23 research outputs found
An objective reduction technique of proteomic mass spectra based on multi-scale fuzzy thresholding
A proteomic approach offers a powerful and complementary tool to genomics. It allows to index and characterize
proteins, and, for example, to compare their levels of expression between healthy and pathological states. Proteomic
analyses are mainly based on the separation of proteins by two-dimensional gel electrophoresis and their subsequent
identification by comparing the data from Mass Spectrometry (SM) analyses to the theoretical ones contained in
databases.
In mass spectrometry, the detector noise, the electronic and chemical noise, sometimes the small amount of peptides
that has to be treated and finally the spectrum reduction noise (due to bad filtering and/or thresholding), can induce
Parasitic Mass Peaks (PMP) and/or hide some Useful Mass Peaks (UMP) of low intensities. The immediate consequence
is that the presence of the PMP and the absence of the UMP will be detrimental to the protein identification quality. In
this article, we propose an original algorithm eliminating the PMP, detecting and amplifying those which are useful. The
preprocessing principle uses a multi-scale analysis technique coupled to a fuzzy thresholding (multi-scale fuzzy
thresholding), a local amplification of the UMP, and finally an adaptive Base Line Correction.
The associated frequencies with the PMP are distributed on all the spectrum pass bandwidth. This leads us to a dyadic
tree structure subband decomposition. The algorithm principle consists of dividing the frequential pass bandwidth of
each masses spectrum into two subbands, a Low and High Frequency (LF,HF) subband, then each subband is in turn
divided into two subbands etc. The HF subbands are then thresholded according to the minimization criterion of the
Shannon fuzzy entropy, and then amplified locally; the base line is calculated in an adaptive way and subtracted from
reconstructed spectrum. To evaluate the quality of this algorithm, we present a comparison of the results obtained by
our algorithm, and those obtained by the DataExplorer software. The latter is a reduction software provided within the
MALDI-TOF spectrometer software package.La protéomique offre une approche puissante et complémentaire à la génomique. Elle permet de répertorier et
caractĂ©riser les protĂ©ines, de comparer leur niveau dâexpression entre un Ă©tat physiologique sain et malade
par exemple. Lâanalyse protĂ©omique se fait essentiellement par lâutilisation de la technique dâĂ©lectrophorĂšse
bidimensionnelle couplĂ©e Ă la technique dâanalyse par SpectromĂ©trie de Masse (SM). La premiĂšre, aidĂ©e par
lâimagerie protĂ©omique, conduit Ă la localisation des protĂ©ines candidates Ă une analyse par SM. La
comparaison des spectres de masses obtenus Ă des bases de donnĂ©es protĂ©iques, conduit Ă lâidentification
des protĂ©ines dâintĂ©rĂȘt en terme de peptides. Le problĂšme qui se pose souvent est que les spectres sont
bruités et pauvres en masses. En effet, le bruit du détecteur, le bruit électronique et chimique, la présence de
peu de matériel protéique et enfin le bruit de la réduction des spectres (mauvais filtrage et/ou seuillage), tous
ces bruits peuvent induire des Pics de Masses Parasites (PMP) et/ou supprimer des Pics de Masses Utiles
(PMU) de faible intensitĂ©. La consĂ©quence immĂ©diate est que la prĂ©sence des PMP et lâabsence des PMU
seront utilisĂ©es au dĂ©pens de la qualitĂ© dâidentification de la protĂ©ine.
Dans cet article, nous proposons un algorithme original éliminant les PMP, détectant et amplifiant ceux utiles.
Le principe du pré-traitement utilise une Analyse Multirésolution (AM) couplée à un seuillage basé sur la
logique floue (seuillage flou multi-Ă©chelle), une amplification locale des PMU, et enfin une correction
adaptative de la Ligne de Base (LB). Les fréquences associées aux PMP sont réparties sur toute la bande
passante du spectre, ce qui nous conduit à une AM dite en arbre. Le principe consiste à découper la bande
passante frĂ©quentielle de chaque spectre de masses en deux sous-bandes, une Basse FrĂ©quence (BF), lâautre
Haute Fréquence (HF), ensuite chaque sous-bande est à son tour découpée en deux sous-bandes etc. Les
sous-bandes HF sont seuillĂ©es selon le critĂšre de minimisation de lâentropie floue de Shannon et amplifiĂ©es
localement, la ligne de base est calculée automatiquement et soustraite du spectre reconstruit. Pour évaluer
la qualité de cet algorithme, nous présentons une comparaison des résultats obtenus par notre algorithme, et
ceux fournis par le spectromĂštre MALDI-TOF (Matrix Assisted Laser Desorption/Ionisation-Time Of Flight), qui
utilise le logiciel « DataExplorer » comme logiciel de réduction
Regulation of the Fruit-Specific PEP Carboxylase SlPPC2 Promoter at Early Stages of Tomato Fruit Development
The SlPPC2 phosphoenolpyruvate carboxylase (PEPC; EC 4.1.1.31) gene from tomato (Solanum lycopersicum) is differentially and specifically expressed in expanding tissues of developing tomato fruit. We recently showed that a 1966 bp DNA fragment located upstream of the ATG codon of the SlPPC2 gene (GenBank AJ313434) confers appropriate fruit-specificity in transgenic tomato. In this study, we further investigated the regulation of the SlPPC2 promoter gene by analysing the SlPPC2 cis-regulating region fused to either the firefly luciferase (LUC) or the ÎČ-glucuronidase (GUS) reporter gene, using stable genetic transformation and biolistic transient expression assays in the fruit. Biolistic analyses of 5âČ SlPPC2 promoter deletions fused to LUC in fruits at the 8th day after anthesis revealed that positive regulatory regions are mostly located in the distal region of the promoter. In addition, a 5âČ UTR leader intron present in the 1966 bp fragment contributes to the proper temporal regulation of LUC activity during fruit development. Interestingly, the SlPPC2 promoter responds to hormones (ethylene) and metabolites (sugars) regulating fruit growth and metabolism. When tested by transient expression assays, the chimeric promoter:LUC fusion constructs allowed gene expression in both fruit and leaf, suggesting that integration into the chromatin is required for fruit-specificity. These results clearly demonstrate that SlPPC2 gene is under tight transcriptional regulation in the developing fruit and that its promoter can be employed to drive transgene expression specifically during the cell expansion stage of tomato fruit. Taken together, the SlPPC2 promoter offers great potential as a candidate for driving transgene expression specifically in developing tomato fruit from various tomato cultivars
Autoantibodies against type I IFNs in patients with life-threatening COVID-19
Interindividual clinical variability in the course of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is vast. We report that at least 101 of 987 patients with life-threatening coronavirus disease 2019 (COVID-19) pneumonia had neutralizing immunoglobulin G (IgG) autoantibodies (auto-Abs) against interferon-w (IFN-w) (13 patients), against the 13 types of IFN-a (36), or against both (52) at the onset of critical disease; a few also had auto-Abs against the other three type I IFNs. The auto-Abs neutralize the ability of the corresponding type I IFNs to block SARS-CoV-2 infection in vitro. These auto-Abs were not found in 663 individuals with asymptomatic or mild SARS-CoV-2 infection and were present in only 4 of 1227 healthy individuals. Patients with auto-Abs were aged 25 to 87 years and 95 of the 101 were men. A B cell autoimmune phenocopy of inborn errors of type I IFN immunity accounts for life-threatening COVID-19 pneumonia in at least 2.6% of women and 12.5% of men
Principles of the data reduction software of the VLTI mid-infrared instrument MIDI (Poster)
International audienc
Principles of the data reduction software of the VLTI mid-infrared instrument MIDI (Poster)
International audienc
Principles of the data reduction software of the VLTI mid-infrared instrument MIDI (Poster)
International audienc
Use of speckle-tracking strain in preload-dependent patients, need for cautious interpretation!
International audienceBackground: In critical patients, left ventricular ejection fraction and fractional shortening are used to reflect left ventricular systolic function. An emerging technique, two-dimensional-strain echocardiography, allows assessment of the left ventricle systolic longitudinal deformation (global longitudinal strain) and the speed at which this deformation occurs (systolic strain rate). This technique is of increasing use in critical patients in intensive care units and in the peri-operative period where preload constantly varies. Our objective, in this prospective single-center observational study, was to evaluate the effect of fluid resuscitation on two-dimensional-strain echocardiography measurements in preload-dependent critically ill patients. We included 49 patients with preload dependence attested by an increase of at least 10% in the left ventricular outflow track velocity-time integral measured by echocardiography during a passive leg raising maneuver. Echocardiography was performed before fluid resuscitation (echocardiography 1) and after preload independency achievement (echocardiography 2).Results: Two-dimensional-strain echocardiography was feasible in 40 (82%) among the 49 patients. With preload dependence correction, the absolute value of global longitudinal strain and systolic strain rate was significantly increased from, respectively, -13.3 +/- 3.5 to -18.4% +/- 4.5 (p < 0.01) and -1.11 s(-1) +/- 0.29 to -1.55 s(-1) +/- 0.55 (p < 0.001). The fluid resuscitation affects GLS and SSR in preload-dependent patients, with a shift, for GLS, from pathological to normal values.Conclusion: In critically ill patients, the assessment of the systolic function by two-dimensional-strain echocardiography needs prior evaluation of preload dependency, in order to adequately interpret this variable. Future studies should assess the ability of global longitudinal strain to guide fluid management in the critically ill patients
TMP/Pd Complex Immobilized on Graphene Oxide for Efficient Pseudocapacitive Energy Storage with Combined Experimental and DFT Study
Designing sophisticated energy sources that can offer a large amount of electricity for various energy storage uses is a pressing need. In this study, Trimethoprim (TMP) was functionalized as a rich supply of nitrogen and oxygen on graphene oxide (FGO-TMP), using graphene oxide layers adorned with trimethoprim functional groups. Then, using a simple approach to synthesize FGO-TMP/Pd complex for supercapacitor applications, palladium ions were reacted and fixed on the FGO-TMP composite surface. The FGO-TMP/Pd composite produced was characterized as a symmetric capacitor with a capacitance of 330F/g at 5 mV sâ1 and high energy and power densities of 60.3 W h Kgâ1 and 1200 W kgâ1, respectively. After 10,000 cycles at 8 A/g, this symmetric device retained 93.7 percent of its original capacitance, proving the remarkable capacitive performance of the developed platform as well as ultra-stability for such sophisticated energy storage devices. Topological analysis of the electron density distribution and its Laplacian at the bonding critical points and Bader atomic charges of the GO layer in both FGO-TMP and FGO-TMP/Pd composites confirms more concentrated bond charges in FGO-TMP/Pd, indicating effective improvement in electrode material behavior in a supercapacitor