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Xu Z, Wei D, Zhang H, Demongeot J. A Novel Mathematical Model That Predicts the Protection Time of SARS-CoV-2 Antibodies. Viruses 2023; 15:v15020586. [PMID: 36851801 PMCID: PMC9962246 DOI: 10.3390/v15020586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
Infectious diseases such as SARS-CoV-2 pose a considerable threat to public health. Constructing a reliable mathematical model helps us quantitatively explain the kinetic characteristics of antibody-virus interactions. A novel and robust model is developed to integrate antibody dynamics with virus dynamics based on a comprehensive understanding of immunology principles. This model explicitly formulizes the pernicious effect of the antibody, together with a positive feedback stimulation of the virus-antibody complex on the antibody regeneration. Besides providing quantitative insights into antibody and virus dynamics, it demonstrates good adaptivity in recapturing the virus-antibody interaction. It is proposed that the environmental antigenic substances help maintain the memory cell level and the corresponding neutralizing antibodies secreted by those memory cells. A broader application is also visualized in predicting the antibody protection time caused by a natural infection. Suitable binding antibodies and the presence of massive environmental antigenic substances would prolong the protection time against breakthrough infection. The model also displays excellent fitness and provides good explanations for antibody selection, antibody interference, and self-reinfection. It helps elucidate how our immune system efficiently develops neutralizing antibodies with good binding kinetics. It provides a reasonable explanation for the lower SARS-CoV-2 mortality in the population that was vaccinated with other vaccines. It is inferred that the best strategy for prolonging the vaccine protection time is not repeated inoculation but a directed induction of fast-binding antibodies. Eventually, this model will inform the future construction of an optimal mathematical model and help us fight against those infectious diseases.
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Affiliation(s)
- Zhaobin Xu
- Department of Life Science, Dezhou University, Dezhou 253023, China
- Correspondence: (Z.X.); (J.D.)
| | - Dongqing Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Hongmei Zhang
- Department of Life Science, Dezhou University, Dezhou 253023, China
| | - Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France
- Correspondence: (Z.X.); (J.D.)
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Lefranc MP, Lefranc G. Antibody Sequence and Structure Analyses Using IMGT ®: 30 Years of Immunoinformatics. Methods Mol Biol 2023; 2552:3-59. [PMID: 36346584 DOI: 10.1007/978-1-0716-2609-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org , the global reference in immunogenetics and immunoinformatics, was created in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS) to manage the huge diversity of the antigen receptors, immunoglobulins (IG) or antibodies, and T cell receptors (TR) of the adaptive immune responses. The founding of IMGT® marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT® standardized analysis of the IG, TR, and major histocompatibility (MH) genes and proteins bridges the gap between sequences and three-dimensional (3D) structures, for all jawed vertebrates from fish to humans. This is achieved through the IMGT Scientific chart rules, based on the IMGT-ONTOLOGY axioms, and primarily CLASSIFICATION (IMGT gene and allele nomenclature) and NUMEROTATION (IMGT unique numbering and IMGT Colliers de Perles). IMGT® comprises seven databases (IMGT/LIGM-DB for nucleotide sequences, IMGT/GENE-DB for genes and alleles, etc.), 17 tools (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/HighV-QUEST for NGS, etc.), and more than 20,000 Web resources. In this chapter, the focus is on the tools for amino acid sequences per domain (IMGT/DomainGapAlign and IMGT/Collier-de-Perles), and on the databases for receptors (IMGT/2Dstructure-DB and IMGT/3D-structure-DB) described per receptor, chain, and domain and, for 3D, with contact analysis, paratope, and epitope. The IMGT/mAb-DB is the query interface for monoclonal antibodies (mAb), fusion proteins for immune applications (FPIA), composite proteins for clinical applications (CPCA), and related proteins of interest (RPI) with links to IMGT® 2D and 3D databases and to the World Health Organization (WHO) International Nonproprietary Names (INN) program lists. The chapter includes the human IG allotypes and antibody engineered variants for effector properties used in the description of therapeutical mAb.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002 CNRS, Université de Montpellier, Montpellier cedex 5, France.
| | - Gérard Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002 CNRS, Université de Montpellier, Montpellier cedex 5, France.
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Schall N, Talamini L, Wilhelm M, Jouvin-Marche E, Muller S. P140 Peptide Leads to Clearance of Autoreactive Lymphocytes and Normalizes Immune Response in Lupus-Prone Mice. Front Immunol 2022; 13:904669. [PMID: 35720371 PMCID: PMC9199391 DOI: 10.3389/fimmu.2022.904669] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
In systemic lupus erythematosus, T cells display multiple abnormalities. They are abnormally activated, secrete pro-inflammatory cytokines, help B cells to generate pathogenic autoantibodies, and provoke the accumulation of autoreactive memory T cells. P140, a synthetic peptide evaluated in phase-III clinical trials for lupus, binds HSPA8/HSC70 chaperone protein. In vitro and in vivo, it interferes with hyperactivated chaperone-mediated autophagy, modifying overexpression of major histocompatibility complex class II molecules and antigen presentation to autoreactive T cells. Here, we show that in P140-treated lupus mice, abnormalities affecting T and B cells are no longer detectable in secondary lymphoid tissue and peripheral blood. Data indicate that P140 acts by depleting hyper-activated autoreactive T and B cells and restores normal immune homeostasis. Our findings suggest that P140 belongs to a new family of non-immunosuppressive immunoregulators that do not correct T and B cell abnormalities but rather contribute to the clearance of deleterious T and B cells.
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Affiliation(s)
- Nicolas Schall
- CNRS and Strasbourg University, Unit Biotechnology and Cell signaling, UMR7242/Strasbourg Drug Discovery and Development Institute (IMS), Strasbourg, France
| | - Laura Talamini
- CNRS and Strasbourg University, Unit Biotechnology and Cell signaling, UMR7242/Strasbourg Drug Discovery and Development Institute (IMS), Strasbourg, France
| | - Maud Wilhelm
- CNRS and Strasbourg University, Unit Biotechnology and Cell signaling, UMR7242/Strasbourg Drug Discovery and Development Institute (IMS), Strasbourg, France
| | - Evelyne Jouvin-Marche
- Institute for Advanced Biosciences, Research Centre Université Grenoble Alpes (UGA)-Inserm U1209-CNRS UMR 5309, La Tronche, France
| | - Sylviane Muller
- CNRS and Strasbourg University, Unit Biotechnology and Cell signaling, UMR7242/Strasbourg Drug Discovery and Development Institute (IMS), Strasbourg, France.,Fédération Hospitalo-Universitaire (FHU) OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg University, Strasbourg, France.,University of Strasbourg Institute for Advanced Study, Strasbourg, France
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Lefranc MP, Lefranc G. IMGT®Homo sapiens IG and TR Loci, Gene Order, CNV and Haplotypes: New Concepts as a Paradigm for Jawed Vertebrates Genome Assemblies. Biomolecules 2022; 12:biom12030381. [PMID: 35327572 PMCID: PMC8945572 DOI: 10.3390/biom12030381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023] Open
Abstract
IMGT®, the international ImMunoGeneTics information system®, created in 1989, by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science which emerged at the interface between immunogenetics and bioinformatics for the study of the adaptive immune responses. IMGT® is based on a standardized nomenclature of the immunoglobulin (IG) and T cell receptor (TR) genes and alleles from fish to humans and on the IMGT unique numbering for the variable (V) and constant (C) domains of the immunoglobulin superfamily (IgSF) of vertebrates and invertebrates, and for the groove (G) domain of the major histocompatibility (MH) and MH superfamily (MhSF) proteins. IMGT® comprises 7 databases, 17 tools and more than 25,000 pages of web resources for sequences, genes and structures, based on the IMGT Scientific chart rules generated from the IMGT-ONTOLOGY axioms and concepts. IMGT® reference directories are used for the analysis of the NGS high-throughput expressed IG and TR repertoires (natural, synthetic and/or bioengineered) and for bridging sequences, two-dimensional (2D) and three-dimensional (3D) structures. This manuscript focuses on the IMGT®Homo sapiens IG and TR loci, gene order, copy number variation (CNV) and haplotypes new concepts, as a paradigm for jawed vertebrates genome assemblies.
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Lefranc MP, Lefranc G. Immunoglobulins or Antibodies: IMGT ® Bridging Genes, Structures and Functions. Biomedicines 2020; 8:E319. [PMID: 32878258 PMCID: PMC7555362 DOI: 10.3390/biomedicines8090319] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
IMGT®, the international ImMunoGeneTics® information system founded in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science at the interface between immunogenetics and bioinformatics. For the first time, the immunoglobulin (IG) or antibody and T cell receptor (TR) genes were officially recognized as 'genes' as well as were conventional genes. This major breakthrough has allowed the entry, in genomic databases, of the IG and TR variable (V), diversity (D) and joining (J) genes and alleles of Homo sapiens and of other jawed vertebrate species, based on the CLASSIFICATION axiom. The second major breakthrough has been the IMGT unique numbering and the IMGT Collier de Perles for the V and constant (C) domains of the IG and TR and other proteins of the IG superfamily (IgSF), based on the NUMEROTATION axiom. IMGT-ONTOLOGY axioms and concepts bridge genes, sequences, structures and functions, between biological and computational spheres in the IMGT® system (Web resources, databases and tools). They provide the IMGT Scientific chart rules to identify, to describe and to analyse the IG complex molecular data, the huge diversity of repertoires, the genetic (alleles, allotypes, CNV) polymorphisms, the IG dual function (paratope/epitope, effector properties), the antibody humanization and engineering.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, Université de Montpellier UM, Centre National de la Recherche Scientifique CNRS, UMR 9002 CNRS-UM, 141 Rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
| | - Gérard Lefranc
- IMGT, The International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, Université de Montpellier UM, Centre National de la Recherche Scientifique CNRS, UMR 9002 CNRS-UM, 141 Rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
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Abraham TS, Flickinger JC, Waldman SA, Snook AE. TCR Retrogenic Mice as a Model To Map Self-Tolerance Mechanisms to the Cancer Mucosa Antigen GUCY2C. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 202:1301-1310. [PMID: 30642983 PMCID: PMC6363846 DOI: 10.4049/jimmunol.1801206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 12/13/2018] [Indexed: 01/21/2023]
Abstract
Characterizing self-tolerance mechanisms and their failure is critical to understand immune homeostasis, cancer immunity, and autoimmunity. However, examination of self-tolerance mechanisms has relied primarily on transgenic mice expressing TCRs targeting well-characterized, but nonphysiologic, model Ags, such as OVA and hemagglutinin. Identifying TCRs directed against bona fide self-antigens is made difficult by the extraordinary diversity of TCRs and the low prevalence of Ag-specific clones (<10-100 naive cells per organism), limiting dissection of tolerance mechanisms restricting immunity to self-proteins. In this study, we isolated and characterized TCRs recognizing the intestinal epithelial cell receptor and colorectal cancer Ag GUCY2C to establish a model to study self-antigen-specific tolerance mechanisms. GUCY2C-specific CD4+ effector T cells were isolated from immunized, nontolerant Gucy2c -/- mice. Next-generation sequencing identified GUCY2C-specific TCRs, which were engineered into CD4+ T cells in vitro to confirm TCR recognition of GUCY2C. Further, the generation of "retrogenic" mice by reconstitution with TCR-transduced hematopoietic stem cells resulted in normal CD4+ T cell development, responsiveness to immunization, and GUCY2C-induced tolerance in recipient mice, recapitulating observations in conventional models. This retrogenic model can be employed to define self-tolerance mechanisms restricting T and B cell responses to GUCY2C to optimize colorectal cancer immunotherapy without autoimmunity.
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Affiliation(s)
- Tara S Abraham
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107
| | - John C Flickinger
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107
| | - Scott A Waldman
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107
| | - Adam E Snook
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107
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Stability, complexity and robustness in population dynamics. Acta Biotheor 2014; 62:243-84. [PMID: 25107273 DOI: 10.1007/s10441-014-9229-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 06/17/2014] [Indexed: 12/21/2022]
Abstract
The problem of stability in population dynamics concerns many domains of application in demography, biology, mechanics and mathematics. The problem is highly generic and independent of the population considered (human, animals, molecules,…). We give in this paper some examples of population dynamics concerning nucleic acids interacting through direct nucleic binding with small or cyclic RNAs acting on mRNAs or tRNAs as translation factors or through protein complexes expressed by genes and linked to DNA as transcription factors. The networks made of these interactions between nucleic acids (considered respectively as edges and nodes of their interaction graph) are complex, but exhibit simple emergent asymptotic behaviours, when time tends to infinity, called attractors. We show that the quantity called attractor entropy plays a crucial role in the study of the stability and robustness of such genetic networks.
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9
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Lefranc MP. IMGT, the International ImMunoGeneTics Information System. Cold Spring Harb Protoc 2011; 2011:595-603. [PMID: 21632786 DOI: 10.1101/pdb.top115] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Marie-Paule Lefranc
- IMGT, international ImMunoGeneTics information system, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Université Montpellier 2, Institut de Génétique Humaine IGH, UPR CNRS 1142, 34396 Montpellier cedex 5, France.
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10
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Lefranc MP. IMGT unique numbering for the variable (V), constant (C), and groove (G) domains of IG, TR, MH, IgSF, and MhSF. Cold Spring Harb Protoc 2011; 2011:633-42. [PMID: 21632789 DOI: 10.1101/pdb.ip85] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Marie-Paule Lefranc
- IMGT, international ImMunoGeneTics information system, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Université Montpellier 2, Institut de Génétique Humaine IGH, UPR CNRS 1142, 34396 Montpellier cedex 5, France.
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Gaudart J, Ghassani M, Mintsa J, Rachdi M, Waku J, Demongeot J. Demography and diffusion in epidemics: malaria and black death spread. Acta Biotheor 2010; 58:277-305. [PMID: 20706773 DOI: 10.1007/s10441-010-9103-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 06/28/2010] [Indexed: 01/14/2023]
Abstract
The classical models of epidemics dynamics by Ross and McKendrick have to be revisited in order to incorporate elements coming from the demography (fecundity, mortality and migration) both of host and vector populations and from the diffusion and mutation of infectious agents. The classical approach is indeed dealing with populations supposed to be constant during the epidemic wave, but the presently observed pandemics show duration of their spread during years imposing to take into account the host and vector population changes as well as the transient or permanent migration and diffusion of hosts (susceptible or infected), as well as vectors and infectious agents. Two examples are presented, one concerning the malaria in Mali and the other the plague at the middle-age.
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Affiliation(s)
- J Gaudart
- LERTIM, EA 3283, Faculty of Medicine, Aix-Marseille University, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France.
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Numerical modelling of the V-J combinations of the T cell receptor TRA/TRD locus. PLoS Comput Biol 2010; 6:e1000682. [PMID: 20174554 PMCID: PMC2824756 DOI: 10.1371/journal.pcbi.1000682] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 01/21/2010] [Indexed: 01/07/2023] Open
Abstract
T-Cell antigen Receptor (TR) repertoire is generated through rearrangements of V and J genes encoding α and β chains. The quantification and frequency for every V-J combination during ontogeny and development of the immune system remain to be precisely established. We have addressed this issue by building a model able to account for Vα-Jα gene rearrangements during thymus development of mice. So we developed a numerical model on the whole TRA/TRD locus, based on experimental data, to estimate how Vα and Jα genes become accessible to rearrangements. The progressive opening of the locus to V-J gene recombinations is modeled through windows of accessibility of different sizes and with different speeds of progression. Furthermore, the possibility of successive secondary V-J rearrangements was included in the modelling. The model points out some unbalanced V-J associations resulting from a preferential access to gene rearrangements and from a non-uniform partition of the accessibility of the J genes, depending on their location in the locus. The model shows that 3 to 4 successive rearrangements are sufficient to explain the use of all the V and J genes of the locus. Finally, the model provides information on both the kinetics of rearrangements and frequencies of each V-J associations. The model accounts for the essential features of the observed rearrangements on the TRA/TRD locus and may provide a reference for the repertoire of the V-J combinatorial diversity. Lymphocytes of the immune system ensure the body defense by the expression of receptors which are specific of targets, termed antigens. Each lymphocyte, deriving from the same original clone, expresses the same unique receptor. To achieve the production of receptors covering the wide variety of antigens, lymphocytes use a specialized genetic mechanism consisting of gene rearrangements. For instance, the genes encoding the receptor of the alpha chain of the T lymphocyte receptor (TRA) spread over a 1500 Kb genetic region which includes around 100 V genes, 60 J genes, and a single C gene. To constitute a functional alpha chain, one of the V and one of the J genes rearrange together to form a single exon. The precise definition of these V-J combinations is essential to understand the repertoire of TRA. We have developed a numerical model simulating all of the V-J combinations of TRA, fitting the available experimental observations obtained from the analysis of TRA in T lymphocytes of the thymus and the blood. Our model gives new insights on the rules controlling the use of V and J genes in providing a dynamic estimation of the total V-J combinations.
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Abstract
We illustrate in this review some applications of systems biology in the medical and biological areas. After a brief summary of time scales experienced by medical -observations and of the general scheme of dynamic systems, we describe how some techniques underlying the complex systems theory can be applied to model medical issues in immunology, medical genetics, developmental morphogenesis, biochemistry, epidemiology, telemedecine and multiple platforms of expertise. In concluding, we will discuss the issue of "clinomics" coupling clinical and -omics data in a unique patient-specific file.
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Affiliation(s)
- Jacques Demongeot
- TIMC-IMAG UMR UJF/CNRS 5525, Université J. Fourier de Grenoble, Faculté de médecine, 38700 La Tronche, France.
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Abbas L, Demongeot J, Glade N. Synchrony in reaction-diffusion models of morphogenesis: applications to curvature-dependent proliferation and zero-diffusion front waves. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2009; 367:4829-4862. [PMID: 19884182 DOI: 10.1098/rsta.2009.0170] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The paper presents the classical age-dependent approach of the morphogenesis in the framework of the von Foerster equation, in which we introduce a new constraint and study a new feature: (i) the new constraint concerns cell proliferation along the contour lines of the cell density, depending on the local curvature such as it favours the amplification of the concavities (like in the gastrulation process) and (ii) the new feature consists of considering, on the cell density surface, a remarkable line (the null mean Gaussian curvature line), on which the normal diffusion vanishes, favouring local coexistence of diffusing morphogens, metabolites or cells, and hence the auto-assemblages of these entities. Two applications to biological multi-agents systems are studied, gastrulation and feather morphogenesis.
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Affiliation(s)
- Lamia Abbas
- Institut National des Sciences Appliquées Rouen, Laboratoire de Mathématiques de l'INSA EA 3226, Place Emile Blondel BP 08, 76131 Mont-Saint-Aignan, France
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RNA relics and origin of life. Int J Mol Sci 2009; 10:3420-3441. [PMID: 20111682 PMCID: PMC2812825 DOI: 10.3390/ijms10083420] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 07/11/2009] [Accepted: 07/28/2009] [Indexed: 11/18/2022] Open
Abstract
A number of small RNA sequences, located in different non-coding sequences and highly preserved across the tree of life, have been suggested to be molecular fossils, of ancient (and possibly primordial) origin. On the other hand, recent years have revealed the existence of ubiquitous roles for small RNA sequences in modern organisms, in functions ranging from cell regulation to antiviral activity. We propose that a single thread can be followed from the beginning of life in RNA structures selected only for stability reasons through the RNA relics and up to the current coevolution of RNA sequences; such an understanding would shed light both on the history and on the present development of the RNA machinery and interactions. After presenting the evidence (by comparing their sequences) that points toward a common thread, we discuss a scenario of genome coevolution (with emphasis on viral infectious processes) and finally propose a plan for the reevaluation of the stereochemical theory of the genetic code; we claim that it may still be relevant, and not only for understanding the origin of life, but also for a comprehensive picture of regulation in present-day cells.
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Jouvin-Marche E, Fuschiotti P, Marche PN. Dynamic Aspects of TCRα Gene Recombination: Qualitative and Quantitative Assessments of the TCRα Chain Repertoire in Man and Mouse. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2009; 650:82-92. [DOI: 10.1007/978-1-4419-0296-2_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Lefranc MP. IMGT, the international ImMunoGeneTics information system for Immunoinformatics. Methods for querying IMGT databases, tools, and Web resources in the context of immunoinformatics. Methods Mol Biol 2008; 409:19-42. [PMID: 18449990 DOI: 10.1007/978-1-60327-118-9_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), was created in 1989 by the Laboratoire d'lmmunoGénétique Moléculaire (LIGM) (Université Montpellier II and CNRS) at Montpellier, France, in order to standardize and manage the complexity of immunogenetics data. IMGT is recognized as the international reference in immunogenetics and immunoinformatics. IMGT is a high quality integrated knowledge resource, specialized in (i) the immunoglobulin (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates; (ii) proteins that belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF); and (iii) related proteins of the immune systems (RPI) of any species. IMGT provides a common access to standardized data from genome, proteome, genetics, and three-dimensional (3D) structures for the IG, TR, MHC, IgSF, MhcSF, and RPI. IMGT interactive on-line tools are provided for genome, sequence, and 3D structure analysis. IMGT Web resources comprise 8,000 HTML pages of synthesis and knowledge (IMGT Scientific chart, IMGT Repertoire, IMGT Education, etc.) and external links (IMGT Bloc-notes and IMGT other accesses).
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Affiliation(s)
- Marie-Paule Lefranc
- Institut Universitaire de France, Laboratoire d'ImmunoGénétique Moléculaire, Université Montpellier II, UPR CNRS 1142, France
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Demongeot J, Glade N, Moreira A. Evolution and RNA relics. a systems biology view. Acta Biotheor 2008; 56:5-25. [PMID: 18273683 DOI: 10.1007/s10441-008-9028-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Accepted: 12/19/2007] [Indexed: 02/05/2023]
Abstract
The genetic code has evolved from its initial non-degenerate wobble version until reaching its present state of degeneracy. By using the stereochemical hypothesis, we revisit the problem of codon assignations to the synonymy classes of amino-acids. We obtain these classes with a simple classifier based on physico-chemical properties of nucleic bases, like hydrophobicity and molecular weight. Then we propose simple RNA (or more generally XNA, with X for D, P or R) ring structures that present, overlap included, one and only one codon by synonymy class as solutions of a combinatory variational problem. We compare these solutions to sequences of present RNAs considered as relics, with a high interspecific invariance, like invariant parts of (t)RNAs and micro-RNAs. We conclude by emphasizing some optimal properties of the genetic code.
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Affiliation(s)
- Jacques Demongeot
- TIMC-IMAG, UMR CNRS 5525, Faculty of Medicine of Grenoble, University J. Fourier, 38 700 La Tronche, France.
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IMGT, the International ImMunoGeneTics Information System for Immunoinformatics : methods for querying IMGT databases, tools, and web resources in the context of immunoinformatics. Mol Biotechnol 2008; 40:101-11. [PMID: 18463990 DOI: 10.1007/s12033-008-9062-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2008] [Indexed: 10/22/2022]
Abstract
IMGT, the International ImMunoGeneTics information system ( http://imgt.cines.fr ), was created in 1989 by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM) (Université Montpellier 2 and CNRS) at Montpellier, France, in order to standardize and manage the complexity of immunogenetics data. IMGT is recognized as the international reference in immunogenetics and immunoinformatics. IMGT is a high quality integrated knowledge resource, specialized in (i) the immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates; (ii) proteins that belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF); and (iii) related proteins of the immune systems (RPI) of any species. IMGT provides a common access to standardized data from genome, proteome, genetics, and three-dimensional (3D) structures for the IG, TR, MHC, IgSF, MhcSF, and RPI. IMGT interactive on-line tools are provided for genome, sequence, and 3D structure analysis. IMGT Web resources comprise 10,000 HTML pages of synthesis and knowledge (IMGT Scientific chart, IMGT Repertoire, IMGT Education, etc.) and external links (IMGT Bloc-notes and IMGT other accesses).
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Mi JQ, Manches O, Wang J, Perron P, Weisbuch S, Marche PN, Renversez JC, Bensa JC, Sotto JJ, Cahn JY, Leroux D, Bonnefoix T. Development of autologous cytotoxic CD4+T clones in a human model of B-cell non-Hodgkin follicular lymphoma. Br J Haematol 2006; 135:324-35. [PMID: 16984392 DOI: 10.1111/j.1365-2141.2006.06294.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Immunotherapy for cancer aims to generate cytotoxic cells that are capable of eradicating tumour cells. It has been well demonstrated that helper, non-cytotoxic CD4(+) T cells are important for the induction and maintenance of anti-tumour immunity exerted by cytotoxic CD8(+) T cells. In contrast, the existence of direct anti-tumour, effector cytotoxic CD4(+) T cells remains elusive, mainly due to the paucity of reliable experimental data, especially in human B-cell non-Hodgkin lymphomas. This study developed an appropriate, autologous follicular B-cell non-Hodgkin follicular lymphoma model, including the in vitro establishment of a malignant, human leucocyte antigen class I (HLA-I) deficient B-cell line, and the generation of three autologous anti-tumour cytotoxic CD4(+) T-cell clones originating from the peripheral blood of the same patient. These three clones were considered as tumour specific, because they were capable of killing the malignant, HLA-I-deficient B-cell line through a classical HLA-II restricted perforin-mediated pathway, but did not lyse the Epstein-Barr virus-infected autologous normal B lymphocytes. All three CD4(+)clones were T-cell receptor Vbeta17-Dbeta1-Jbeta1.2 and exhibited an identical complementarity-determining region 3, suggesting the immunodominance of a single peptide antigen presented by tumour cells. Such lymphoma models would provide a useful tool for in vivo expansion and the adoptive transfer of selected CD4(+) cytotoxic cells in immunotherapeutic strategies.
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Affiliation(s)
- Jian-Qing Mi
- Institut National de la Santé et de la Recherche Médicale [Inserm E353, Lymphoma Research Group (Molecular Bases of Tumor Progression)], Université Joseph Fourier, La Tronche, France.
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Baum TP, Hierle V, Pasqual N, Bellahcene F, Chaume D, Lefranc MP, Jouvin-Marche E, Marche PN, Demongeot J. IMGT/GeneInfo: T cell receptor gamma TRG and delta TRD genes in database give access to all TR potential V(D)J recombinations. BMC Bioinformatics 2006; 7:224. [PMID: 16640788 PMCID: PMC1482724 DOI: 10.1186/1471-2105-7-224] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Accepted: 04/26/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Adaptative immune repertoire diversity in vertebrate species is generated by recombination of variable (V), diversity (D) and joining (J) genes in the immunoglobulin (IG) loci of B lymphocytes and in the T cell receptor (TR) loci of T lymphocytes. These V-J and V-D-J gene rearrangements at the DNA level involve recombination signal sequences (RSS). Whereas many data exist, they are scattered in non specialized resources with different nomenclatures (eg. flat files) and are difficult to extract. DESCRIPTION IMGT/GeneInfo is an online information system that provides, through a user-friendly interface, exhaustive information resulting from the complex mechanisms of T cell receptor V-J and V-D-J recombinations. T cells comprise two populations which express the alphabeta and gammadelta TR, respectively. The first version of the system dealt with the Homo sapiens and Mus musculus TRA and TRB loci whose gene rearrangements allow the synthesis of the alphabeta TR chains. In this paper, we present the second version of IMGT/GeneInfo where we complete the database for the Homo sapiens and Mus musculus TRG and TRD loci along with the introduction of a quality control procedure for existing and new data. We also include new functionalities to the four loci analysis, giving, to date, a very informative tool which allows to work on V(D)J genes of all TR loci in both human and mouse species. IMGT/GeneInfo provides more than 59,000 rearrangement combinations with a full gene description which is freely available at http://imgt.cines.fr/GeneInfo. CONCLUSION IMGT/GeneInfo allows all TR information sequences to be in the same spot, and are now available within two computer-mouse clicks. This is useful for biologists and bioinformaticians for the study of T lymphocyte V(D)J gene rearrangements and their applications in immune response analysis.
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Affiliation(s)
- Thierry-Pascal Baum
- Laboratoire TIMC-IMAG-CNRS UMR 5525, Techniques de l'Imagerie, de la Modélisation et de la Cognition; Université Joseph Fourier, Grenoble 1, Faculté de Médecine, Domaine de la Merci, 38706 La Tronche, France
| | - Vivien Hierle
- Laboratoire TIMC-IMAG-CNRS UMR 5525, Techniques de l'Imagerie, de la Modélisation et de la Cognition; Université Joseph Fourier, Grenoble 1, Faculté de Médecine, Domaine de la Merci, 38706 La Tronche, France
| | - Nicolas Pasqual
- Laboratoire d'Immunochimie, CEA-Grenoble/DRDC/ICH; INSERM U548; Université Joseph Fourier Grenoble 1, 17 rue des Martyrs, 38054 Grenoble Cedex 09, France
- ImmunID Technologies, 17 rue des Martyrs, 38054 Grenoble Cedex 09, France
| | - Fatena Bellahcene
- Laboratoire d'Immunochimie, CEA-Grenoble/DRDC/ICH; INSERM U548; Université Joseph Fourier Grenoble 1, 17 rue des Martyrs, 38054 Grenoble Cedex 09, France
- ImmunID Technologies, 17 rue des Martyrs, 38054 Grenoble Cedex 09, France
| | - Denys Chaume
- Laboratoire d'ImmunoGénétique Moléculaire, LIGM; Université Montpellier II, UPR CNRS 1142, IGH, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Marie-Paule Lefranc
- Laboratoire d'ImmunoGénétique Moléculaire, LIGM; Université Montpellier II, UPR CNRS 1142, IGH, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
- Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
| | - Evelyne Jouvin-Marche
- Laboratoire d'Immunochimie, CEA-Grenoble/DRDC/ICH; INSERM U548; Université Joseph Fourier Grenoble 1, 17 rue des Martyrs, 38054 Grenoble Cedex 09, France
| | - Patrice Noël Marche
- Laboratoire d'Immunochimie, CEA-Grenoble/DRDC/ICH; INSERM U548; Université Joseph Fourier Grenoble 1, 17 rue des Martyrs, 38054 Grenoble Cedex 09, France
| | - Jacques Demongeot
- Laboratoire TIMC-IMAG-CNRS UMR 5525, Techniques de l'Imagerie, de la Modélisation et de la Cognition; Université Joseph Fourier, Grenoble 1, Faculté de Médecine, Domaine de la Merci, 38706 La Tronche, France
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Lefranc MP. IMGT, the international ImMunoGeneTics information system: a standardized approach for immunogenetics and immunoinformatics. Immunome Res 2005; 1:3. [PMID: 16305737 PMCID: PMC1312312 DOI: 10.1186/1745-7580-1-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2005] [Accepted: 09/20/2005] [Indexed: 11/10/2022] Open
Abstract
IMGT, the international ImMunoGeneTics information system http://imgt.cines.fr, was created in 1989 by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM) (Université Montpellier II and CNRS) at Montpellier, France. IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune system (RPI) of any species which belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF). IMGT consists of five databases, ten on-line tools and more than 8,000 HTML pages of Web resources. IMGT provides a common access to standardized data from genome, genetics, proteome and three-dimensional structures. The accuracy and the consistency of IMGT data are based on IMGT-ONTOLOGY, a semantic specification of terms to be used in immunogenetics and immunoinformatics. IMGT-ONTOLOGY comprises six main concepts: IDENTIFICATION, CLASSIFICATION, DESCRIPTION, NUMEROTATION, ORIENTATION and OBTENTION. Based on these concepts, the controlled vocabulary and the annotation rules necessary for the immunogenetics data identification, classification, description and numbering and for the management of IMGT knowledge are defined in the IMGT Scientific chart. IMGT is the international reference in immunogenetics and immunoinformatics for medical research (repertoire analysis of the IG antibody sites and of the TR recognition sites in autoimmune and infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research (IG and TR repertoires in farm and wild life species), genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (single chain Fragment variable (scFv), phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (detection and follow up of residual diseases) and therapeutical approaches (grafts, immunotherapy, vaccinology). IMGT is freely available at http://imgt.cines.fr.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT, the international ImMunoGeneTics information system, Université Montpellier II, Institut Universitaire de France, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Montpellier, France.
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Giudicelli V, Chaume D, Lefranc MP. IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res 2005; 33:D256-61. [PMID: 15608191 PMCID: PMC539964 DOI: 10.1093/nar/gki010] [Citation(s) in RCA: 369] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IMGT/GENE-DB is the comprehensive IMGT genome database for immunoglobulin (IG) and T cell receptor (TR) genes from human and mouse, and, in development, from other vertebrates. IMGT/GENE-DB is the international reference for the IG and TR gene nomenclature and works in close collaboration with the HUGO Nomenclature Committee, Mouse Genome Database and genome committees for other species. IMGT/GENE-DB allows a search of IG and TR genes by locus, group and subgroup, which are CLASSIFICATION concepts of IMGT-ONTOLOGY. Short cuts allow the retrieval gene information by gene name or clone name. Direct links with configurable URL give access to information usable by humans or programs. An IMGT/GENE-DB entry displays accurate gene data related to genome (gene localization), allelic polymorphisms (number of alleles, IMGT reference sequences, functionality, etc.) gene expression (known cDNAs), proteins and structures (Protein displays, IMGT Colliers de Perles). It provides internal links to the IMGT sequence databases and to the IMGT Repertoire Web resources, and external links to genome and generalist sequence databases. IMGT/GENE-DB manages the IMGT reference directory used by the IMGT tools for IG and TR gene and allele comparison and assignment, and by the IMGT databases for gene data annotation. IMGT/GENE-DB is freely available at http://imgt.cines.fr.
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Affiliation(s)
- Véronique Giudicelli
- IMGT, the international ImMunoGeneTics information system, Laboratoire d'ImmunoGénétique Moléculaire, LIGM, Université Montpellier II, Institut de Génétique Humaine, IGH, UPR CNRS 1142, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
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Lefranc MP, Giudicelli V, Kaas Q, Duprat E, Jabado-Michaloud J, Scaviner D, Ginestoux C, Clément O, Chaume D, Lefranc G. IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res 2005; 33:D593-7. [PMID: 15608269 PMCID: PMC540019 DOI: 10.1093/nar/gki065] [Citation(s) in RCA: 231] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The international ImMunoGeneTics information system® (IMGT) (http://imgt.cines.fr), created in 1989, by the Laboratoire d'ImmunoGénétique Moléculaire LIGM (Université Montpellier II and CNRS) at Montpellier, France, is a high-quality integrated knowledge resource specializing in the immunoglobulins (IGs), T cell receptors (TRs), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune systems (RPI) that belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF). IMGT includes several sequence databases (IMGT/LIGM-DB, IMGT/PRIMER-DB, IMGT/PROTEIN-DB and IMGT/MHC-DB), one genome database (IMGT/GENE-DB) and one three-dimensional (3D) structure database (IMGT/3Dstructure-DB), Web resources comprising 8000 HTML pages (IMGT Marie-Paule page), and interactive tools. IMGT data are expertly annotated according to the rules of the IMGT Scientific chart, based on the IMGT-ONTOLOGY concepts. IMGT tools are particularly useful for the analysis of the IG and TR repertoires in normal physiological and pathological situations. IMGT is used in medical research (autoimmune diseases, infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research, biotechnology related to antibody engineering (phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (clonalities, detection and follow up of residual diseases) and therapeutical approaches (graft, immunotherapy and vaccinology). IMGT is freely available at http://imgt.cines.fr.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT, the international ImMunoGeneTics information system Université Montpellier II, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
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Giudicelli V, Chaume D, Lefranc MP. IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis. Nucleic Acids Res 2004; 32:W435-40. [PMID: 15215425 PMCID: PMC441550 DOI: 10.1093/nar/gkh412] [Citation(s) in RCA: 224] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2004] [Revised: 04/01/2004] [Accepted: 04/01/2004] [Indexed: 11/14/2022] Open
Abstract
IMGT/V-QUEST, for 'V-QUEry and STandardization', is an integrated software program which analyses the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences. The extraordinary diversity of the IG and TR repertoires (10(12) antibodies and 10(12) TR per individual) results from several mechanisms at the DNA level: the combinatorial diversity of the variable (V), diversity (D) and joining (J) genes, the N-diversity and, for IG, the somatic mutations. IMGT/V-QUEST identifies the V, D and J genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. IMGT/V-QUEST delimits the structurally important features, frameworks and complementarity-determining regions (the last of these forming the antigen binding site), on the basis of the IMGT unique numbering. The tool localizes the somatic mutations of the IG rearranged sequences. IMGT/V-QUEST also dynamically displays a graphical two-dimensional representation, or IMGT Collier de Perles, of the IG and TR variable regions. Moreover, IMGT/V-QUEST can interact with IMGT/JunctionAnalysis for the detailed description of the V-J and V-D-J junctions, and with IMGT/PhyloGene for the construction of phylogenetic trees. IMGT/V-QUEST is currently available for human and mouse, and partly for non-human primates, sheep, chondrichthyes and teleostei. IMGT/V-QUEST is freely available at http://imgt.cines.fr.
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Affiliation(s)
- Véronique Giudicelli
- IMGT, the international ImMunoGeneTics information system, Laboratoire d'ImmunoGénétique Moléculaire, LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, 141 rue de la Cardonille, F-34396 Montpellier Cedex 5, France
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Lefranc MP. IMGT-ONTOLOGY and IMGT databases, tools and Web resources for immunogenetics and immunoinformatics. Mol Immunol 2004; 40:647-60. [PMID: 14644091 DOI: 10.1016/j.molimm.2003.09.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The international ImMunoGeneTics information system (IMGT; http://imgt.cines.fr), is a high quality integrated information system specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), and related proteins of the immune system (RPI) of human and other vertebrates, created in 1989, by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM; Université Montpellier II and CNRS) at Montpellier, France. IMGT provides a common access to standardized data which include nucleotide and protein sequences, oligonucleotide primers, gene maps, genetic polymorphisms, specificities, 2D and 3D structures. IMGT consists of several sequence databases (IMGT/LIGM-DB, IMGT/MHC-DB, IMGT/PRIMER-DB), one genome database (IMGT/GENE-DB) and one 3D structure database (IMGT/3Dstructure-DB), interactive tools for sequence analysis (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/PhyloGene, IMGT/Allele-Align), for genome analysis (IMGT/GeneSearch, IMGT/GeneView, IMGT/LocusView) and for 3D structure analysis (IMGT/StructuralQuery), and Web resources ("IMGT Marie-Paule page") comprising 8000 HTML pages. IMGT other accesses include SRS, FTP, search by BLAST, etc. By its high quality and its easy data distribution, IMGT has important implications in medical research (repertoire in autoimmune diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research, genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (single chain Fragment variable (scFv), phage displays, combinatorial libraries) and therapeutical approaches (grafts, immunotherapy). IMGT is freely available at http://imgt.cines.fr.
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Affiliation(s)
- Marie-Paule Lefranc
- Laboratoire d'ImmunoGénétique Moléculaire, LIGM, Institut de Génétique Humaine IGH, Université Montpellier II, UPR CNRS 1142, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France.
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