34 results on '"Felicori, L."'
Search Results
2. Biochemical and immunological characteristics of Peruvian Loxosceles laeta spider venom: Neutralization of its toxic effects by anti-loxoscelic antivenoms
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Guimarães, G., Dias-Lopes, C., Duarte, C.G., Felicori, L., Machado de Avila, R.A., Figueiredo, L.F.M., de Moura, J., Faleiro, B.T., Barro, J., Flores, K., Silva, W., Tintaya, B., Yarleque, A., Bonilla, C., Kalapothakis, E., Salas, C.E., and Chávez-Olortegui, C.
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- 2013
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3. Generation and characterization of a recombinant chimeric protein (rCpLi) consisting of B-cell epitopes of a dermonecrotic protein from Loxosceles intermedia spider venom
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Mendes, T.M., Oliveira, D., Figueiredo, L.F.M., Machado-de-Avila, R.A., Duarte, C.G., Dias-Lopes, C., Guimarães, G., Felicori, L., Minozzo, J.C., and Chávez-Olortegui, C.
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- 2013
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4. Systems and Synthetic Biology Applied to Health
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Mendes, T., primary, Castiglione, F., additional, Tieri, P., additional, and Felicori, L., additional
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- 2017
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5. List of Contributors
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Alvarenga, L.M., primary, Antunes, F., additional, Basso, A.M.M., additional, Billiald, P., additional, Callese, T., additional, Carvalho, K.A.T., additional, Castiglione, F., additional, Castilho, L.R., additional, Corrêa-Velloso, J.C., additional, Dalagostin, O., additional, de Cássia Oliveira Paiva, N., additional, Degrave, W.M.S., additional, Dellagostin, O.A., additional, de Medeiros, R.V.B., additional, de Moura, J., additional, Dias-Souza, M.V., additional, Edgar, L., additional, Felicori, L., additional, Felix, S.R., additional, Fendrich, R., additional, Gentile, C., additional, Gomes, A.Q., additional, Goulart, V.A.M., additional, Grossi-de-Sa, M.F., additional, Guedes, D., additional, Igel, D., additional, Jorge, S., additional, Katari, R., additional, Lima, H., additional, Marasco, D., additional, Marinho, H.S., additional, McNamara, K., additional, Mendes, T., additional, Mendonça-Lima, L., additional, Mondal, S., additional, Mor, A., additional, Nakamura, R., additional, Nardi Drummond, R.M., additional, Nascimento, I.C., additional, Ndoja, S., additional, Nery, A.A., additional, Nolasco, S., additional, Orlando, G., additional, Pandey, A., additional, Parreira, R.C., additional, Pelegrini, P.B., additional, Perottoni, C., additional, Pinto, M.C.X., additional, Prado, G.S., additional, Real, C., additional, Reddy, I.J., additional, Resende, R.R., additional, Sanson, R.K., additional, Santos, V.L., additional, Scheuer, T., additional, Severo, M.G., additional, Soares, H., additional, Soccol, C.R., additional, Souza, L.T., additional, Tamburrini, R., additional, Thomaz-Soccol, V., additional, Tieri, P., additional, Tonelli, F.C.P., additional, Tonelli, F.M.P., additional, Ulrich, H., additional, Vandenberghe, L.P.S., additional, Vitola, F., additional, Zambon, J.P., additional, and Zeferino, A.S., additional
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- 2017
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6. Protection against the toxic effects of Loxosceles intermedia spider venom elicited by mimotope peptides
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de Moura, J., Felicori, L., Moreau, V., Guimarães, G., Dias-Lopes, C., Molina, L., Alvarenga, L.M., Fernandes, P., Frézard, F., Ribeiro, R.R., Fleury, C., Nguyen, C., Molina, F., Granier, C., and Chávez-Olórtegui, C.
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- 2011
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7. Design of antibody-reactive peptides from discontinuous parts of scorpion toxins
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Alvarenga, L., Moreau, V., Felicori, L., Nguyen, C., Duarte, C., Chavez-Olortegui, C., Molina, F., Martin-Eauclaire, M.-F., and Granier, C.
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- 2010
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8. A protective immune response against lethal, dermonecrotic and hemorrhagic effects of Loxosceles intermedia venom elicited by a 27-residue peptide
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Dias-Lopes, C., Guimarães, G., Felicori, L., Fernandes, P., Emery, L., Kalapothakis, E., Nguyen, C., Molina, F., Granier, C., and Chávez-Olórtegui, C.
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- 2010
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9. Immunodiagnosis of human neurocysticercosis using a synthetic peptide selected by phage-display
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Hell, R.C.R., Amim, P., de Andrade, H.M., de Avila, R.A.M., Felicori, L., Oliveira, A.G., Oliveira, C.A., Nascimento, E., Tavares, C.A.P., Granier, C., and Chávez-Olórtegui, C.
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- 2009
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10. Functional characterization and epitope analysis of a recombinant dermonecrotic protein from Loxosceles intermedia spider
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Felicori, L., Araujo, S.C., Machado de Ávila, R.A., Sanchez, E.F., Granier, C., Kalapothakis, E., and Chávez-Olórtegui, C.
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- 2006
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11. 9 - Systems and Synthetic Biology Applied to Health
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Mendes, T., Castiglione, F., Tieri, P., and Felicori, L.
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- 2017
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12. EPI-peptide designer: a tool for designing peptide ligand libraries based on epitope–paratope interactions
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Viart, B., primary, Dias-Lopes, C., additional, Kozlova, E., additional, Oliveira, C. F. B., additional, Nguyen, C., additional, Neshich, G., additional, Chávez-Olórtegui, C., additional, Molina, F., additional, and Felicori, L. F., additional
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- 2016
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13. The C-terminal mutation beyond the catalytic site of brown spider phospholipase D significantly impacts its biological activities.
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Cunha LC, Barreto LP, Valadares VS, Oliveira CFB, Vuitika L, Vilela MP, Cino EA, Silva AHM, Nagem RAP, Chávez-Olórtegui C, Dias-Lopes C, Molina F, and Felicori L
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- Animals, Catalytic Domain, Sphingomyelin Phosphodiesterase, Phosphoric Diester Hydrolases genetics, Mutation, Recombinant Proteins genetics, Recombinant Proteins chemistry, Phospholipase D genetics, Phospholipase D chemistry, Phospholipase D metabolism, Spiders genetics, Spider Venoms genetics, Spider Venoms chemistry
- Abstract
Loxosceles spider envenomation results in dermonecrosis, principally due to phospholipases D (PLDs) present in the venom. These enzymes have a strongly conserved sequence,
273 ATXXDNPW280 , in the C-terminal region (SMD-tail) that make contact with β-sheets of the TIM barrel, in which the amino acids Asp277 and Trp280 establish the energetically strongest contacts. The SMD-tail is conserved in PLDs from different species but absent in the non-toxic PLD ancestral glycerophosphodiester phosphodiesterases (GDPDs). This work aims to understand the role of the C-terminal region in the structural stability and/or function of phospholipases D. Through site-directed mutagenesis of the rLiD1 protein (recombinant Loxosceles intermedia dermonecrotic protein 1), we produced two mutants: rLiD1D277A and rLiD1W280A (both with sphingomyelinase activity), in which Asp277 and Trp280 were replaced by alanine. rLiD1D277A showed similar sphingomyelinase activity but at least 2 times more dermonecrotic activity than rLiD1 (wild-type protein). Conversely, while the rLiD1W280A displayed a slight increase in sphingomyelinase activity, its biological activity was similar or lower compared to rLiD1, potentially due to its decreased thermostability and formation of amyloid aggregates. In conclusion, these new findings provide evidence that SMD-tail mutants impact the structure and function of these proteins and point out that residues outside the active site can even increase the function of these enzymes., Competing Interests: Declaration of competing interest The authors declare that the research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.)- Published
- 2023
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14. Molecular and Cellular Biomarkers of COVID-19 Prognosis: Protocol for the Prospective Cohort TARGET Study.
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Kurizky P, Nóbrega OT, Soares AASM, Aires RB, Albuquerque CP, Nicola AM, Albuquerque P, Teixeira-Carvalho A, Naves LA, Fontes W, Luz IS, Felicori L, Gomides APM, Mendonça-Silva DL, Espindola LS, Martins-Filho OA, de Lima SMB, Mota LMH, and Gomes CM
- Abstract
Background: Since the beginning of the COVID-19 pandemic, the world's attention has been focused on better understanding the relation between the human host and the SARS-CoV-2 virus, as its action has led to hundreds of thousands of deaths., Objective: In this context, we decided to study certain consequences of the abundant cytokine release over the innate and adaptive immune systems, inflammation, and hemostasis, comparing mild and severe forms of COVID-19., Methods: To accomplish these aims, we will analyze demographic characteristics, biochemical tests, immune biomarkers, leukocyte phenotyping, immunoglobulin profile, hormonal release (cortisol and prolactin), gene expression, thromboelastometry, neutralizing antibodies, metabolic profile, and neutrophil function (reactive oxygen species production, neutrophil extracellular trap production, phagocytosis, migration, gene expression, and proteomics). A total of 200 reverse transcription polymerase chain reaction-confirmed patients will be enrolled and divided into two groups: mild/moderate or severe/critical forms of COVID-19. Blood samples will be collected at different times: at inclusion and after 9 and 18 days, with an additional 3-day sample for severe patients. We believe that this information will provide more knowledge for future studies that will provide more robust and useful clinical information that may allow for better decisions at the front lines of health care., Results: The recruitment began in June 2020 and is still in progress. It is expected to continue until February 2021. Data analysis is scheduled to start after all data have been collected. The coagulation study branch is complete and is already in the analysis phase., Conclusions: This study is original in terms of the different parameters analyzed in the same sample of patients with COVID-19. The project, which is currently in the data collection phase, was approved by the Brazilian Committee of Ethics in Human Research (CAAE 30846920.7.0000.0008)., Trial Registration: Brazilian Registry of Clinical Trials RBR-62zdkk; https://ensaiosclinicos.gov.br/rg/RBR-62zdkk., International Registered Report Identifier (irrid): DERR1-10.2196/24211., (©Patricia Kurizky, Otávio T Nóbrega, Alexandre Anderson De Sousa Munhoz Soares, Rodrigo Barbosa Aires, Cleandro Pires De Albuquerque, André Moraes Nicola, Patrícia Albuquerque, Andréa Teixeira-Carvalho, Luciana Ansaneli Naves, Wagner Fontes, Isabelle Souza Luz, Liza Felicori, Ana Paulo Monteiro Gomides, Dayde Lane Mendonça-Silva, Laila Salmen Espindola, Olindo Assis Martins-Filho, Sheila Maria Barbosa de Lima, Licia Maria Henrique Mota, Ciro Martins Gomes. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 04.03.2021.)
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- 2021
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15. Antigenic and Substrate Preference Differences between Scorpion and Spider Dermonecrotic Toxins, a Comparative Investigation.
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Ben Yekhlef R, Felicori L, Santos LH, F B Oliveira C, Fadhloun R, Torabi E, Shahbazzadeh D, Pooshang Bagheri K, Salgado Ferreira R, and Borchani L
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- Animals, Antivenins immunology, Cross Reactions, Epitopes, Hemolysis drug effects, Insect Bites and Stings enzymology, Lysophosphatidylcholines metabolism, Necrosis, Phospholipase D immunology, Phospholipase D metabolism, Phosphoric Diester Hydrolases immunology, Scorpion Venoms enzymology, Scorpion Venoms immunology, Skin enzymology, Skin pathology, Sphingomyelins metabolism, Spider Venoms enzymology, Spider Venoms immunology, Substrate Specificity, Antivenins pharmacology, Brown Recluse Spider enzymology, Brown Recluse Spider immunology, Phospholipase D toxicity, Phosphoric Diester Hydrolases toxicity, Scorpion Venoms toxicity, Scorpions enzymology, Scorpions immunology, Skin drug effects, Spider Venoms toxicity
- Abstract
The Hemiscorpius lepturus scorpion and brown spider Loxosceles intermedia represent a public health problem in Asia and America, respectively. Although distinct, these organisms contain similar toxins responsible for the principal clinical signs of envenomation. To better understand the properties of these toxins, we designed a study to compare recombinant Heminecrolysin (rHNC) and rLiD1, the major phospholipase D toxins of scorpion and spider venom, respectively. Using a competitive ELISA and a hemolytic inhibition test, we come to spot a cross reaction between scorpion and spider venoms along with an epitopic similarity between rHNC and rLiD1 associated with neutralizing antibodies. Results show that the ability of the rHNC to hydrolyze lysophosphatidylcholine (LPC) is equivalent to that of rLiD1 to hydrolyze sphingomyelin and vice-versa. rHNC exclusively catalyze transphosphatidylation of LPC producing cyclic phosphatidic acid (cPA). The in-silico analysis of hydrogen bonds between LPC and toxins provides a possible explanation for the higher transphosphatidylase activity of rHNC. Interestingly, for the first time, we reveal that lysophosphatidic acid (LPA) can be a substrate for both enzymes using cellular and enzymatic assays. The finding of the usage of LPA as a substrate as well as the formation of cPA as an end product could shed more light on the molecular basis of Hemiscorpius lepturus envenomation as well as on loxoscelism.
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- 2020
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16. PEPOP 2.0: new approaches to mimic non-continuous epitopes.
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Demolombe V, de Brevern AG, Felicori L, NGuyen C, Machado de Avila RA, Valera L, Jardin-Watelet B, Lavigne G, Lebreton A, Molina F, and Moreau V
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- Amino Acid Sequence, Animals, Antibodies, Monoclonal immunology, Epitopes chemistry, Immune Sera, Internet, Mice, Peptides blood, Peptides chemistry, Peptides immunology, Protein Domains, Proteins chemistry, Computational Biology methods, Epitopes metabolism, Software
- Abstract
Background: Bioinformatics methods are helpful to identify new molecules for diagnostic or therapeutic applications. For example, the use of peptides capable of mimicking binding sites has several benefits in replacing a protein which is difficult to produce, or toxic. Using peptides is less expensive. Peptides are easier to manipulate, and can be used as drugs. Continuous epitopes predicted by bioinformatics tools are commonly used and these sequential epitopes are used as is in further experiments. Numerous discontinuous epitope predictors have been developed but only two bioinformatics tools have been proposed so far to predict peptide sequences: Superficial and PEPOP 2.0. PEPOP 2.0 can generate series of peptide sequences that can replace continuous or discontinuous epitopes in their interaction with their cognate antibody., Results: We have developed an improved version of PEPOP (PEPOP 2.0) dedicated to answer to experimentalists' need for a tool able to handle proteins and to turn them into peptides. The PEPOP 2.0 web site has been reorganized by peptide prediction category and is therefore better formulated to experimental designs. Since the first version of PEPOP, 32 new methods of peptide design were developed. In total, PEPOP 2.0 proposes 35 methods in which 34 deal specifically with discontinuous epitopes, the most represented epitope type in nature., Conclusion: Through the presentation of its user-friendly, well-structured new web site conceived in close proximity to experimentalists, we report original methods that show how PEPOP 2.0 can assist biologists in dealing with discontinuous epitopes.
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- 2019
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17. Computational B-cell epitope identification and production of neutralizing murine antibodies against Atroxlysin-I.
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Kozlova EEG, Cerf L, Schneider FS, Viart BT, NGuyen C, Steiner BT, de Almeida Lima S, Molina F, Duarte CG, Felicori L, Chávez-Olórtegui C, and Machado-de-Ávila RA
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- Algorithms, Amino Acid Sequence, Amino Acids chemistry, Animals, Decision Trees, Epitope Mapping, Epitopes, B-Lymphocyte chemistry, Female, Immunization, Metalloproteases metabolism, Mice, Inbred BALB C, Models, Molecular, Peptides chemistry, ROC Curve, Reproducibility of Results, Antibodies, Neutralizing biosynthesis, Computational Biology methods, Epitopes, B-Lymphocyte immunology, Snake Venoms immunology
- Abstract
Epitope identification is essential for developing effective antibodies that can detect and neutralize bioactive proteins. Computational prediction is a valuable and time-saving alternative for experimental identification. Current computational methods for epitope prediction are underused and undervalued due to their high false positive rate. In this work, we targeted common properties of linear B-cell epitopes identified in an individual protein class (metalloendopeptidases) and introduced an alternative method to reduce the false positive rate and increase accuracy, proposing to restrict predictive models to a single specific protein class. For this purpose, curated epitope sequences from metalloendopeptidases were transformed into frame-shifted Kmers (3 to 15 amino acid residues long). These Kmers were decomposed into a matrix of biochemical attributes and used to train a decision tree classifier. The resulting prediction model showed a lower false positive rate and greater area under the curve when compared to state-of-the-art methods. Our predictions were used for synthesizing peptides mimicking the predicted epitopes for immunization of mice. A predicted linear epitope that was previously undetected by an experimental immunoassay was able to induce neutralizing-antibody production in mice. Therefore, we present an improved prediction alternative and show that computationally identified epitopes can go undetected during experimental mapping.
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- 2018
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18. Venomous Arachnid Diagnostic Assays, Lessons from Past Attempts.
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Dias-Lopes C, Paiva AL, Guerra-Duarte C, Molina F, and Felicori L
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- Animals, Antivenins therapeutic use, Biological Assay, Diagnostic Tests, Routine, Humans, Spider Bites drug therapy, Spider Bites diagnosis, Spider Venoms analysis
- Abstract
Diagnostic tests for arachnid accidents remain unavailable for patients and clinicians. Together with snakes, these accidents are still a global medical concern, and are recognized as neglected tropical issues. Due to arachnid toxins' fast mechanism of action, quick detection and quantification of venom is required to accelerate treatment decisions, rationalize therapy, and reduce costs and patient risks. This review aims to understand the current limitations for arachnid venom identification and quantification in biological samples. We benchmarked the already existing initiatives regarding test requirements (sample or biomarkers of choice), performances (time, detection limit, sensitivity and specificity) and their validation (on animal models or on samples from envenomed humans). Our analysis outlines unmet needs for improving diagnosis and consequently treatment of arachnid accidents. Hence, based on lessons from past attempts, we propose a road map for raising best practice guidelines, leading to recommendations for future progress in the development of arachnid diagnostic assays.
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- 2018
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19. Searching whole genome sequences for biochemical identification features of emerging and reemerging pathogenic Corynebacterium species.
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Santos AS, Ramos RT, Silva A, Hirata R Jr, Mattos-Guaraldi AL, Meyer R, Azevedo V, Felicori L, and Pacheco LGC
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- ATP-Binding Cassette Transporters genetics, Corynebacterium classification, Corynebacterium metabolism, Fructokinases genetics, Phosphoenolpyruvate Sugar Phosphotransferase System genetics, Phosphoglucomutase genetics, Phylogeny, Polymorphism, Genetic, Bacterial Proteins genetics, Bacterial Typing Techniques methods, Corynebacterium genetics, Genome, Bacterial
- Abstract
Biochemical tests are traditionally used for bacterial identification at the species level in clinical microbiology laboratories. While biochemical profiles are generally efficient for the identification of the most important corynebacterial pathogen Corynebacterium diphtheriae, their ability to differentiate between biovars of this bacterium is still controversial. Besides, the unambiguous identification of emerging human pathogenic species of the genus Corynebacterium may be hampered by highly variable biochemical profiles commonly reported for these species, including Corynebacterium striatum, Corynebacterium amycolatum, Corynebacterium minutissimum, and Corynebacterium xerosis. In order to identify the genomic basis contributing for the biochemical variabilities observed in phenotypic identification methods of these bacteria, we combined a comprehensive literature review with a bioinformatics approach based on reconstruction of six specific biochemical reactions/pathways in 33 recently released whole genome sequences. We used data retrieved from curated databases (MetaCyc, PathoSystems Resource Integration Center (PATRIC), The SEED, TransportDB, UniProtKB) associated with homology searches by BLAST and profile Hidden Markov Models (HMMs) to detect enzymes participating in the various pathways and performed ab initio protein structure modeling and molecular docking to confirm specific results. We found a differential distribution among the various strains of genes that code for some important enzymes, such as beta-phosphoglucomutase and fructokinase, and also for individual components of carbohydrate transport systems, including the fructose-specific phosphoenolpyruvate-dependent sugar phosphotransferase (PTS) and the ribose-specific ATP-binging cassette (ABC) transporter. Horizontal gene transfer plays a role in the biochemical variability of the isolates, as some genes needed for sucrose fermentation were seen to be present in genomic islands. Noteworthy, using profile HMMs, we identified an enzyme with putative alpha-1,6-glycosidase activity only in some specific strains of C. diphtheriae and this may aid to understanding of the differential abilities to utilize glycogen and starch between the biovars.
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- 2018
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20. Efficient differentiation of Corynebacterium striatum, Corynebacterium amycolatum and Corynebacterium xerosis clinical isolates by multiplex PCR using novel species-specific primers.
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Santos CS, Ramos JN, Vieira VV, Pinheiro CS, Meyer R, Alcantara-Neves NM, Ramos RT, Silva A, Hirata R Jr, Felicori L, de Alegría Puig CR, Navas J, Azevedo V, Mattos-Guaraldi AL, and Pacheco LGC
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- Corynebacterium isolation & purification, Corynebacterium Infections microbiology, DNA Primers genetics, DNA-Directed RNA Polymerases genetics, Humans, RNA, Ribosomal, 16S genetics, Corynebacterium classification, Corynebacterium genetics, Corynebacterium Infections diagnosis, Molecular Typing methods, Multiplex Polymerase Chain Reaction methods
- Abstract
A multiplex-PCR (mPCR) assay was designed with species-specific primers which generate amplicons of 226bp, 434bp and 106bp for differentiating the species C. striatum, C. amycolatum, and C. xerosis, respectively. mPCR results were 100% in agreement with identifications achieved by 16S rRNA and rpoB gene sequencing and by VITEK-MS., (Copyright © 2017 Elsevier B.V. All rights reserved.)
- Published
- 2017
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21. Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners.
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Felicori L, Jameson KH, Roblin P, Fogg MJ, Garcia-Garcia T, Ventroux M, Cherrier MV, Bazin A, Noirot P, Wilkinson AJ, Molina F, Terradot L, and Noirot-Gros MF
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- Amino Acid Motifs, Amino Acid Sequence, Bacillus subtilis genetics, Bacillus subtilis metabolism, Bacterial Proteins chemistry, Bacterial Proteins genetics, Binding Sites, DNA-Binding Proteins chemistry, DNA-Binding Proteins genetics, Intracellular Space, Models, Molecular, Molecular Sequence Data, Mutation, Position-Specific Scoring Matrices, Protein Binding, Protein Conformation, Protein Interaction Domains and Motifs, Protein Interaction Mapping methods, Protein Multimerization, Protein Transport, Sequence Alignment, Structure-Activity Relationship, Zinc metabolism, Bacterial Proteins metabolism, DNA Replication, DNA-Binding Proteins metabolism, Multiprotein Complexes metabolism
- Abstract
YabA negatively regulates initiation of DNA replication in low-GC Gram-positive bacteria. The protein exerts its control through interactions with the initiator protein DnaA and the sliding clamp DnaN. Here, we combined X-ray crystallography, X-ray scattering (SAXS), modeling and biophysical approaches, with in vivo experimental data to gain insight into YabA function. The crystal structure of the N-terminal domain (NTD) of YabA solved at 2.7 Å resolution reveals an extended α-helix that contributes to an intermolecular four-helix bundle. Homology modeling and biochemical analysis indicates that the C-terminal domain (CTD) of YabA is a small Zn-binding domain. Multi-angle light scattering and SAXS demonstrate that YabA is a tetramer in which the CTDs are independent and connected to the N-terminal four-helix bundle via flexible linkers. While YabA can simultaneously interact with both DnaA and DnaN, we found that an isolated CTD can bind to either DnaA or DnaN, individually. Site-directed mutagenesis and yeast-two hybrid assays identified DnaA and DnaN binding sites on the YabA CTD that partially overlap and point to a mutually exclusive mode of interaction. Our study defines YabA as a novel structural hub and explains how the protein tetramer uses independent CTDs to bind multiple partners to orchestrate replication initiation in the bacterial cell., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2016
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22. PnPP-19, a Synthetic and Nontoxic Peptide Designed from a Phoneutria nigriventer Toxin, Potentiates Erectile Function via NO/cGMP.
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Silva CN, Nunes KP, Torres FS, Cassoli JS, Santos DM, Almeida Fde M, Matavel A, Cruz JS, Santos-Miranda A, Nunes AD, Castro CH, Machado de Ávila RA, Chávez-Olórtegui C, Láuar SS, Felicori L, Resende JM, Camargos ER, Borges MH, Cordeiro MN, Peigneur S, Tytgat J, and de Lima ME
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- Animals, Disease Models, Animal, Enzyme-Linked Immunosorbent Assay, Erectile Dysfunction physiopathology, Male, Mice, Neurotoxins, Patch-Clamp Techniques, Rats, Rats, Sprague-Dawley, Cyclic GMP metabolism, Erectile Dysfunction drug therapy, Neuropeptides pharmacology, Nitric Oxide Synthase Type I metabolism, Penile Erection drug effects
- Abstract
Purpose: We designed a peptide, PnPP-19, comprising the potential active core of the Phoneutria nigriventer native toxin PnTx2-6. We investigated its role on erectile function, and its toxicity and immunogenicity., Materials and Methods: Erectile function was evaluated by the intracavernous pressure-to-mean arterial pressure ratio during electrical field stimulation on rat pelvic ganglia. Cavernous strips were contracted with phenylephrine and relaxation was induced by electrical field stimulation with or without PnPP-19 (10(-8) M). Activity on sodium channels was evaluated by electrophysiological screening of transfected channels on Xenopus oocytes and dorsal root ganglion cells. Antibodies were detected by indirect enzyme-linked immunosorbent assay in mice previously treated with the peptide. Histopathological studies were performed with mouse organs treated with different doses of PnPP-19., Results: PnPP-19 was able to potentiate erection at 4 and 8 Hz in vivo and ex vivo. It showed no toxicity and low immunogenicity in mice, and did not affect sodium channels or rat hearts. PnPP-19 increased cyclic guanosine monophosphate levels at 8 Hz. This effect was inhibited by L-NAME (10(-4) M). Erectile function was partially inhibited by 7-nitroindazole (10(-5) M), a selective inhibitor of neuronal nitric oxide synthase., Conclusions: PnPP-19 potentiates erection in vivo and ex vivo via the nitric oxide/cyclic guanosine monophosphate pathway. It does not affect sodium channels or rat hearts and shows no toxicity and low immunogenicity. These findings make it a promising candidate as a novel drug in the therapy of erectile dysfunction., (Copyright © 2015 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.)
- Published
- 2015
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23. Protein-Protein and Peptide-Protein Interactions of NudE-Like 1 (Ndel1): A Protein Involved in Schizophrenia.
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Hayashi MA, Felicori LF, Fresqui MA, and Yonamine CM
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- Amino Acid Sequence, Carrier Proteins chemistry, Humans, Molecular Sequence Data, Nerve Tissue Proteins metabolism, Peptides chemistry, Protein Binding, Carrier Proteins metabolism, Peptides metabolism, Protein Interaction Maps, Schizophrenia metabolism
- Abstract
Schizophrenia (SCZ) is a devastating chronic mental disease determined by genetic and environmental factors, which susceptibility may involve an impaired neural migration during the neurodevelopmental process. Several candidate risk genes potentially associated with SCZ were related to the formation of protein complexes that ultimately mediate alterations in the neuroplasticity. The most studied SCZ risk gene is the Disrupted-in-Schizophrenia 1 (DISC1) gene, which functions seem to depend on the binding with cytoskeleton proteins, as the Nuclear-distribution gene E homolog like-1 (Ndel1) protein among others. Interestingly, Ndel1 is the only binding partner of DISC1 proteins with oligopeptidase activity, besides playing roles in multiple processes, including cytoskeletal organization, cell signaling, neuron migration, and neurite outgrowth. It is still not clear if the protein-protein interaction between Ndel1 and DISC1 is enough to explain all cellular functions attributed to these proteins, but there are several lines of evidence suggesting the importance of the catalytic activity of Ndel1 for the neurite outgrowth and neuron migration during embryogenesis. Recent works of the group have demonstrated the modulation of Ndel1 activity by DISC1, which is hypothetically impaired in SCZ patients. In fact, more recently, we also showed a lower Ndel1 activity in the plasma of SCZ patients compared to control health subjects, but the physiopathological significance of this feature is still unknown. Here we discuss Ndel1 ligands involved in protein-protein complex formations related to neurodevelopmental diseases, as (1) lissencephaly or Miller-Dieker Syndrome (MDS), which is characterized by the typical craniofacial features and abnormal smooth cerebral surface, and as (2) SCZ, since they both seem to be determined by defects in neuronal migration. Although impaired lissencephaly protein Lis1 complex formation with Ndel1 is the leading cause of lissencephaly, this binding does not affect Ndel1 oligopeptidase activity. On the other hand, although MDS and SCZ may be both determined by an abnormal neuronal migration, DISC1 complex formation with Ndel1 was shown to inhibit Ndel1 activity. Also differently of MDS, SCZ needs inputs from environmental factors, while lissencephaly is not likely dependent or affected by the environment. Several other proteins and peptide ligands were described for Ndel1, Lis1 and DISC1, thanks to the employment of biochemical, immunochemical, and biological (using cells or living animals) assays, including heterologous expression and also simply by purification from nature of these proteins in the complex form. Effects of the post-translational modifications of these proteins are also discussed here. Taken together, the data presented here show in essence how protein-protein and proteinpeptide interactions can underlie fundamental processes as cell division, maturation and migration, necessary for adequate formation of a complex structured tissue as the brain. A special attention was given to Ndel1 as this protein binds to either proteins or peptides, besides having proteolytic activity. Moreover, Ndel1 seems to be the key protein underlying two seemingly unrelated diseases with highly complex etiology, as lissencephaly and SCZ.
- Published
- 2015
- Full Text
- View/download PDF
24. Classification epitopes in groups based on their protein family.
- Author
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Kozlova E, Viart B, de Avila R, Felicori L, and Chavez-Olortegui C
- Subjects
- Amino Acid Sequence, Amino Acids chemistry, Area Under Curve, Data Mining, Databases, Protein, Decision Trees, Epitopes, B-Lymphocyte chemistry, Regression Analysis, Support Vector Machine, Computational Biology methods, Epitopes, B-Lymphocyte classification, Proteins chemistry
- Abstract
Background: The humoral immune system response is based on the interaction between antibodies and antigens for the clearance of pathogens and foreign molecules. The interaction between these proteins occurs at specific positions known as antigenic determinants or B-cell epitopes. The experimental identification of epitopes is costly and time consuming. Therefore the use of in silico methods, to help discover new epitopes, is an appealing alternative due the importance of biomedical applications such as vaccine design, disease diagnostic, anti-venoms and immune-therapeutics. However, the performance of predictions is not optimal been around 70% of accuracy. Further research could increase our understanding of the biochemical and structural properties that characterize a B-cell epitope., Results: We investigated the possibility of linear epitopes from the same protein family to share common properties. This hypothesis led us to analyze physico-chemical (PCP) and predicted secondary structure (PSS) features of a curated dataset of epitope sequences available in the literature belonging to two different groups of antigens (metalloproteinases and neurotoxins). We discovered statistically significant parameters with data mining techniques which allow us to distinguish neurotoxin from metalloproteinase and these two from random sequences. After a five cross fold validation we found that PCP based models obtained area under the curve values (AUC) and accuracy above 0.9 for regression, decision tree and support vector machine., Conclusions: We demonstrated that antigen's family can be inferred from properties within a single group of linear epitopes (metalloproteinases or neurotoxins). Also we discovered the characteristics that represent these two epitope groups including their similarities and differences with random peptides and their respective amino acid sequence. These findings open new perspectives to improve epitope prediction by considering the specific antigen's protein family. We expect that these findings will help to improve current computational mapping methods based on physico-chemical due it's potential application during epitope discovery.
- Published
- 2015
- Full Text
- View/download PDF
25. Identification of new sphingomyelinases D in pathogenic fungi and other pathogenic organisms.
- Author
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Dias-Lopes C, Neshich IA, Neshich G, Ortega JM, Granier C, Chávez-Olortegui C, Molina F, and Felicori L
- Subjects
- Amino Acid Motifs genetics, Amino Acid Sequence, Animals, Arthropod Proteins chemistry, Arthropod Proteins genetics, Arthropod Proteins metabolism, Aspergillus flavus enzymology, Aspergillus flavus genetics, Bacterial Proteins chemistry, Bacterial Proteins genetics, Bacterial Proteins metabolism, Biocatalysis, Catalytic Domain, Corynebacterium pseudotuberculosis classification, Corynebacterium pseudotuberculosis genetics, Fungal Proteins chemistry, Fungal Proteins genetics, Fungal Proteins metabolism, Fungi classification, Fungi genetics, Ixodes classification, Ixodes genetics, Models, Molecular, Molecular Sequence Data, Phosphoric Diester Hydrolases chemistry, Phosphoric Diester Hydrolases genetics, Phylogeny, Protein Structure, Secondary, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Sphingomyelins chemistry, Sphingomyelins metabolism, Spiders classification, Spiders genetics, Corynebacterium pseudotuberculosis enzymology, Fungi enzymology, Ixodes enzymology, Phosphoric Diester Hydrolases metabolism, Spiders enzymology
- Abstract
Sphingomyelinases D (SMases D) or dermonecrotic toxins are well characterized in Loxosceles spider venoms and have been described in some strains of pathogenic microorganisms, such as Corynebacterium sp. After spider bites, the SMase D molecules cause skin necrosis and occasional severe systemic manifestations, such as acute renal failure. In this paper, we identified new SMase D amino acid sequences from various organisms belonging to 24 distinct genera, of which, 19 are new. These SMases D share a conserved active site and a C-terminal motif. We suggest that the C-terminal tail is responsible for stabilizing the entire internal structure of the SMase D Tim barrel and that it can be considered an SMase D hallmark in combination with the amino acid residues from the active site. Most of these enzyme sequences were discovered from fungi and the SMase D activity was experimentally confirmed in the fungus Aspergillus flavus. Because most of these novel SMases D are from organisms that are endowed with pathogenic properties similar to those evoked by these enzymes alone, they might be associated with their pathogenic mechanisms.
- Published
- 2013
- Full Text
- View/download PDF
26. Elementary flux modes analysis of functional domain networks allows a better metabolic pathway interpretation.
- Author
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Pérès S, Felicori L, and Molina F
- Subjects
- Adenosine Triphosphate biosynthesis, Algorithms, Bacillus subtilis enzymology, Bacillus subtilis metabolism, Catalysis, Citric Acid Cycle, Computer Simulation, Systems Biology, Metabolic Networks and Pathways, Models, Biological
- Abstract
Metabolic network analysis is an important step for the functional understanding of biological systems. In these networks, enzymes are made of one or more functional domains often involved in different catalytic activities. Elementary flux mode (EFM) analysis is a method of choice for the topological studies of these enzymatic networks. In this article, we propose to use an EFM approach on networks that encompass available knowledge on structure-function. We introduce a new method that allows to represent the metabolic networks as functional domain networks and provides an application of the algorithm for computing elementary flux modes to analyse them. Any EFM that can be represented using the classical representation can be represented using our functional domain network representation but the fine-grained feature of functional domain networks allows to highlight new connections in EFMs. This methodology is applied to the tricarboxylic acid cycle (TCA cycle) of Bacillus subtilis, and compared to the classical analyses. This new method of analysis of the functional domain network reveals that a specific inhibition on the second domain of the lipoamide dehydrogenase (pdhD) component of pyruvate dehydrogenase complex leads to the loss of all fluxes. Such conclusion was not predictable in the classical approach.
- Published
- 2013
- Full Text
- View/download PDF
27. Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism.
- Author
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Buescher JM, Liebermeister W, Jules M, Uhr M, Muntel J, Botella E, Hessling B, Kleijn RJ, Le Chat L, Lecointe F, Mäder U, Nicolas P, Piersma S, Rügheimer F, Becher D, Bessieres P, Bidnenko E, Denham EL, Dervyn E, Devine KM, Doherty G, Drulhe S, Felicori L, Fogg MJ, Goelzer A, Hansen A, Harwood CR, Hecker M, Hubner S, Hultschig C, Jarmer H, Klipp E, Leduc A, Lewis P, Molina F, Noirot P, Peres S, Pigeonneau N, Pohl S, Rasmussen S, Rinn B, Schaffer M, Schnidder J, Schwikowski B, Van Dijl JM, Veiga P, Walsh S, Wilkinson AJ, Stelling J, Aymerich S, and Sauer U
- Subjects
- Algorithms, Bacterial Proteins metabolism, Computer Simulation, Data Interpretation, Statistical, Gene Expression Regulation, Bacterial, Genome, Bacterial, Metabolome, Metabolomics, Models, Biological, Operon, Promoter Regions, Genetic, Transcription Factors metabolism, Transcription, Genetic, Adaptation, Physiological, Bacillus subtilis genetics, Bacillus subtilis metabolism, Gene Regulatory Networks, Glucose metabolism, Malates metabolism, Metabolic Networks and Pathways genetics
- Abstract
Adaptation of cells to environmental changes requires dynamic interactions between metabolic and regulatory networks, but studies typically address only one or a few layers of regulation. For nutritional shifts between two preferred carbon sources of Bacillus subtilis, we combined statistical and model-based data analyses of dynamic transcript, protein, and metabolite abundances and promoter activities. Adaptation to malate was rapid and primarily controlled posttranscriptionally compared with the slow, mainly transcriptionally controlled adaptation to glucose that entailed nearly half of the known transcription regulation network. Interactions across multiple levels of regulation were involved in adaptive changes that could also be achieved by controlling single genes. Our analysis suggests that global trade-offs and evolutionary constraints provide incentives to favor complex control programs.
- Published
- 2012
- Full Text
- View/download PDF
28. Cardiotoxic effects of Loxosceles intermedia spider venom and the recombinant venom toxin rLiD1.
- Author
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Dias-Lopes C, Felicori L, Guimarães G, Gomes ER, Roman-Campos D, Duarte H, Damasceno D, Martins M, Kalapothakis E, Almeida AP, Granier C, Cruz JS, Guatimosim S, and Chávez-Olórtegui C
- Subjects
- Animals, Antigens analysis, Calcium metabolism, Cardiotoxins immunology, Cardiotoxins isolation & purification, Cells, Cultured, Creatine Kinase blood, Creatine Kinase, MB Form blood, Enzyme-Linked Immunosorbent Assay, Female, In Vitro Techniques, Male, Mice, Mice, Inbred BALB C, Mice, Inbred C57BL, Myocytes, Cardiac drug effects, Patch-Clamp Techniques, Phosphoric Diester Hydrolases immunology, Phosphoric Diester Hydrolases isolation & purification, Phosphoric Diester Hydrolases metabolism, Phosphoric Diester Hydrolases pharmacology, Recombinant Fusion Proteins, Spider Venoms immunology, Spider Venoms isolation & purification, Cardiotoxins toxicity, Heart drug effects, Myocardium pathology, Phosphoric Diester Hydrolases toxicity, Spider Venoms toxicity
- Abstract
Loxosceles spider bites cause many human injuries worldwide. Injections in mice of whole Loxosceles (L.) intermedia venom or a recombinant toxin (rLiD1) produce systemic symptoms similar to those detected in envenomed humans. This animal model was used to characterize the effects of Loxosceles intermedia venom in cardiac tissues. L. intermedia antigens were detected by ELISA in kidney, heart, lung and liver of experimentally envenomed mice. In addition, rLiD1 binding to cardiomyocytes was demonstrated by immunofluorescence and confocal microscopy. Furthermore, isolated perfused heart preparations and ventricular cardiomyocytes from envenomed mice showed heart function impairment, and a significant increase of I(Ca,L) density and intracellular Ca(2+) transients, respectively. Thus, L. intermedia spider venom, as shown through the use of the recombinant toxin rLiD1, causes cardiotoxic effects and a protein from the sphingomyelinase D family plays a key role in heart dysfunction. Thus, L. intermedia spider venom and the Loxtox rLiD1 play a key role in heart dysfunction., (Copyright © 2010 Elsevier Ltd. All rights reserved.)
- Published
- 2010
- Full Text
- View/download PDF
29. BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks.
- Author
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Rialle S, Felicori L, Dias-Lopes C, Pérès S, El Atia S, Thierry AR, Amar P, and Molina F
- Subjects
- Databases, Factual, Models, Biological, Programming Languages, Protein Biosynthesis, Proteins, Software, Computational Biology methods, Computer Simulation, Computer-Aided Design, Systems Biology methods
- Abstract
Motivation: Synthetic biology studies how to design and construct biological systems with functions that do not exist in nature. Biochemical networks, although easier to control, have been used less frequently than genetic networks as a base to build a synthetic system. To date, no clear engineering principles exist to design such cell-free biochemical networks., Results: We describe a methodology for the construction of synthetic biochemical networks based on three main steps: design, simulation and experimental validation. We developed BioNetCAD to help users to go through these steps. BioNetCAD allows designing abstract networks that can be implemented thanks to CompuBioTicDB, a database of parts for synthetic biology. BioNetCAD enables also simulations with the HSim software and the classical Ordinary Differential Equations (ODE). We demonstrate with a case study that BioNetCAD can rationalize and reduce further experimental validation during the construction of a biochemical network., Availability and Implementation: BioNetCAD is freely available at http://www.sysdiag.cnrs.fr/BioNetCAD. It is implemented in Java and supported on MS Windows. CompuBioTicDB is freely accessible at http://compubiotic.sysdiag.cnrs.fr/.
- Published
- 2010
- Full Text
- View/download PDF
30. Computing biological functions using BioPsi, a formal description of biological processes based on elementary bricks of actions.
- Author
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Pérès S, Felicori L, Rialle S, Jobard E, and Molina F
- Subjects
- Biological Phenomena, Glycolysis, Peptide Hydrolases chemistry, Peptide Hydrolases metabolism, Signal Transduction, Computational Biology methods
- Abstract
Motivation: In the available databases, biological processes are described from molecular and cellular points of view, but these descriptions are represented with text annotations that make it difficult to handle them for computation. Consequently, there is an obvious need for formal descriptions of biological processes., Results: We present a formalism that uses the BioPsi concepts to model biological processes from molecular details to networks. This computational approach, based on elementary bricks of actions, allows us to calculate on biological functions (e.g. process comparison, mapping structure-function relationships, etc.). We illustrate its application with two examples: the functional comparison of proteases and the functional description of the glycolysis network. This computational approach is compatible with detailed biological knowledge and can be applied to different kinds of systems of simulation., Availability: www.sysdiag.cnrs.fr/publications/supplementary-materials/BioPsi_Manager/., Supplementary Information: Supplementary data are available at Bioinformatics online.
- Published
- 2010
- Full Text
- View/download PDF
31. An in vivo protective response against toxic effects of the dermonecrotic protein from Loxosceles intermedia spider venom elicited by synthetic epitopes.
- Author
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Felicori L, Fernandes PB, Giusta MS, Duarte CG, Kalapothakis E, Nguyen C, Molina F, Granier C, and Chávez-Olórtegui C
- Subjects
- Animals, Edema prevention & control, Epitope Mapping, Female, Hemorrhage prevention & control, Necrosis prevention & control, Rabbits, Vaccines, Synthetic immunology, Epitopes immunology, Insect Bites and Stings immunology, Phosphoric Diester Hydrolases immunology, Spider Venoms antagonists & inhibitors, Spider Venoms immunology, Spiders
- Abstract
Loxoscelism is a necrotic-hemolytic syndrome caused by bites of brown spiders belonging to the genus Loxosceles. Many approaches for the treatment of Loxosceles poisoning have already been proposed, among which administration of specific antivenom is thought to be the more specific. We have evaluated the use of peptides as immunogen to raise in rabbits an antibody response that could protect animals from a challenge by the Loxtox isoform LiD1, one of the main toxic component of Loxosceles intermedia venom. Six antigenic regions of LiD1 were mapped by using the SPOT method. The corresponding peptides were further chemically synthesized, mixed, and used as immunogens in rabbits. Control animal received recombinant LiD1 alone or together with peptides. We found that the rabbit antibody response to peptides was cross-reactive with LiD1, although only one peptide from the mix of six was immunogenic. The dermonecrotic, hemorrhagic and oedema forming activities induced by LiD1 in naïve rabbits were inhibited by 82%, 35% and 35% respectively, by preincubation of LiD1 with anti-peptide antibodies prepared from immunized rabbits. Animals that were immunized with peptides or LiD1r, were found to be protected from the dermonecrotic, hemorrhagic and oedema forming activities induced by a challenge with LiD1. The protection conferred by peptides was, however, lower than that provided by the peptide protein combination or by the full-length protein. These results encourage us in the utilization of synthetic peptides for therapeutic serum development or vaccination approaches.
- Published
- 2009
- Full Text
- View/download PDF
32. [Patient at hemorrhagic risk. Prevention and local control].
- Author
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Boschetti P, Abbate GG, and Felicori L
- Subjects
- Aged, Gelatin Sponge, Absorbable, Humans, Male, Middle Aged, Risk Factors, Anticoagulants adverse effects, Blood Coagulation Disorders, Dental Care for Persons with Disabilities, Hemostatic Techniques, Oral Hemorrhage prevention & control
- Abstract
The Authors make a short analysis of the main alterations of the coagulative system and of the anticoagulant medicines, used in patients with normal hemostasis, but suffering from cardiovascular disease. It is underlined the importance of a close collaboration between the odontologist and the hematologist or the general practitioner, to be able to make a correct pre-operating prophylaxis, if necessary. All the local procedures that the odontologist must prepare to prevent or at least stop the possible hemorrhagic troubles are finally analysed.
- Published
- 1990
33. [Periodontology and reconstructive dentistry: analysis of the dimension of biological width].
- Author
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Checchi L and Felicori L
- Subjects
- Humans, Periodontal Diseases prevention & control, Dental Restoration, Permanent, Dentures, Gingiva analysis, Periodontium anatomy & histology
- Published
- 1987
34. [Periodontology and reconstructive dentistry. Operative technic].
- Author
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Checchi L and Felicori L
- Subjects
- Gingivectomy, Humans, Tooth Movement Techniques, Crowns, Dental Restoration, Permanent, Periodontal Diseases surgery
- Published
- 1988
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