revealed the presence of the StAR mRNA in male and female adrenals, in tests and ovaries, but not in the liver or kidneys of either sex. Whole hamster adrenals revealed the presence of four mRNAs of 0.65, 1.7, 3.1 and 5.25 kb, respectively. In addition, ACTH regulates the expression of StAR mRNA in hamster adrenals. Indeed, when groups of hamsters were injected with ACTH and sacrificed at different times after treatment, only the 0.65 kb form of the StAR mRNA did not increase, whereas the other forms increased at varying levels. These results might suggest that the expression of the StAR protein in hamster adrenals depends upon different genes, different promoters, or different polyadenylation signal sites. In conclusion, these results indicate that in vivo, StAR is regulated by ACTH, suggesting the participation of this protein in controlling the transformation of cholesterol to pregnenolone, a key regulatory step in corticosteroidogenesis.

Adrenal Glands↗
PubMed1996

Characterization of the hamster CYP11B2 gene regulatory regions.

We have isolated a hamster CYP11B2 gene encoding the cytochrome P450 aldosterone synthase. In comparison with the CYP11B2 gene of other species, cis-elements named Ad1, Ad2, Ad3, and Ad4, were identified in the 5'-untranslated region of the hamster gene. Mouse adrenal tumor cells were transiently transfected with chimaeric reporter constructs, fused to the bacterial chloramphenicol acyltransferase (CAT) reporter gene, to study the regulation of expression of the hamster CYP11B2 gene. The highest basal expression was obtained with the -130 bp construct. Decreasing the length of the regulatory region of the CYP11B2 gene beyond that of -130 bp, to exclude Ad2 and Ad1 elements, resulted in successive decreases in CAT activity. Increasing the length of the regulatory region beyond that of -130 bp also resulted in a reduction of CAT activity, indicating the presence of inhibitory cis-elements in this area of the gene. Forskolin stimulated the CAT activity of all constructs, the highest of which occurred with the -130 bp construct, indicating that the gene is controlled by the PKA signalling pathway. TPA, however, had no stimulatory effects on any of these constructs. Staurosporine, an inhibitor of the PKC pathway, stimulated cells transfected with the different constructs in a similar manner as forskolin, indicating that PKC might act, at least in Y-1 cells, as a negative regulator on the hamster CYP11B2 promoter.

Adrenal Cortex Neoplasms↗
PubMed1996

Some effects of a low sodium intake on the expression of P450 aldosterone synthase in the hamster adrenal cortex: immunoblotting, immunofluorescent and immuno-gold electron microscopic studies.

In the current work we studied the effects of a low sodium intake on P450 aldosterone synthase (P450aldo) in the adrenal cortex of male hamsters by Western blotting analysis. We also investigated the zonal distribution of P450aldo with a specific antibody using immunofluorescence and immuno-gold electron microscopy. Western blotting analysis revealed a progressive induction of P450aldo in the adrenals of hamsters kept on a low sodium diet, with two-, four- and eightfold increases after 2, 4 and 21 days on the diet. Immunofluorescence microscopy showed that P450aldo was confined to the zona glomerulosa (ZG) cells. Electron microscopy showed P450aldo to be located in the mitochondria of ZG cells. When hamsters were maintained on a low sodium intake for 2, 11 and 21 days, P450aldo was still found only in the ZG; the ZG appeared either unchanged or sometimes slightly enlarged. Moreover, at days 11 and 21, the intensity of the immunofluorescent signal was much stronger in the ZG of hamsters on the low sodium intake than in controls. Hence, immunocytochemistry using the colloidal-gold technique showed P450aldo to be more abundant in the mitochondria of the experimental animals than in controls. To conclude, P450aldo is present only in the ZG of hamster adrenals and sodium restriction appears to induce its expression by stimulating production within individual ZG cells rather than by stimulating a proliferation of the ZG cells.

Adrenal Cortex↗