Biomedical subjects
Publications and source records attributed to Olivier Bastien.
Cardiac resynchronization therapy improves symptoms and survival in chronic heart failure patients, but has been poorly studied in the acute heart failure setting. We report the case of successful cardiac resynchronization therapy in the early postoperative period after cardiac surgery in a patient with left bundle branch block and proven ventricular dyssynchrony.
The organization and mining of malaria genomic and post-genomic data is important to significantly increase the knowledge of the biology of its causative agents, and is motivated, on a longer term, by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should, therefore, be as reliable and versatile as possible. In this context, five aspects of the organization and mining of malaria genomic and post-genomic data were examined: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes, particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Recent progress towards a grid-enabled chemogenomic knowledge space is discussed.
A fast, reliable capillary zone electrophoresis (CZE) method with indirect UV detection was optimized and validated to determine the main organic acids contained in plants. Citric, malic, succinic, oxalic, formic, fumaric, acetic acids, and phosphate were quantified. A rapid separation while keeping a good resolution was obtained by optimizing capillary length, separation voltage, electrolyte composition, and pH. Analyses were performed in a 30 cm uncoated fused-silica capillary (length to the detector window) in the co-electroosmotic mode with reversed electroosmotic flow and anodic detection using a -30 kV separation voltage. The pH 9.0 electrolyte contained 3 x 10(-4)mol/L tetradecyltrimethylammonium and 10(-2)mol/L trimellitate. Separation with baseline return was achieved in 100 s. Linearity, detection limits, repeatability, reproducibility, and recoveries were evaluated. Mean precision values of 0.2 and 3.4% for migration times and time-corrected peak areas, respectively, enabled accurate identification and quantification whether in standard solutions or in samples. Such performances were perfectly adapted to high-throughput routine determinations of organic acids in research or industry. Organic acids were assayed in different plant tissues and cells, including sycamore, arabidopsis, buttercup, and pea. Citrate and malate were the most abundant in all plants tested with concentrations reaching 18.9 and 22.3 micromol/g fresh matter, respectively. Cadmium effect on pea leaves metabolism was also assessed.
BACKGROUND: The aim of this study was to assess the influence of IL-10 and TGFbeta1 gene polymorphisms on the development of acute rejection and coronary disease in pediatric heart transplant recipients. METHODS: Patients were classified as either Rejectors or Nonrejectors. Coronary artery disease (CAD) was diagnosed by angiography or on macroscopic examination. Genotyping PCR-SSP were performed for IL-10 and TGFbeta1 (codon 10 and 25) in 111 patients. Thirty-nine were Rejectors and 31 developed CAD. RESULTS: The proportion of IL-10 low-producers was higher in Rejectors than in Nonrejectors (respectively 46% versus 22%, P=0.009). IL-10 gene polymorphism was not associated with CAD. TGFbeta1-codon10-25 high-producers were 92.3% in Rejectors and 75% in Nonrejectors (P=0.026), 93.5% in patients with CAD and 76.2% in patients free from CAD (P=0.037). TGFbeta1-codon25 high-production separately analyzed correlated with CAD (31/31 high-producers in CAD=100% versus 69/80 in noCAD patients=86.2%, P=0.03). TGFbeta1-codon10 gene polymorphisms were not associated with CAD. CONCLUSION: IL-10 low-producers have an increased risk of acute rejection. High-expressors of TGFbeta1-codon10-25 have an increased risk of acute rejection and CAD, while TGFbeta1-codon25 high-production is associated with coronary disease. Genetic polymorphism may reveal patients at high-risk in whom therapies and monitoring should be adjusted.
Toxoplasma gondii is an obligate intracellular parasite that contains a relic plastid, called the apicoplast, deriving from a secondary endosymbiosis with an ancestral alga. Metabolic labelling experiments using [14C]acetate led to a substantial production of numerous glycero- and sphingo-lipid classes in extracellular tachyzoites. Syntheses of all these lipids were affected by the herbicide haloxyfop, demonstrating that their de novo syntheses necessarily required a functional apicoplast fatty acid synthase II. The complex metabolic profiles obtained and a census of glycerolipid metabolism gene candidates indicate that synthesis is probably scattered in the apicoplast membranes [possibly for PA (phosphatidic acid), DGDG (digalactosyldiacylglycerol) and PG (phosphatidylglycerol)], the endoplasmic reticulum (for major phospholipid classes and ceramides) and mitochondria (for PA, PG and cardiolipid). Based on a bioinformatic analysis, it is proposed that apicoplast produced acyl-ACP (where ACP is acyl-carrier protein) is transferred to glycerol-3-phosphate for apicoplast glycerolipid synthesis. Acyl-ACP is also probably transported outside the apicoplast stroma and irreversibly converted into acyl-CoA. In the endoplasmic reticulum, acyl-CoA may not be transferred to a three-carbon backbone by an enzyme similar to the cytosolic plant glycerol-3-phosphate acyltransferase, but rather by a dual glycerol-3-phosphate/dihydroxyacetone-3-phosphate acyltransferase like in animal and yeast cells. We further showed that intracellular parasites could also synthesize most of their lipids from scavenged host cell precursors. The observed appearance of glycerolipids specific to either the de novo pathway in extracellular parasites (unknown glycerolipid 1 and the plant like DGDG), or the intracellular stages (unknown glycerolipid 8), may explain the necessary coexistence of both de novo parasitic acyl-lipid synthesis and recycling of host cell compounds.
To get more insight into plant cell response to cadmium (Cd) stress, both proteomic and metabolomic "differential display" analyses were performed on Arabidopsis thaliana cells exposed to different concentrations of the toxic chemical. After a 24 h treatment, soluble proteins extracted from untreated and treated cells were separated by 2-D-PAGE and image analyses were performed to quantify and compare protein levels. Proteins up- and down-regulated in response to Cd were identified by MS and mapped into specific metabolic pathways and cellular processes, highlighting probable activation of the carbon, nitrogen, and sulfur metabolic pathways. For some of these proteins, Northern blot and RT-PCR analyses were performed to test transcript accumulation in response to Cd. In parallel, metabolite profiling analyses by LC coupled to ESI MS were initiated to better characterize the metabolic adaptation to the chemical stress. This study revealed that the main variation at the metabolite level came from the presence of six different families of phytochelatins, in A. thaliana cells treated with Cd, whose accumulation increases with Cd concentrations. Taken together these data provide an overview of the molecular and cellular changes elicited by Cd exposure.
BACKGROUND: Left ventricular stroke area by transoesophageal echocardiographic automated border detection has been shown to be strongly correlated to left ventricular stroke volume. Respiratory variations in left ventricular stroke volume or its surrogates are good predictors of fluid responsiveness in mechanically ventilated patients. We hypothesised that respiratory variations in left ventricular stroke area (DeltaSA) can predict fluid responsiveness. METHODS: Eighteen mechanically ventilated patients undergoing coronary artery bypass grafting were studied immediately after induction of anaesthesia. Stroke area was measured on a beat-to-beat basis using transoesophageal echocardiographic automated border detection. Haemodynamic and echocardiographic data were measured at baseline and after volume expansion induced by a passive leg raising manoeuvre. Responders to passive leg raising manoeuvre were defined as patients presenting a more than 15% increase in cardiac output. RESULTS: Cardiac output increased significantly in response to volume expansion induced by passive leg raising (from 2.16 +/- 0.79 litres per minute to 2.78 +/- 1.08 litres per minute; p < 0.01). DeltaSA decreased significantly in response to volume expansion (from 17% +/- 7% to 8% +/- 6%; p < 0.01). DeltaSA was higher in responders than in non-responders (20% +/- 5% versus 10% +/- 5%; p < 0.01). A cutoff DeltaSA value of 16% allowed fluid responsiveness prediction with a sensitivity of 92% and a specificity of 83%. DeltaSA at baseline was related to the percentage increase in cardiac output in response to volume expansion (r = 0.53, p < 0.01). CONCLUSION: DeltaSA by transoesophageal echocardiographic automated border detection is sensitive to changes in preload, can predict fluid responsiveness, and can quantify the effects of volume expansion on cardiac output. It has potential clinical applications.
Monogalactosyldiacylglycerol (MGDG), the major lipid of plant and algal plastids, is synthesized by MGD (or MGDG synthase), a dimeric and membrane-bound glycosyltransferase of the plastid envelope that catalyzes the transfer of a galactosyl group from a UDP-galactose donor onto a diacylglycerol acceptor. Although this enzyme is essential for biogenesis, and therefore an interesting target for herbicide design, no structural information is available. MGD monomers share sequence similarity with MURG, a bacterial glycosyltransferase catalyzing the transfer of N-acetyl-glucosamine on Lipid 1. Using the x-ray structure of Escherichia coli MURG as a template, we computed a model for the fold of Spinacia oleracea MGD. This structural prediction was supported by site-directed mutagenesis analyses. The predicted monomer architecture is a double Rossmann fold. The binding site for UDP-galactose was predicted in the cleft separating the two Rossmann folds. Two short segments of MGD (beta2-alpha2 and beta6-beta7 loops) have no counterparts in MURG, and their structure could not be determined. Combining the obtained model with phylogenetic and biochemical information, we collected evidence supporting the beta2-alpha2 loop in the N-domain as likely to be involved in diacylglycerol binding. Additionally, the monotopic insertion of MGD in one membrane leaflet of the plastid envelope occurs very likely at the level of hydrophobic amino acids of the N-terminal domain.
BACKGROUND: Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction. RESULTS: We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space) and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP) allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. CONCLUSION: The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.
Results from a French multicentre survey on the use of inotropes after cardiac surgery are presented. Consideration of these findings, which strictly apply only to France, highlights the importance of developing monitoring strategies to help in decision making regarding therapy with inotropes in this context.
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Automatic comparison of compositionally biased genomes, such as that of the malarial causative agent Plasmodium falciparum (82% adenosine + thymidine), with genomes of average composition, is currently limited. Indeed, popular tools such as BLAST require that amino acid distributions be similar in aligned sequences. However, the P. falciparum genome is so biased that six amino acids account for more than 50% of the protein composition. One reason for the comparison methods failure lies in the compositional difference between the query and the subject proteomes, which is not taken into account in the amino acid substitution matrices. This paper introduces a method to derive substitution matrices, in particular BLOSUM 62, in the frame of the information theory. It allows the construction of non-symmetrical matrices, taking into account the non-symmetric amino acid distributions. The dirAtPf family of matrices allowing the comparison of P. falciparum and A. thaliana is given as an example. This paper further provides an analysis of the obtained matrices in the frame of the information theory, supporting the discrimination advantage they bring.
OBJECTIVE: Many changes have occurred in the natural history and the management of active infectious endocarditis (AIE) in recent years. Therefore, the records of patients admitted in a tertiary care specialized hospital presenting with the Duke criteria were reviewed. METHODS: Adults operated on to treat AIE were included during a 3-year period. Patients presenting with AIE associated with a pacemaker were not included. Bacteriologic investigations included blood cultures, intraoperative samplings (including polymerase chain reaction), and serologies. Clinical and bacteriologic factors associated with hospital mortality were studied by univariate regression analysis (p < 0.05). RESULTS: Ninety-eight of 164 patients (60%) admitted with the diagnosis of AIE underwent valvular surgery. The duration between the beginning of AIE and surgery was 23 +/- 16 (mean +/- standard deviation) days. Only 45 patients had a previous history of valvular disease. Seventy-two patients presented with aortic and 41 with mitral valve AIE. Fifty suffered from embolic events. Streptococcus species were responsible in 64 cases (23 were Streptococcus bovis) and Staphylococcus species in 24 cases. Death occurred postoperatively in 19 patients. The factors associated with fatal outcome were preoperative hemodynamic instability, age, Parsonnet and Simplified Acute Physiology Score II scores, diabetes mellitus, preexisting valvulopathy, antiarrhythmic treatment, hypoalbuminemia, renal dysfunction, duration of extracorporeal circulation, and red cell allogeneic transfusions. The type of bacteria did not influence mortality. The mean intensive care unit and hospital stays were 10 and 39 days, respectively. Eleven patients suffered from neurologic sequelae; 2 years later, 2 of them presented with severe deficit and 1 had died. CONCLUSIONS: AIE necessitating cardiac surgery should be considered as a severe and resource-consuming disease.
Comparative genomic analysis of the malaria causative agent, Plasmodium falciparum, with other eukaryotes for which the complete genome is available, revealed that the genome from P. falciparum was more similar to the genome of a plant, Arabidopsis thaliana, than to other non-apicomplexan taxa. Plant-like sequences are thought to result from horizontal gene transfers after a secondary endosymbiosis involving an algal ancestor. The use of the A. thaliana genome and proteome as a reference gives an opportunity to refine our understanding of the extreme compositional bias in the P. falciparum genome that leads to a proteome-wide amino acid bias. A set of pairs of non-redundant protein homologues was selected owing to rigorous genome-wide sequence comparison methods. The introduction of A. thaliana as a reference was a mean to weight the magnitude of the protein evolutionary divergence in P. falciparum. The correlation of the amino acid proportions with evolutionary time supports the hypothesis that amino acids encoded by GC-rich codons are directionally substituted into amino acids encoded by AT-rich codons in the P. falciparum proteome. The long-term deviation of codons in malarial sequences appears as a possible consequence of a genome-wide tri-nucleotidic signature imprinting. Additionally, this study suggests possible working guidelines to improve the accuracy of P. falciparum sequence comparisons, for homology searches and phylogenetic studies.
OBJECTIVE: The objective of the study was to perform a descriptive approach of the current use of catecholamines by French physicians. DESIGN: A questionnaire of 12 questions with 4 items established by a group of French intensivists. POPULATION: French physicians from 433 departments working in the following practicing areas: intensive care unit (ICU), emergency department, and pre-hospital setting. MEASUREMENTS: Responding physicians were asked about the catecholamine that they would select in various clinical settings. RESULTS: The response rate was 82%. Of the responding physicians, 277 (78%) worked in an ICU, 28 (8%) in an emergency department, and 21 (6%) in a pre-hospital setting. Dobutamine was chosen for patients with cardiogenic shock by 90% of the respondents. Norepinephrine was the first choice agent as vasopressor in patients with septic shock in 52% of the cases. Dopamine was selected in a clinical setting requiring an optimization of regional blood flow, as in the concept of high-risk surgical patients. Dopexamine was used as a second or third choice agent to improve regional blood flow and cardiac output. The indications of epinephrine for anaphylactic shock and cardio-circulatory arrest were obvious for more than 90% of responding physicians. CONCLUSION: A lack of standardization appears in the use of catecholamines by French physicians, particularly for improvement of regional circulation and management of high-risk surgical patients. Guidelines that define the place of each catecholamine in these settings are required to improve the quality of prescription.
MOTIVATION: Different automatic methods of sequence alignments are routinely used as a starting point for homology searches and function inference. Confidence in an alignment probability is one of the major fundamentals of massive automatic genome-scale pairwise comparisons, for clustering of putative orthologs and paralogs, sequenced genome annotation or multiple-genomic tree constructions. Extreme value distribution based on the Karlin-Altschul model, usually advised for large-scale comparisons are not always valid, particularly in the case of comparisons of non-biased with nucleotide-biased genomes (such that of Plasmodium falciparum). Z-values estimates based on Monte Carlo technics, can be calculated experimentally for any alignment output, whatever the method used. Empirically, a Z-value higher than approximately 8 is supposed reasonable to assess that an alignment score is significant, but this arbitrary figure was never theoretically justified. RESULTS: In this paper, we used the Bienaymé-Chebyshev inequality to demonstrate a theorem of the upper limit of an alignment score probability (or P-value). This theorem implies that a computed Z-value is a statistical test, a single-linkage clustering criterion and that 1/Z-value(2) is an upper limit to the probability of an alignment score whatever the actual probability law is. Therefore, this study provides the missing theoretical link between a Z-value cut-off used for an automatic clustering of putative orthologs and/or paralogs, and the corresponding statistical risk in such genome-scale comparisons (using non-biased or biased genomes).
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Since the first case in 1987, 159 patients underwent heart mechanical assist device as a bridge to transplantation or as potential post transplanted recovery (right ventricular failure or graft failure) or in case of unsuccessful weaning of cardiopulmonary bypass. Survival rate of patients under assist device waiting either for heart transplantation or for functional recovery was 75.4%. 67.7% of them were transplanted (1 year survival rate 63%). Improvement of cardiac assist device technology and new method of intensive care allowed the observation of 6 myocardial recovery without transplantation 4 after more than 3 weeks of cardiac support. The increase in cardiac assist duration (mean duration = 103 days in 2001) because of organ shortage, led to a change in patients medical care. Unexpected interactions between cardiac treatments and anaesthetic drugs should lead anaesthetists to a better understanding of the failing heart pathophysiology. Consequently, anaesthetists well conduct appropriately anaesthesia and perioperative monitoring. Technical and conceptual evolution should allow some patient, to come back home and to fully recover without the need of transplantation.