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 caractériser les protéines, de comparer leur niveau d’expression entre un état physiologique sain et malade par exemple. L’analyse protéomique se fait essentiellement par l’utilisation de la technique d’électrophorèse bidimensionnelle couplée à la technique d’analyse par Spectrométrie de Masse (SM). La première, aidée par l’imagerie protéomique, conduit à la localisation des protéines candidates à une analyse par SM. La comparaison des spectres de masses obtenus à des bases de données protéiques, conduit à l’identification des protéines d’intérêt en terme de peptides. Le problème 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 intensité. La conséquence immédiate est que la présence des PMP et l’absence des PMU seront utilisées au dépens de la qualité d’identification de la protéine. 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-échelle), 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 fréquentielle de chaque spectre de masses en deux sous-bandes, une Basse Fréquence (BF), l’autre Haute Fréquence (HF), ensuite chaque sous-bande est à son tour découpée en deux sous-bandes etc. Les sous-bandes HF sont seuillées selon le critère de minimisation de l’entropie floue de Shannon et amplifiées 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 spectromètre 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 β-glucuronidase (GUS) reporter gene, using stable genetic transformation and biolistic transient expression assays in the fruit. Biolistic analyses of 5′ 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 5′ 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

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 s−1 and high energy and power densities of 60.3 W h Kg−1 and 1200 W kg−1, 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

Autoantibodies neutralizing type I IFNs are present in ~4% of uninfected individuals over 70 years old and account for ~20% of COVID-19 deaths

Circulating autoantibodies (auto-Abs) neutralizing high concentrations (10 ng/ml; in plasma diluted 1:10) of IFN-α and/or IFN-ω are found in about 10% of patients with critical COVID-19 (coronavirus disease 2019) pneumonia but not in individuals with asymptomatic infections. We detect auto-Abs neutralizing 100-fold lower, more physiological, concentrations of IFN-α and/or IFN-ω (100 pg/ml; in 1:10 dilutions of plasma) in 13.6% of 3595 patients with critical COVID-19, including 21% of 374 patients >80 years, and 6.5% of 522 patients with severe COVID-19. These antibodies are also detected in 18% of the 1124 deceased patients (aged 20 days to 99 years; mean: 70 years). Moreover, another 1.3% of patients with critical COVID-19 and 0.9% of the deceased patients have auto-Abs neutralizing high concentrations of IFN-β. We also show, in a sample of 34,159 uninfected individuals from the general population, that auto-Abs neutralizing high concentrations of IFN-α and/or IFN-ω are present in 0.18% of individuals between 18 and 69 years, 1.1% between 70 and 79 years, and 3.4% >80 years. Moreover, the proportion of individuals carrying auto-Abs neutralizing lower concentrations is greater in a subsample of 10,778 uninfected individuals: 1% of individuals 80 years. By contrast, auto-Abs neutralizing IFN-β do not become more frequent with age. Auto-Abs neutralizing type I IFNs predate SARS-CoV-2 infection and sharply increase in prevalence after the age of 70 years. They account for about 20% of both critical COVID-19 cases in the over 80s and total fatal COVID-19 cases

Autoantibodies against type I IFNs in patients with life-threatening COVID-19

International audienceInterindividual 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-ω (IFN-ω) (13 patients), against the 13 types of IFN-α (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