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Martinez-Barnetche J, Godoy-Lozano EE, Saint Remy-Hernández S, Pacheco-Olvera DL, Téllez-Sosa J, Valdovinos-Torres H, Pastelin-Palacios R, Mena H, Zambrano L, López-Macías C. Characterization of immunoglobulin loci in the gigantic genome of Ambystoma mexicanum. Front Immunol 2023; 14:1039274. [PMID: 36776846 PMCID: PMC9911811 DOI: 10.3389/fimmu.2023.1039274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/06/2023] [Indexed: 01/28/2023] Open
Abstract
Background The axolotl, Ambystoma mexicanum is a unique biological model for complete tissue regeneration. Is a neotenic endangered species and is highly susceptible to environmental stress, including infectious disease. In contrast to other amphibians, the axolotl is particularly vulnerable to certain viral infections. Like other salamanders, the axolotl genome is one of the largest (32 Gb) and the impact of genome size on Ig loci architecture is unknown. To better understand the immune response in axolotl, we aimed to characterize the immunoglobulin loci of A. mexicanum and compare it with other model vertebrates. Methods The most recently published genome sequence of A. mexicanum (V6) was used for alignment-based annotation and manual curation using previously described axolotl Ig sequences or reference sequences from other vertebrates. Gene models were further curated using A. mexicanum spleen RNA-seq data. Human, Xenopus tropicalis, Danio rerio (zebrafish), and eight tetrapod reference genomes were used for comparison. Results Canonical A. mexicanum heavy chain (IGH), lambda (IGL), sigma (IGS), and the putative surrogate light chain (SLC) loci were identified. No kappa locus was found. More than half of the IGHV genes and the IGHF gene are pseudogenes and there is no clan I IGHV genes. Although the IGH locus size is proportional to genome size, we found local size restriction in the IGHM gene and the V gene intergenic distances. In addition, there were V genes with abnormally large V-intron sizes, which correlated with loss of gene functionality. Conclusion The A. mexicanum immunoglobulin loci share the same general genome architecture as most studied tetrapods. Consistent with its large genome, Ig loci are larger; however, local size restrictions indicate evolutionary constraints likely to be imposed by high transcriptional demand of certain Ig genes, as well as the V(D)J recombination over very long genomic distance ranges. The A. mexicanum has undergone an extensive process of Ig gene loss which partially explains a reduced potential repertoire diversity that may contribute to its impaired antibody response.
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Affiliation(s)
- Jesús Martinez-Barnetche
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico,*Correspondence: Jesús Martinez-Barnetche, ; Constantino López-Macías,
| | | | - Stephanie Saint Remy-Hernández
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico,Unidad de Investigación Médica en Inmunoquímica, UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, México City, Mexico
| | - Diana Laura Pacheco-Olvera
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico,Unidad de Investigación Médica en Inmunoquímica, UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, México City, Mexico
| | - Juan Téllez-Sosa
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Humberto Valdovinos-Torres
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | | | - Horacio Mena
- Laboratorio de Restauración Ecológica, Instituto de Biología. Universidad Nacional Autónoma de México, México City, Mexico
| | - Luis Zambrano
- Laboratorio de Restauración Ecológica, Instituto de Biología. Universidad Nacional Autónoma de México, México City, Mexico
| | - Constantino López-Macías
- Unidad de Investigación Médica en Inmunoquímica, UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, México City, Mexico,*Correspondence: Jesús Martinez-Barnetche, ; Constantino López-Macías,
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Rodríguez-Santiago J, Rodríguez-Medina N, Tamayo-Legorreta EM, Silva-Sánchez J, Téllez-Sosa J, Duran-Bedolla J, Aguilar-Vera A, Lecona-Valera AN, Garza-Ramos U, Alpuche-Aranda C. Molecular and Genomic Insights of mcr-1-Producing Escherichia coli Isolates from Piglets. Antibiotics (Basel) 2022; 11:antibiotics11020157. [PMID: 35203760 PMCID: PMC8868104 DOI: 10.3390/antibiotics11020157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 02/04/2023] Open
Abstract
The use of colistin in food-producing animals favors the emergence and spread of colistin-resistant strains. Here, we investigated the occurrence and molecular mechanisms of colistin resistance among E. coli isolates from a Mexican piglet farm. A collection of 175 cephalosporin-resistant colonies from swine fecal samples were recovered. The colistin resistance phenotype was identified by rapid polymyxin test and the mcr-type genes were screened by PCR. We assessed the colistin-resistant strains by antimicrobial susceptibility test, pulse-field gel electrophoresis, plasmid profile, and mating experiments. Whole-Genome Sequencing data was used to explore the resistome, virulome, and mobilome of colistin-resistant strains. A total of four colistin-resistant E. coli were identified from the cefotaxime-resistant colonies. All harbored the plasmid-borne mcr-1 gene, which was located on conjugative 170-kb IncHI-2 plasmid co-carrying ESBLs genes. Thus, high antimicrobial resistance rates were observed for several antibiotic families. In the RC2-007 strain, the mcr-1 gene was located as part of a prophage carried on non-conjugative 100-kb-plasmid, which upon being transformed into K. variicola strain increased the polymyxin resistance 2-fold. The genomic analysis showed a broad resistome and virulome. Our findings suggest that colistin resistance followed independent acquisition pathways as clonal and non-genetically related mcr-1-harboring strains were identified. These E. coli isolates represent a reservoir of antibiotic resistance and virulence genes in animals for human consumption which could be potentially propagated into other interfaces.
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Affiliation(s)
- Jonathan Rodríguez-Santiago
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Nadia Rodríguez-Medina
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Elsa María Tamayo-Legorreta
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Jesús Silva-Sánchez
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Juan Téllez-Sosa
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Josefina Duran-Bedolla
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Alejandro Aguilar-Vera
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62100, Morelos, Mexico;
| | - Alba Neri Lecona-Valera
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
| | - Ulises Garza-Ramos
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
- Correspondence: (U.G.-R.); (C.A.-A.)
| | - Celia Alpuche-Aranda
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca 62100, Morelos, Mexico; (J.R.-S.); (N.R.-M.); (E.M.T.-L.); (J.S.-S.); (J.T.-S.); (J.D.-B.); (A.N.L.-V.)
- Correspondence: (U.G.-R.); (C.A.-A.)
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Alvarado-Delgado A, Martínez-Barnetche J, Téllez-Sosa J, Rodríguez MH, Gutiérrez-Millán E, Zumaya-Estrada FA, Saldaña-Navor V, Rodríguez MC, Tello-López Á, Lanz-Mendoza H. Prediction of neuropeptide precursors and differential expression of adipokinetic hormone/corazonin-related peptide, hugin and corazonin in the brain of malaria vector Nyssorhynchus albimanus during a Plasmodium berghei infection. Current Research in Insect Science 2021; 1:100014. [PMID: 36003598 PMCID: PMC9387463 DOI: 10.1016/j.cris.2021.100014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/02/2022]
Abstract
We describe precursors that predicted at least sixty neuropeptides in Ny. albimanus. At least 16 precursors are encoded in the Ny. albimanus brain. Myosuppressin neuropeptide precursor was identified in Ny albimanus. acp and hugin transcripts increased in Ny. albimanus brains infected with P. berghei.
Insect neuropeptides, play a central role in the control of many physiological processes. Based on an analysis of Nyssorhynchus albimanus brain transcriptome a neuropeptide precursor database of the mosquito was described. Also, we observed that adipokinetic hormone/corazonin-related peptide (ACP), hugin and corazonin encoding genes were differentially expressed during Plasmodium infection. Transcriptomic data from Ny. albimanus brain identified 29 pre-propeptides deduced from the sequences that allowed the prediction of at least 60 neuropeptides. The predicted peptides include isoforms of allatostatin C, orcokinin, corazonin, adipokinetic hormone (AKH), SIFamide, capa, hugin, pigment-dispersing factor, adipokinetic hormone/corazonin-related peptide (ACP), tachykinin-related peptide, trissin, neuropeptide F, diuretic hormone 31, bursicon, crustacean cardioactive peptide (CCAP), allatotropin, allatostatin A, ecdysis triggering hormone (ETH), diuretic hormone 44 (Dh44), insulin-like peptides (ILPs) and eclosion hormone (EH). The analysis of the genome of An. albimanus and the generated transcriptome, provided evidence for the identification of myosuppressin neuropeptide precursor. A quantitative analysis documented increased expression of precursors encoding ACP peptide, hugin and corazonin in the mosquito brain after Plasmodium berghei infection. This work represents an initial effort to characterize the neuropeptide precursors repertoire of Ny. albimanus and provides information for understanding neuroregulation of the mosquito response during Plasmodium infection.
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Rodriguez MC, Martínez-Barnetche J, Lecona-Valera AN, Téllez-Sosa J, Argotte-Ramos RS, Alvarado-Delgado A, Ovilla MT, Saldaña-Navor V, Rodriguez MH. Expression of Heat shock protein 70 (Hsp70-1) in Plasmodium berghei ookinetes and its participation in midgut mosquito infection. Mol Biochem Parasitol 2020; 240:111337. [PMID: 33147473 DOI: 10.1016/j.molbiopara.2020.111337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/22/2020] [Accepted: 10/28/2020] [Indexed: 10/23/2022]
Abstract
The heat shock protein family 70 (Hsp70) comprises chaperone proteins that play major multiple roles in Plasmodium asexual and sexual development. In this study, we analyzed the expression of Hsp70-1 in gametocytes, gametes, zygotes, and its participation in ookinete formation and their transition into oocysts. A monoclonal antibody against recombinant Hsp70-1 revealed its presence in zygotes and micronemes of ookinetes. Compared to wild type parasites, Hsp70-1 knockout ookinetes produced fewer oocysts in Plasmodium-susceptible Anopheles albimanus mosquitoes. This may indicate a defective transformation of ookinetes into oocysts in the absence of Hsp70-1. The presence of this protein in micronemes suggests its participation in mosquito infection, probably aiding to the adequate structural conformation of proteins in charge of motility, recognition and invasion of the insect midgut epithelium.
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Affiliation(s)
- Maria Carmen Rodriguez
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, C. P. 62100, Cuernavaca, Morelos, Mexico
| | - Jesús Martínez-Barnetche
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, C. P. 62100, Cuernavaca, Morelos, Mexico
| | - Alba N Lecona-Valera
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, C. P. 62100, Cuernavaca, Morelos, Mexico
| | - Juan Téllez-Sosa
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, C. P. 62100, Cuernavaca, Morelos, Mexico
| | - Rocio S Argotte-Ramos
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, C. P. 62100, Cuernavaca, Morelos, Mexico
| | - Alejandro Alvarado-Delgado
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, C. P. 62100, Cuernavaca, Morelos, Mexico
| | - Marbella T Ovilla
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, C. P. 62100, Cuernavaca, Morelos, Mexico
| | - Vianey Saldaña-Navor
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, C. P. 62100, Cuernavaca, Morelos, Mexico
| | - Mario H Rodriguez
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Av. Universidad 655, C. P. 62100, Cuernavaca, Morelos, Mexico.
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Hernández-Castro R, Rodríguez-Santiago J, Téllez-Sosa J, Bravo-Romero S, Silva-Sánchez J, Sánchez-Pérez A, Avalos-Téllez R, Martínez-Chavarría LC, Xicohtencatl-Cortes J, Garza-Ramos U. Molecular and genome characterization of colistin-resistant Escherichia coli isolates from wild sea lions (Zalophus californianus). Braz J Microbiol 2020; 51:2009-2014. [PMID: 32897511 DOI: 10.1007/s42770-020-00371-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 08/26/2020] [Indexed: 02/06/2023] Open
Abstract
Using molecular and whole-genome sequencing tools, we investigated colistin-resistant Escherichia coli isolates from wild sea lions. Two unrelated E. coli colistin-resistant isolates, ST8259 and ST4218, were identified, both belonging to the B2 phylogroup and different serotypes. Polymorphisms in PmrA, PmrB, and PhoQ proteins were identified, and the role of PmrB and PhoQ in contributing to colistin resistance was determined by complementation assays. However, the mutations characterized in the present study are not involved in colistin resistance, which have been described in E. coli isolates from clinical settings. Therefore, the acquired mutations in pmrB and phoQ genes in resistance to colistin in bacteria related to marine environment animals are different. This work contributes to the surveillance and characterization of colistin resistance in Escherichia coli obtained from animals from aquatic environments.
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Affiliation(s)
- Rigoberto Hernández-Castro
- Departamento Ecología de Agentes Patógenos, Hospital General "Dr. Manuel Gea González", Ciudad de México, Mexico
| | - Jonathan Rodríguez-Santiago
- Laboratorio de Resistencia Bacteriana; Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, Mexico
| | - Juan Téllez-Sosa
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, Mexico
| | - Sugey Bravo-Romero
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, Mexico
| | - Jesús Silva-Sánchez
- Laboratorio de Resistencia Bacteriana; Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, Mexico
| | - Alejandro Sánchez-Pérez
- Laboratorio de Resistencia Bacteriana; Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, Mexico
| | - Rosalia Avalos-Téllez
- Área de Protección de Flora y Fauna. Islas del Golfo de California, Baja California, CONANP, SEMARNAT. Bahía de Los Ángeles, 22980, Ensenada, Baja California, Mexico
| | - Luary Carolina Martínez-Chavarría
- Departamento de Patología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Coyoacán, 04510, Ciudad de México, Mexico
| | - Juan Xicohtencatl-Cortes
- Laboratorio de Bacteriología Intestinal, Hospital Infantil de México Dr. Federico Gómez, Cuauhtémoc, 06720, Ciudad de México, Mexico
| | - Ulises Garza-Ramos
- Laboratorio de Resistencia Bacteriana; Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, Mexico.
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Bautista D, Vásquez C, Ayala-Ramírez P, Téllez-Sosa J, Godoy-Lozano E, Martínez-Barnetche J, Franco M, Angel J. Differential Expression of IgM and IgD Discriminates Two Subpopulations of Human Circulating IgM +IgD +CD27 + B Cells That Differ Phenotypically, Functionally, and Genetically. Front Immunol 2020; 11:736. [PMID: 32435242 PMCID: PMC7219516 DOI: 10.3389/fimmu.2020.00736] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/31/2020] [Indexed: 01/17/2023] Open
Abstract
The origin and function of blood IgM+IgD+CD27+ B cells is controversial, and they are considered a heterogeneous population. Previous staining of circulating B cells of healthy donors with rotavirus fluorescent virus-like particles allowed us to differentiate two subsets of IgM+IgD+CD27+: IgMhi and IgMlo B cells. Here, we confirmed this finding and compared the phenotype, transcriptome, in vitro function, and Ig gene repertoire of these two subsets. Eleven markers phenotypically discriminated both subsets (CD1c, CD69, IL21R, CD27, MTG, CD45RB, CD5, CD184, CD23, BAFFR, and CD38) with the IgMhi phenotypically resembling previously reported marginal zone B cells and the IgMlo resembling both naïve and memory B cells. Transcriptomic analysis showed that both subpopulations clustered close to germinal center-experienced IgM only B cells with a Principal Component Analysis, but differed in expression of 78 genes. Moreover, IgMhi B cells expressed genes characteristic of previously reported marginal zone B cells. After stimulation with CpG and cytokines, significantly (p < 0.05) higher frequencies (62.5%) of IgMhi B cells proliferated, compared with IgMlo B cells (35.37%), and differentiated to antibody secreting cells (14.22% for IgMhi and 7.19% for IgMlo). IgMhi B cells had significantly (p < 0.0007) higher frequencies of mutations in IGHV and IGKV regions, IgMlo B cells had higher usage of IGHJ6 genes (p < 0.0001), and both subsets differed in their HCDR3 properties. IgMhi B cells shared most of their shared IGH clonotypes with IgM only memory B cells, and IgMlo B cells with IgMhi B cells. These results support the notion that differential expression of IgM and IgD discriminates two subpopulations of human circulating IgM+IgD+CD27+ B cells, with the IgMhi B cells having similarities with previously described marginal zone B cells that passed through germinal centers, and the IgMlo B cells being the least differentiated amongst the IgM+CD27+ subsets.
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Affiliation(s)
- Diana Bautista
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Camilo Vásquez
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Paola Ayala-Ramírez
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Juan Téllez-Sosa
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Ernestina Godoy-Lozano
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Jesús Martínez-Barnetche
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Manuel Franco
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Juana Angel
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
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Gomez-Gamboa L, Barrios-Camacho H, Duran-Bedolla J, Sánchez-Perez A, Reyna-Flores F, Perozo-Mena A, Zabala I, Rodriguez-Medina N, Martínez-Barnetche J, Téllez-Sosa J, Valdovinos-Torres H, Garza-Ramos U. Molecular and genetic characterization of carbapenemase-producing bacteria in Venezuela. J Chemother 2019; 31:349-353. [PMID: 31046636 DOI: 10.1080/1120009x.2019.1607452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Carbapenem-resistant Gram-negative bacteria isolated in Venezuela have been poorly characterized. The present study characterized a total of 34 isolates obtained from 27 patients; five of these patients were multi-infected. The bacterial species identified were Klebsiella pneumoniae (17), Pseudomonas aeruginosa (9), and Acinetobacter baumannii (8). From these isolates, 85% were identified as carbapenemase-producing bacteria, and the identified carbapenemase genes were blaKPC-2 (10/29 [34.4%]), blaVIM-type (7/29 [24.1%]), blaOXA-23 (7/29 [24.1%]), blaNDM-1 (8/29 [27.5%]), and the coexistence of blaOXA-23/blaNDM-1 (2/29 [6.8%]). Patient 1 was multi-infected by K. pneumoniae ST11 and ST2413 isolates harbouring the blaNDM-1 and blaKPC-2 genes, respectively. The other patients were multi-infected by two or three different bacterial species such as ESBL-producing K. pneumoniae isolates, P. aeruginosa harbouring the blaVIM-type gene, K. pneumoniae ST147 harbouring the blaKPC-2 gene and by A. baumannii harbouring the blaOXA-23 gene. The blaNDM-1 gene in A. baumannii is flanked by an uncommon genetic structure, whereas blaNDM-1 gene in K. pneumoniae revealed a common structure described in different plasmids from Enterobacteriaceae isolates. This study provides new information about the epidemiology of carbapenemase-producing bacteria in clinical setting in Venezuela.
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Affiliation(s)
- Liliana Gomez-Gamboa
- Department of Tropical and Infectious Diseases School of Medicine, University of Zulia , Maracaibo , Venezuela
| | - Humberto Barrios-Camacho
- Instituto Nacional de Salud Pública (INSP), CISEI Laboratorio de Resistencia Bacteriana , Cuernavaca , Morelos , Mexico
| | - Josefina Duran-Bedolla
- Instituto Nacional de Salud Pública (INSP), CISEI Laboratorio de Resistencia Bacteriana , Cuernavaca , Morelos , Mexico
| | - Alejandro Sánchez-Perez
- Instituto Nacional de Salud Pública (INSP), CISEI Laboratorio de Resistencia Bacteriana , Cuernavaca , Morelos , Mexico
| | - Fernando Reyna-Flores
- Instituto Nacional de Salud Pública (INSP), CISEI Laboratorio de Resistencia Bacteriana , Cuernavaca , Morelos , Mexico
| | - Armindo Perozo-Mena
- Laboratory of Bacteriology Department of Microbiology Faculty of Medicine. University of Zulia, Maracaibo , Venezuela
| | - Irene Zabala
- Genetics and Molecular Biology Laboratory Faculty of Science, University of Zulia , Maracaibo , Venezuela
| | - Nadia Rodriguez-Medina
- Instituto Nacional de Salud Pública (INSP), CISEI Laboratorio de Resistencia Bacteriana , Cuernavaca , Morelos , Mexico
| | - Jesús Martínez-Barnetche
- Instituto Nacional de Salud Pública (INSP), CISEI, Departamento de Inmunología , Cuernavaca , Morelos , Mexico
| | - Juan Téllez-Sosa
- Instituto Nacional de Salud Pública (INSP), CISEI, Departamento de Inmunología , Cuernavaca , Morelos , Mexico
| | - Humberto Valdovinos-Torres
- Instituto Nacional de Salud Pública (INSP), CISEI, Departamento de Inmunología , Cuernavaca , Morelos , Mexico
| | - Ulises Garza-Ramos
- Instituto Nacional de Salud Pública (INSP), CISEI Laboratorio de Resistencia Bacteriana , Cuernavaca , Morelos , Mexico
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8
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Kuri-Magaña H, Collado-Torres L, Jaffe AE, Valdovinos-Torres H, Ovilla-Muñoz M, Téllez-Sosa J, Bonifaz LC, Martínez-Barnetche J. Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses. Front Immunol 2018; 9:2679. [PMID: 30519242 PMCID: PMC6260145 DOI: 10.3389/fimmu.2018.02679] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 10/30/2018] [Indexed: 12/22/2022] Open
Abstract
Antibody class switch recombination (CSR) to IgG, IgA, or IgE is a hallmark of adaptive immunity, allowing antibody function diversification beyond IgM. CSR involves a deletion of the IgM/IgD constant region genes placing a new acceptor Constant gene, downstream of the VDJH exon. CSR depends on non-coding (CSRnc) transcription of donor Iμ and acceptor IH exons, located 5′ upstream of each CH coding gene. Although, our knowledge of the role of CSRnc transcription has advanced greatly, its extension and importance in healthy and diseased humans is scarce. We analyzed CSRnc transcription in 70,603 publicly available RNA-seq samples, including GTEx, TCGA, and the Sequence Read Archive using recount2, an online resource consisting of normalized RNA-seq gene and exon counts, as well as, coverage BigWig files that can be programmatically accessed through R. CSRnc transcription was validated with a qRT-PCR assay for Iμ, Iγ3, and Iγ1 in humans in response to vaccination. We mapped IH transcription for the human IGH locus, including the less understood IGHD gene. CSRnc transcription was restricted to B cells and is widely distributed in normal adult tissues, but predominant in blood, spleen, MALT-containing tissues, visceral adipose tissue and some so-called “immune privileged” tissues. However, significant Iγ4 expression was found even in non-lymphoid fetal tissues. CSRnc expression in cancer tissues mimicked the expression of their normal counterparts, with notable pattern changes in some common cancer subsets. CSRnc transcription in tumors appears to result from tumor infiltration by B cells, since CSRnc transcription was not detected in corresponding tumor-derived immortal cell lines. Additionally, significantly increased Iδ transcription in ileal mucosa in Crohn's disease with ulceration was found. In conclusion, CSRnc transcription occurs in multiple anatomical locations beyond classical secondary lymphoid organs, representing a potentially useful marker of effector B cell responses in normal and pathological immune responses. The pattern of IH exon expression may reveal clues of the local immune response (i.e., cytokine milieu) in health and disease. This is a great example of how the public recount2 data can be used to further our understanding of transcription, including regions outside the known transcriptome.
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Affiliation(s)
- Helena Kuri-Magaña
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Baltimore, MD, United States.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Baltimore, MD, United States.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, United States.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Humberto Valdovinos-Torres
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Marbella Ovilla-Muñoz
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Juan Téllez-Sosa
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Laura C Bonifaz
- Unidad de Investigación Medica en Inmunoquímica, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Jesús Martínez-Barnetche
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
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9
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Martínez-Barnetche J, Lavore A, Beliera M, Téllez-Sosa J, Zumaya-Estrada FA, Palacio V, Godoy-Lozano E, Rivera-Pomar R, Rodríguez MH. Adaptations in energy metabolism and gene family expansions revealed by comparative transcriptomics of three Chagas disease triatomine vectors. BMC Genomics 2018; 19:296. [PMID: 29699489 PMCID: PMC5921304 DOI: 10.1186/s12864-018-4696-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 04/18/2018] [Indexed: 12/17/2022] Open
Abstract
Background Chagas disease is a parasitic infection caused by Trypanosoma cruzi. It is an important public health problem affecting around seven to eight million people in the Americas. A large number of hematophagous triatomine insect species, occupying diverse natural and human-modified ecological niches transmit this disease. Triatomines are long-living hemipterans that have evolved to explode different habitats to associate with their vertebrate hosts. Understanding the molecular basis of the extreme physiological conditions including starvation tolerance and longevity could provide insights for developing novel control strategies. We describe the normalized cDNA, full body transcriptome analysis of three main vectors in North, Central and South America, Triatoma pallidipennis, T. dimidiata and T. infestans. Results Two-thirds of the de novo assembled transcriptomes map to the Rhodnius prolixus genome and proteome. A Triatoma expansion of the calycin family and two types of protease inhibitors, pacifastins and cystatins were identified. A high number of transcriptionally active class I transposable elements was documented in T. infestans, compared with T. dimidiata and T. pallidipennis. Sequence identity in Triatoma-R. prolixus 1:1 orthologs revealed high sequence divergence in four enzymes participating in gluconeogenesis, glycogen synthesis and the pentose phosphate pathway, indicating high evolutionary rates of these genes. Also, molecular evidence suggesting positive selection was found for several genes of the oxidative phosphorylation I, III and V complexes. Conclusions Protease inhibitors and calycin-coding gene expansions provide insights into rapidly evolving processes of protease regulation and haematophagy. Higher evolutionary rates in enzymes that exert metabolic flux control towards anabolism and evidence for positive selection in oxidative phosphorylation complexes might represent genetic adaptations, possibly related to prolonged starvation, oxidative stress tolerance, longevity, and hematophagy and flight reduction. Overall, this work generated novel hypothesis related to biological adaptations to extreme physiological conditions and diverse ecological niches that sustain Chagas disease transmission. Electronic supplementary material The online version of this article (10.1186/s12864-018-4696-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jesús Martínez-Barnetche
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Andrés Lavore
- Centro de Bioinvestigaciones (CeBio) and Centro de Investigación y Transferencia del Noroeste de Buenos Aires (CITNOBA-CONICET), Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Pergamino, Argentina
| | - Melina Beliera
- Centro de Bioinvestigaciones (CeBio) and Centro de Investigación y Transferencia del Noroeste de Buenos Aires (CITNOBA-CONICET), Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Pergamino, Argentina
| | - Juan Téllez-Sosa
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Federico A Zumaya-Estrada
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Victorio Palacio
- Centro de Bioinvestigaciones (CeBio) and Centro de Investigación y Transferencia del Noroeste de Buenos Aires (CITNOBA-CONICET), Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Pergamino, Argentina
| | - Ernestina Godoy-Lozano
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Rolando Rivera-Pomar
- Centro de Bioinvestigaciones (CeBio) and Centro de Investigación y Transferencia del Noroeste de Buenos Aires (CITNOBA-CONICET), Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Pergamino, Argentina.,Laboratorio de Genética y Genómica Funcional. Centro Regional de Estudios Genómicos. Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mario Henry Rodríguez
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México.
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10
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Mora-Velandia LM, Castro-Escamilla O, Méndez AG, Aguilar-Flores C, Velázquez-Avila M, Tussié-Luna MI, Téllez-Sosa J, Maldonado-García C, Jurado-Santacruz F, Ferat-Osorio E, Martínez-Barnetche J, Pelayo R, Bonifaz LC. A Human Lin - CD123 + CD127 low Population Endowed with ILC Features and Migratory Capabilities Contributes to Immunopathological Hallmarks of Psoriasis. Front Immunol 2017; 8:176. [PMID: 28303135 PMCID: PMC5332395 DOI: 10.3389/fimmu.2017.00176] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 02/07/2017] [Indexed: 02/06/2023] Open
Abstract
Innate lymphoid cells (ILC) are members of a heterogeneous family with a lymphoid origin that mimics the T helper (Th) cytokine profile. ILC are involved in early effector cytokine-mediated responses during infections in peripheral tissues. ILC also play an important role in chronic skin inflammatory diseases, including psoriasis. Although classical ILC express CD127, it has been recently reported that the presence of non-classical CD127- ILC populations and an early ILC precursor (EILP) CD127low. ILC development has predominately been investigated in mouse models. However, in humans, different transcription factors have been described for ILC identification. NFIL3 (nuclear factor, IL-3 regulated) is crucial for ILC development in response to IL-7. CD123 (IL-3Rα) is usually used to exclude basophils during ILC identification, however, it is unknown if in response to IL-3, NFIL3 could be relevant to induce ILC features in Lin- CD123+ populations in addition, is also unknown whether peripheral blood (PB) population with ILC features may have skin-homing potential to participate in skin inflammatory chronic diseases. Here, we report a Lin- CD123+ CD127low CD7+ CLA+ population that share some phenotypic properties with basophils, but expresses several transcription factors for ILC commitment such as inhibitor of DNA binding 2 (Id2), NFIL3, promyelocytic leukemia zinc finger (PLZF), thymocyte selection-associated high-mobility group box protein (TOX), and T cell factor-1 (TCF-1). In addition, this population expresses different ILC markers: CD132, CD90, CD161, α4 integrin, c-Kit, CRTH2, AhR, and IL-23R. IL-3 prevents apoptosis and increases their NFIL3, TOX, and PLZF expression. In PB, the CD123+ CD127low population is predominantly a conspicuous population that expresses T-bet and RORγt. The Lin- CD123+ CD127low population in PB has a limited Th type cytokine expression and highly expresses IL-8. The Lin- CD123+ CD127low population expresses skin-homing receptors (cutaneous lymphocyte antigen and CXCR4) and transmigrates through endothelial cells in response to SDF-1. An equivalent Lin- CD123low population was identified in control skin, which shows a broader phenotypic diversity and cytokine production, including IL-22 and IL-17. Remarkably, the CD123low population in the lesion and non-lesion skin of psoriasis patients expresses IL-17 and IL-22. Our findings suggest the identification of an alternative Lin- CD123+ CD127low population with ILC features endowed with migratory capabilities that might contribute to immunopathological hallmarks of psoriasis.
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Affiliation(s)
- Luz María Mora-Velandia
- Unidad de Investigación Médica en Inmunoquímica Hospital de Especialidades Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico; Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Octavio Castro-Escamilla
- Unidad de Investigación Médica en Inmunoquímica Hospital de Especialidades Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico; Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Andrés González Méndez
- Unidad de Investigación Médica en Inmunoquímica Hospital de Especialidades Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social , Mexico City , Mexico
| | - Cristina Aguilar-Flores
- Unidad de Investigación Médica en Inmunoquímica Hospital de Especialidades Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social , Mexico City , Mexico
| | - Martha Velázquez-Avila
- Unidad de Investigación en Enfermedades Oncológicas, Hospital de Oncología, Centro Médico Nacional 'Siglo XXI' , Mexico City , Mexico
| | - María Isabel Tussié-Luna
- División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico; Unidad de Investigación en Virología y Cáncer, Hospital Infantil de México "Federico Gómez", Mexico City, Mexico
| | - Juan Téllez-Sosa
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública , Cuernavaca, Morelos , Mexico
| | - César Maldonado-García
- Centro Dermatológico "Dr. Ladislao de la Pascua", Secretaria de Salud de la Ciudad de México , Mexico City , Mexico
| | - Fermín Jurado-Santacruz
- Centro Dermatológico "Dr. Ladislao de la Pascua", Secretaria de Salud de la Ciudad de México , Mexico City , Mexico
| | - Eduardo Ferat-Osorio
- Unidad de Investigación Médica en Inmunoquímica Hospital de Especialidades Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social , Mexico City , Mexico
| | - Jesus Martínez-Barnetche
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública , Cuernavaca, Morelos , Mexico
| | - Rosana Pelayo
- Unidad de Investigación en Enfermedades Oncológicas, Hospital de Oncología, Centro Médico Nacional 'Siglo XXI' , Mexico City , Mexico
| | - Laura C Bonifaz
- Unidad de Investigación Médica en Inmunoquímica Hospital de Especialidades Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social , Mexico City , Mexico
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11
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Hernández-Flores KG, Calderón-Garcidueñas AL, Mellado-Sánchez G, Ruiz-Ramos R, Sánchez-Vargas LA, Thomas-Dupont P, Izaguirre-Hernández IY, Téllez-Sosa J, Martínez-Barnetche J, Wood L, Paterson Y, Cedillo-Barrón L, López-Franco O, Vivanco-Cid H. Evaluation of the safety and adjuvant effect of a detoxified listeriolysin O mutant on the humoral response to dengue virus antigens. Clin Exp Immunol 2017; 188:109-126. [PMID: 27886660 DOI: 10.1111/cei.12906] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2016] [Indexed: 01/14/2023] Open
Abstract
Listeriolysin O (LLO) has been proposed as a potential carrier or adjuvant molecule in the vaccination field. However, the cytotoxic and pro-apoptotic effects of LLO are the major limitations for this purpose. Here, we have performed a preclinical safety evaluation and characterized a new potential adjuvant application for a non-cytolytic LLO mutant (dtLLO) to enhance and modulate the immune response against the envelope (E) protein from dengue virus. In addition, we have studied the adjuvant effects of dtLLO on human immune cells and the role of membrane cholesterol for the binding and proinflammatory property of the toxoid. Our in-vivo results in the murine model confirmed that dtLLO is a safer molecule than wild-type LLO (wtLLO), with a significantly increased survival rate for mice challenged with dtLLO compared with mice challenged with wtLLO (P < 0·001). Histopathological analysis showed non-toxic effects in key target organs such as brain, heart, liver, spleen, kidney and lung after challenge with dtLLO. In vitro, dtLLO retained the capacity of binding to plasma membrane cholesterol on the surface of murine and human immune cells. Immunization of 6-8-week-old female BALB/c mice with a combination of dtLLO mixed with E protein elicited a robust specific humoral response with isotype diversification of immunoglobulin (Ig)G antibodies (IgG1 and IgG2a). Finally, we demonstrated that cholesterol and lipid raft integrity are required to induce a proinflammatory response by human cells. Taken together, these findings support a potential use of the dtLLO mutant as a safe and effective adjuvant molecule in vaccination.
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Affiliation(s)
- K G Hernández-Flores
- Instituto de Investigaciones Médico-Biológicas, Universidad Veracruzana, Veracruz City, Veracruz, México.,Doctorado en Ciencias Biomédicas, Centro de Investigaciones Biomédicas, Universidad Veracruzana, Xalapa Veracruz, México
| | | | - G Mellado-Sánchez
- Instituto de Investigaciones Médico-Biológicas, Universidad Veracruzana, Veracruz City, Veracruz, México
| | - R Ruiz-Ramos
- Instituto de Medicina Forense, Universidad Veracruzana, Boca del Río Veracruz, México
| | - L A Sánchez-Vargas
- Instituto de Investigaciones Médico-Biológicas, Universidad Veracruzana, Veracruz City, Veracruz, México.,Doctorado en Ciencias Biomédicas, Centro de Investigaciones Biomédicas, Universidad Veracruzana, Xalapa Veracruz, México
| | - P Thomas-Dupont
- Instituto de Investigaciones Médico-Biológicas, Universidad Veracruzana, Veracruz City, Veracruz, México.,Doctorado en Ciencias Biomédicas, Centro de Investigaciones Biomédicas, Universidad Veracruzana, Xalapa Veracruz, México
| | - I Y Izaguirre-Hernández
- Instituto de Investigaciones Médico-Biológicas, Universidad Veracruzana, Veracruz City, Veracruz, México.,Doctorado en Ciencias Biomédicas, Centro de Investigaciones Biomédicas, Universidad Veracruzana, Xalapa Veracruz, México
| | - J Téllez-Sosa
- Departamento de Inmunología, Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Cuernavaca, México
| | - J Martínez-Barnetche
- Departamento de Inmunología, Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Cuernavaca, México
| | - L Wood
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Y Paterson
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - L Cedillo-Barrón
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados IPN, Ciudad de México, México
| | - O López-Franco
- Centro de Estudios y Servicios en Salud. Universidad Veracruzana, Veracruz City, Veracruz, México
| | - H Vivanco-Cid
- Instituto de Investigaciones Médico-Biológicas, Universidad Veracruzana, Veracruz City, Veracruz, México
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12
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Duran-Bedolla J, Téllez-Sosa J, Valdovinos-Torres H, Pavón N, Buelna-Chontal M, Tello-López AT, Argotte-Ramos R, Rodríguez MH, Rodríguez MC. Cellular stress associated with the differentiation of Plasmodium berghei ookinetes. Biochem Cell Biol 2016; 95:310-317. [PMID: 28177775 DOI: 10.1139/bcb-2016-0028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
For malaria transmission, Plasmodium parasites must develop in the mosquito vector. Oxidative stress in the insect midgut, triggered by environmental changes (e.g., pH and temperature), influences the cellular signaling involved in differentiation from gametocytes to mobile ookinetes for the purpose of parasite survival. Oxidative stress activates the homeostatic response to stress characterized by the phosphorylation eIF2α, the attenuation of protein synthesis, and the transcription of genes participating in the unfolded protein response and antioxidant processes, forming a part of an integrated stress response (ISR). We hypothesized that ISR operates during the differentiation of gametocytes to ookinetes to assure Plasmodium survival. Using in-vitro conditions resembling the mosquito midgut conditions, we cultured Plasmodium berghei gametocytes to ookinetes and evaluated the redox balance by detecting reactive oxygen species and superoxide dismutase activity. Additionally, we evaluated the phosphorylation of eIF2α, the attenuation of the global protein synthesis, and the gene expression of cellular stress markers (e.g., endoplasmic reticulum chaperones and antioxidant molecules, measured by reverse-transcription quantitative polymerase chain reaction), finding that these processes were all taking place, probably to improve survival during the differentiation of Plasmodium berghei ookinetes.
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Affiliation(s)
- Josefina Duran-Bedolla
- a Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Avenida Universidad 655, C.P. 62100, Cuernavaca, Morelos, México
| | - Juan Téllez-Sosa
- a Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Avenida Universidad 655, C.P. 62100, Cuernavaca, Morelos, México
| | - Humberto Valdovinos-Torres
- a Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Avenida Universidad 655, C.P. 62100, Cuernavaca, Morelos, México
| | - Natalia Pavón
- b Departamento de Farmacología and Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología, Ignacio Chávez, Juan Badiano # 1, Col. Sección XVI, C.P. 014080, Tlalpan, D.F., México
| | - Mabel Buelna-Chontal
- b Departamento de Farmacología and Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología, Ignacio Chávez, Juan Badiano # 1, Col. Sección XVI, C.P. 014080, Tlalpan, D.F., México
| | - Angel T Tello-López
- a Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Avenida Universidad 655, C.P. 62100, Cuernavaca, Morelos, México
| | - Rocio Argotte-Ramos
- a Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Avenida Universidad 655, C.P. 62100, Cuernavaca, Morelos, México
| | - Mario Henry Rodríguez
- a Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Avenida Universidad 655, C.P. 62100, Cuernavaca, Morelos, México
| | - María Carmen Rodríguez
- a Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Avenida Universidad 655, C.P. 62100, Cuernavaca, Morelos, México
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13
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Audirac-Chalifour A, Torres-Poveda K, Bahena-Román M, Téllez-Sosa J, Martínez-Barnetche J, Cortina-Ceballos B, López-Estrada G, Delgado-Romero K, Burguete-García AI, Cantú D, García-Carrancá A, Madrid-Marina V. Cervical Microbiome and Cytokine Profile at Various Stages of Cervical Cancer: A Pilot Study. PLoS One 2016; 11:e0153274. [PMID: 27115350 PMCID: PMC4846060 DOI: 10.1371/journal.pone.0153274] [Citation(s) in RCA: 226] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/25/2016] [Indexed: 12/27/2022] Open
Abstract
Cervical cancer (CC) is caused by high-risk human papillomavirus persistence due to the immunosuppressive tumor microenvironment mediated by cytokines. Vaginal microbiota determines the presence of certain cytokines locally. We assessed the association between cervical microbiota diversity and the histopathological diagnosis of each stage of CC, and we evaluated mRNA cervical expression levels of IL-4, IL-6, IL-10, TGF-β1, TNF-α and IFN-γ across the histopathological diagnosis and specific bacterial clusters. We determined the cervical microbiota by high throughput sequencing of 16S rDNA amplicons and classified it in community state types (CST). Mean difference analyses between alpha-diversity and histopathological diagnosis were carried out, as well as a β-diversity analysis within the histological diagnosis. Cervical cytokine mRNA expression was analyzed across the CSTs and the histopathological diagnoses. We found a significant difference in microbiota's diversity in NCL-HPV negative women vs those with squamous intraepithelial lesions (SIL) and CC(p = 0.006, p = 0.036).When β-diversity was evaluated, the CC samples showed the highest variation within groups (p<0.0006) and the largest distance compared to NCL-HPV negative ones (p<0.00001). The predominant bacteria in women with normal cytology were L. crispatus and L. iners, whereas for SIL, it was Sneathia spp. and for CC, Fusobacterium spp. We found higher median cervical levels of IL-4 and TGF-β1 mRNA in the CST dominated by Fusobacterium spp. These results suggest that the cervical microbiota may be implicated in cervical cancer pathology. Further cohort studies are needed to validate these findings.
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Affiliation(s)
- Astride Audirac-Chalifour
- Dirección de Infecciones Crónicas y Cáncer, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública (INSP) (Chronic Infectious Diseases and Cancer Division, Center for Research on Infectious Diseases, National Institute of Public Health), Cuernavaca, Morelos, Mexico
| | - Kirvis Torres-Poveda
- Dirección de Infecciones Crónicas y Cáncer, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública (INSP) (Chronic Infectious Diseases and Cancer Division, Center for Research on Infectious Diseases, National Institute of Public Health), Cuernavaca, Morelos, Mexico
| | - Margarita Bahena-Román
- Dirección de Infecciones Crónicas y Cáncer, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública (INSP) (Chronic Infectious Diseases and Cancer Division, Center for Research on Infectious Diseases, National Institute of Public Health), Cuernavaca, Morelos, Mexico
| | - Juan Téllez-Sosa
- Dirección de Infecciones Crónicas y Cáncer, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública (INSP) (Chronic Infectious Diseases and Cancer Division, Center for Research on Infectious Diseases, National Institute of Public Health), Cuernavaca, Morelos, Mexico
| | - Jesús Martínez-Barnetche
- Dirección de Infecciones Crónicas y Cáncer, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública (INSP) (Chronic Infectious Diseases and Cancer Division, Center for Research on Infectious Diseases, National Institute of Public Health), Cuernavaca, Morelos, Mexico
| | - Bernardo Cortina-Ceballos
- Dirección de Infecciones Crónicas y Cáncer, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública (INSP) (Chronic Infectious Diseases and Cancer Division, Center for Research on Infectious Diseases, National Institute of Public Health), Cuernavaca, Morelos, Mexico
| | | | - Karina Delgado-Romero
- Centro de Atención para la Salud de la Mujer (CAPASAM) (Center for Women’s Health), Health Services of the State of Morelos, Cuernavaca, Mexico
| | - Ana I. Burguete-García
- Dirección de Infecciones Crónicas y Cáncer, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública (INSP) (Chronic Infectious Diseases and Cancer Division, Center for Research on Infectious Diseases, National Institute of Public Health), Cuernavaca, Morelos, Mexico
| | - David Cantú
- Division of Clinical Research, Instituto Nacional de Cancerología (INCan), SS, Mexico City, Mexico
| | | | - Vicente Madrid-Marina
- Dirección de Infecciones Crónicas y Cáncer, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública (INSP) (Chronic Infectious Diseases and Cancer Division, Center for Research on Infectious Diseases, National Institute of Public Health), Cuernavaca, Morelos, Mexico
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Cortina-Ceballos B, Godoy-Lozano EE, Sámano-Sánchez H, Aguilar-Salgado A, Velasco-Herrera MDC, Vargas-Chávez C, Velázquez-Ramírez D, Romero G, Moreno J, Téllez-Sosa J, Martínez-Barnetche J. Reconstructing and mining the B cell repertoire with ImmunediveRsity. MAbs 2016; 7:516-24. [PMID: 25875140 PMCID: PMC4622655 DOI: 10.1080/19420862.2015.1026502] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The B cell antigen receptor repertoire is highly diverse and constantly modified by clonal selection. High-throughput DNA sequencing (HTS) of the lymphocyte repertoire (Rep-Seq) represents a promising technology to explore such diversity ex-vivo and assist in the identification of antigen-specific antibodies based on molecular signatures of clonal selection. Therefore, integrative tools for repertoire reconstruction and analysis from antibody sequences are needed. We developed ImmunediveRity, a stand-alone pipeline primarily based in R programming for the integral analysis of B cell repertoire data generated by HTS. The pipeline integrates GNU software and in house scripts to perform quality filtering, sequencing noise correction and repertoire reconstruction based on V, D and J segment assignment, clonal origin and unique heavy chain identification. Post-analysis scripts generate a wealth of repertoire metrics that in conjunction with a rich graphical output facilitates sample comparison and repertoire mining. Its performance was tested with raw and curated human and mouse 454-Roche sequencing benchmarks providing good approximations of repertoire structure. Furthermore, ImmunediveRsity was used to mine the B cell repertoire of immunized mice with a model antigen, allowing the identification of previously validated antigen-specific antibodies, and revealing different and unexpected clonal diversity patterns in the post-immunization IgM and IgG compartments. Although ImmunediveRsity is similar to other recently developed tools, it offers significant advantages that facilitate repertoire analysis and repertoire mining. ImmunediveRsity is open source and free for academic purposes and it runs on 64 bit GNU/Linux and MacOS. Available at: https://bitbucket.org/ImmunediveRsity/immunediversity/
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Affiliation(s)
- Bernardo Cortina-Ceballos
- a Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública (CISEI-INSP); Cuernavaca , Morelos , México
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15
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Godoy-Lozano EE, Téllez-Sosa J, Sánchez-González G, Sámano-Sánchez H, Aguilar-Salgado A, Salinas-Rodríguez A, Cortina-Ceballos B, Vivanco-Cid H, Hernández-Flores K, Pfaff JM, Kahle KM, Doranz BJ, Gómez-Barreto RE, Valdovinos-Torres H, López-Martínez I, Rodriguez MH, Martínez-Barnetche J. Lower IgG somatic hypermutation rates during acute dengue virus infection is compatible with a germinal center-independent B cell response. Genome Med 2016; 8:23. [PMID: 26917418 PMCID: PMC4766701 DOI: 10.1186/s13073-016-0276-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 02/03/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The study of human B cell response to dengue virus (DENV) infection is critical to understand serotype-specific protection and the cross-reactive sub-neutralizing response. Whereas the first is beneficial and thus represents the ultimate goal of vaccination, the latter has been implicated in the development of severe disease, which occurs in a small, albeit significant, fraction of secondary DENV infections. Both primary and secondary infections are associated with the production of poly-reactive and cross-reactive IgG antibodies. METHODS To gain insight into the effect of DENV infection on the B cell repertoire, we used VH region high-throughput cDNA sequencing of the peripheral blood IgG B cell compartment of 19 individuals during the acute phase of infection. For 11 individuals, a second sample obtained 6 months later was analyzed for comparison. Probabilities of sequencing antibody secreting cells or memory B cells were estimated using second-order Monte Carlo simulation. RESULTS We found that in acute disease there is an increase in IgG B cell diversity and changes in the relative use of segments IGHV1-2, IGHV1-18, and IGHV1-69. Somewhat unexpectedly, an overall low proportion of somatic hypermutated antibody genes was observed during the acute phase plasmablasts, particularly in secondary infections and those cases with more severe disease. CONCLUSIONS Our data are consistent with an innate-like antiviral recognition system mediated by B cells using defined germ-line coded B cell receptors, which could provide a rapid germinal center-independent antibody response during the early phase of infection. A model describing concurrent T-dependent and T-independent B cell responses in the context of DENV infection is proposed, which incorporates the selection of B cells using hypomutated IGHV segments and their potential role in poly/cross-reactivity. Its formal demonstration could lead to a definition of its potential implication in antibody-dependent enhancement, and may contribute to rational vaccine development efforts.
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Affiliation(s)
| | - Juan Téllez-Sosa
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Gilberto Sánchez-González
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Hugo Sámano-Sánchez
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Andrés Aguilar-Salgado
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Aarón Salinas-Rodríguez
- Centro de Investigación en Evaluación y Encuestas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Bernardo Cortina-Ceballos
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Héctor Vivanco-Cid
- Instituto de Investigaciones Médico-Biológicas, Universidad Veracruzana, Veracruz, Veracruz, México
| | - Karina Hernández-Flores
- Instituto de Investigaciones Médico-Biológicas, Universidad Veracruzana, Veracruz, Veracruz, México
| | | | | | | | - Rosa Elena Gómez-Barreto
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Humberto Valdovinos-Torres
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | | | - Mario H Rodriguez
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Jesús Martínez-Barnetche
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México.
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16
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Valdés-Alemán J, Téllez-Sosa J, Ovilla-Muñoz M, Godoy-Lozano E, Velázquez-Ramírez D, Valdovinos-Torres H, Gómez-Barreto RE, Martinez-Barnetche J. Hybridization-based antibody cDNA recovery for the production of recombinant antibodies identified by repertoire sequencing. MAbs 2013; 6:493-501. [PMID: 24492293 DOI: 10.4161/mabs.27435] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
High-throughput sequencing of the antibody repertoire is enabling a thorough analysis of B cell diversity and clonal selection, which may improve the novel antibody discovery process. Theoretically, an adequate bioinformatic analysis could allow identification of candidate antigen-specific antibodies, requiring their recombinant production for experimental validation of their specificity. Gene synthesis is commonly used for the generation of recombinant antibodies identified in silico. Novel strategies that bypass gene synthesis could offer more accessible antibody identification and validation alternatives. We developed a hybridization-based recovery strategy that targets the complementarity-determining region 3 (CDRH3) for the enrichment of cDNA of candidate antigen-specific antibody sequences. Ten clonal groups of interest were identified through bioinformatic analysis of the heavy chain antibody repertoire of mice immunized with hen egg white lysozyme (HEL). cDNA from eight of the targeted clonal groups was recovered efficiently, leading to the generation of recombinant antibodies. One representative heavy chain sequence from each clonal group recovered was paired with previously reported anti-HEL light chains to generate full antibodies, later tested for HEL-binding capacity. The recovery process proposed represents a simple and scalable molecular strategy that could enhance antibody identification and specificity assessment, enabling a more cost-efficient generation of recombinant antibodies.
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Affiliation(s)
- Javier Valdés-Alemán
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México; Programa de Ingeniería en Biotecnología; Universidad Politécnica del Estado de Morelos; Jiutepec, México
| | - Juan Téllez-Sosa
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Marbella Ovilla-Muñoz
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Elizabeth Godoy-Lozano
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Daniel Velázquez-Ramírez
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Humberto Valdovinos-Torres
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Rosa E Gómez-Barreto
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
| | - Jesús Martinez-Barnetche
- Departamento de Inmunología; Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública; Cuernavaca, México
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17
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Téllez-Sosa J, Rodríguez MH, Gómez-Barreto RE, Valdovinos-Torres H, Hidalgo AC, Cruz-Hervert P, Luna RS, Carrillo-Valenzo E, Ramos C, García-García L, Martínez-Barnetche J. Using high-throughput sequencing to leverage surveillance of genetic diversity and oseltamivir resistance: a pilot study during the 2009 influenza A(H1N1) pandemic. PLoS One 2013; 8:e67010. [PMID: 23843978 PMCID: PMC3699567 DOI: 10.1371/journal.pone.0067010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 05/17/2013] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Influenza viruses display a high mutation rate and complex evolutionary patterns. Next-generation sequencing (NGS) has been widely used for qualitative and semi-quantitative assessment of genetic diversity in complex biological samples. The "deep sequencing" approach, enabled by the enormous throughput of current NGS platforms, allows the identification of rare genetic viral variants in targeted genetic regions, but is usually limited to a small number of samples. METHODOLOGY AND PRINCIPAL FINDINGS We designed a proof-of-principle study to test whether redistributing sequencing throughput from a high depth-small sample number towards a low depth-large sample number approach is feasible and contributes to influenza epidemiological surveillance. Using 454-Roche sequencing, we sequenced at a rather low depth, a 307 bp amplicon of the neuraminidase gene of the Influenza A(H1N1) pandemic (A(H1N1)pdm) virus from cDNA amplicons pooled in 48 barcoded libraries obtained from nasal swab samples of infected patients (n = 299) taken from May to November, 2009 pandemic period in Mexico. This approach revealed that during the transition from the first (May-July) to second wave (September-November) of the pandemic, the initial genetic variants were replaced by the N248D mutation in the NA gene, and enabled the establishment of temporal and geographic associations with genetic diversity and the identification of mutations associated with oseltamivir resistance. CONCLUSIONS NGS sequencing of a short amplicon from the NA gene at low sequencing depth allowed genetic screening of a large number of samples, providing insights to viral genetic diversity dynamics and the identification of genetic variants associated with oseltamivir resistance. Further research is needed to explain the observed replacement of the genetic variants seen during the second wave. As sequencing throughput rises and library multiplexing and automation improves, we foresee that the approach presented here can be scaled up for global genetic surveillance of influenza and other infectious diseases.
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Affiliation(s)
- Juan Téllez-Sosa
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Mario Henry Rodríguez
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Rosa E. Gómez-Barreto
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Humberto Valdovinos-Torres
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Ana Cecilia Hidalgo
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Pablo Cruz-Hervert
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - René Santos Luna
- Centro de Información para Decisiones en Salud Pública, Instituto Nacional de Salud Pública, Cuernavaca, México
| | | | - Celso Ramos
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Lourdes García-García
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Jesús Martínez-Barnetche
- Centro de Investigaciones sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
- * E-mail:
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18
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Martínez-Barnetche J, Gómez-Barreto RE, Ovilla-Muñoz M, Téllez-Sosa J, López DEG, Dinglasan RR, Mohien CU, MacCallum RM, Redmond SN, Gibbons JG, Rokas A, Machado CA, Cazares-Raga FE, González-Cerón L, Hernández-Martínez S, López MHR. Transcriptome of the adult female malaria mosquito vector Anopheles albimanus. BMC Genomics 2012; 13:207. [PMID: 22646700 PMCID: PMC3442982 DOI: 10.1186/1471-2164-13-207] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 05/30/2012] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Human Malaria is transmitted by mosquitoes of the genus Anopheles. Transmission is a complex phenomenon involving biological and environmental factors of humans, parasites and mosquitoes. Among more than 500 anopheline species, only a few species from different branches of the mosquito evolutionary tree transmit malaria, suggesting that their vectorial capacity has evolved independently. Anopheles albimanus (subgenus Nyssorhynchus) is an important malaria vector in the Americas. The divergence time between Anopheles gambiae, the main malaria vector in Africa, and the Neotropical vectors has been estimated to be 100 My. To better understand the biological basis of malaria transmission and to develop novel and effective means of vector control, there is a need to explore the mosquito biology beyond the An. gambiae complex. RESULTS We sequenced the transcriptome of the An. albimanus adult female. By combining Sanger, 454 and Illumina sequences from cDNA libraries derived from the midgut, cuticular fat body, dorsal vessel, salivary gland and whole body, we generated a single, high-quality assembly containing 16,669 transcripts, 92% of which mapped to the An. darlingi genome and covered 90% of the core eukaryotic genome. Bidirectional comparisons between the An. gambiae, An. darlingi and An. albimanus predicted proteomes allowed the identification of 3,772 putative orthologs. More than half of the transcripts had a match to proteins in other insect vectors and had an InterPro annotation. We identified several protein families that may be relevant to the study of Plasmodium-mosquito interaction. An open source transcript annotation browser called GDAV (Genome-Delinked Annotation Viewer) was developed to facilitate public access to the data generated by this and future transcriptome projects. CONCLUSIONS We have explored the adult female transcriptome of one important New World malaria vector, An. albimanus. We identified protein-coding transcripts involved in biological processes that may be relevant to the Plasmodium lifecycle and can serve as the starting point for searching targets for novel control strategies. Our data increase the available genomic information regarding An. albimanus several hundred-fold, and will facilitate molecular research in medical entomology, evolutionary biology, genomics and proteomics of anopheline mosquito vectors. The data reported in this manuscript is accessible to the community via the VectorBase website (http://www.vectorbase.org/Other/AdditionalOrganisms/).
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Affiliation(s)
- Jesús Martínez-Barnetche
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Rosa E Gómez-Barreto
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Marbella Ovilla-Muñoz
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Juan Téllez-Sosa
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - David E García López
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Rhoel R Dinglasan
- Johns Hopkins Bloomberg School of Public Health. Department of Molecular Microbiology & Immunology, Johns Hopkins Malaria Research Institute, Baltimore, MD, 21205, USA
| | - Ceereena Ubaida Mohien
- Johns Hopkins Bloomberg School of Public Health. Department of Molecular Microbiology & Immunology, Johns Hopkins Malaria Research Institute, Baltimore, MD, 21205, USA
- Department of Molecular & Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert M MacCallum
- Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Seth N Redmond
- Pasteur Institut, 28 Rue Du Docteur Roux, Paris, 75015, France
| | - John G Gibbons
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Febe E Cazares-Raga
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav-IPN, México, DF, México
| | - Lilia González-Cerón
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula, Chiapas, México
| | - Salvador Hernández-Martínez
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Mario H Rodríguez López
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
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Izquierdo J, Venkova-Canova T, Ramírez-Romero MA, Téllez-Sosa J, Hernández-Lucas I, Sanjuan J, Cevallos MA. An antisense RNA plays a central role in the replication control of a repC plasmid. Plasmid 2005; 54:259-77. [PMID: 16005966 DOI: 10.1016/j.plasmid.2005.05.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2005] [Revised: 05/17/2005] [Accepted: 05/17/2005] [Indexed: 11/23/2022]
Abstract
The widespread replicons of repABC and repC families from alpha-proteobacteria share high similarity in their replication initiator proteins (RepC). Here we describe the minimal region required for stable replication of a member of the repC family, the low copy-number plasmid pRmeGR4a from Sinorizobium meliloti GR4. This region contains only two genes: one encoding the initiator protein RepC (46.8 kDa) and other, an antisense RNA (67 nt). Mapping of transcriptional start sites and promoter regions of both genes showed that the antisense RNA is nested within the repC mRNA leader. The constitutively expressed countertranscribed RNA (ctRNA) forms a single stem-loop structure that acts as an intrinsic rho-independent terminator. The ctRNA is a strong trans-incompatibility factor and negative regulator of repC expression. Based on structural and functional similarities between members of the repC and repABC families we propose a model of their evolutionary relationship.
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MESH Headings
- Amino Acid Sequence
- Conjugation, Genetic
- DNA Replication
- DNA, Bacterial
- Gene Expression Regulation, Bacterial
- Genes, Bacterial
- Glucuronidase/analysis
- Glucuronidase/metabolism
- Molecular Sequence Data
- Molecular Weight
- Mutagenesis, Site-Directed
- Phylogeny
- Plasmids/chemistry
- Plasmids/genetics
- Plasmids/metabolism
- Promoter Regions, Genetic
- RNA, Antisense/genetics
- RNA, Antisense/physiology
- RNA, Bacterial/genetics
- RNA, Bacterial/physiology
- RNA, Messenger/genetics
- Replicon
- Rhizobium etli/genetics
- Sequence Homology, Amino Acid
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Affiliation(s)
- Javier Izquierdo
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos, Mexico
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20
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Soberón N, Venkova-Canova T, Ramírez-Romero MA, Téllez-Sosa J, Cevallos MA. Incompatibility and the partitioning site of the repABC basic replicon of the symbiotic plasmid from Rhizobium etli. Plasmid 2004; 51:203-16. [PMID: 15109827 DOI: 10.1016/j.plasmid.2004.01.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2003] [Revised: 01/20/2004] [Indexed: 11/19/2022]
Abstract
The basic replicon of the symbiotic plasmid (p42d) of Rhizobium etli CE3 is constituted by the repABC operon. Whereas RepC is essential for plasmid replication, RepA and RepB are involved in plasmid partitioning. Three incompatibility regions have been previously identified in this plasmid: the first one encodes RepA, a partitioning protein that also down-regulates the repABC transcription. The second region is situated within the repB-repC intergenic sequence (inc(alpha)), and the last one, inc(beta), is located in a 502 bp EcoRI fragment spanning the last 72-bp of the coding region of repC and the following downstream sequence. In this paper we show that: (1) The inc(beta) region is required for plasmid partitioning. (2) A 16-bp palindrome sequence, located 40 bp downstream of the repC gene of plasmid p42d, is necessary and sufficient to induce incompatibility towards the parental plasmid, and accounts for all the incompatibility properties of this region (inc(beta)). (3). The palindrome is the DNA target site for RepB binding. With these findings we propose that inc(beta) contains the partitioning site (par site) of the basic replicon of plasmid p42d, and that the 16-bp palindrome is the core sequence to nucleate the RepB binding.
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Affiliation(s)
- Nora Soberón
- Programa de Evolución Molecular, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos
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21
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Téllez-Sosa J, Soberón N, Vega-Segura A, Torres-Márquez ME, Cevallos MA. The Rhizobium etli cyaC product: characterization of a novel adenylate cyclase class. J Bacteriol 2002; 184:3560-8. [PMID: 12057950 PMCID: PMC135151 DOI: 10.1128/jb.184.13.3560-3568.2002] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2001] [Accepted: 04/07/2002] [Indexed: 11/20/2022] Open
Abstract
Adenylate cyclases (ACs) catalyze the formation of 3',5'-cyclic AMP (cAMP) from ATP. A novel AC-encoding gene, cyaC, was isolated from Rhizobium etli by phenotypic complementation of an Escherichia coli cya mutant. The functionality of the cyaC gene was corroborated by its ability to restore cAMP accumulation in an E. coli cya mutant. Further, overexpression of a malE::cyaC fusion protein allowed the detection of significant AC activity levels in cell extracts of an E. coli cya mutant. CyaC is unrelated to any known AC or to any other protein exhibiting a currently known function. Thus, CyaC represents the first member of a novel class of ACs (class VI). Hypothetical genes of unknown function similar to cyaC have been identified in the genomes of the related bacterial species Mesorhizobium loti, Sinorhizobium meliloti, and Agrobacterium tumefaciens. The cyaC gene is cotranscribed with a gene similar to ohr of Xanthomonas campestris and is expressed only in the presence of organic hydroperoxides. The physiological performance of an R. etli cyaC mutant was indistinguishable from that of the wild-type parent strain both under free-living conditions and during symbiosis.
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Affiliation(s)
- Juan Téllez-Sosa
- Programa de Evolución Molecular, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, C.P. 62210, Cuernavaca, Morelos
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Ramírez-Romero MA, Téllez-Sosa J, Barrios H, Pérez-Oseguera A, Rosas V, Cevallos MA. RepA negatively autoregulates the transcription of the repABC operon of the Rhizobium etli symbiotic plasmid basic replicon. Mol Microbiol 2001; 42:195-204. [PMID: 11679078 DOI: 10.1046/j.1365-2958.2001.02621.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The basic replicon of Rhizobium etli CE3, like other members of the repABC plasmid family, is constituted by the repABC operon. RepC is essential for replication, and RepA and RepB play a role in plasmid segregation. It has been shown that deletion derivatives lacking the repAB genes have an increased copy number, indicating that these genes participate in the control of plasmid copy number. RepA is also a trans-incompatibility factor. To understand the regulation of the repABC operon, in this paper: (i) the transcription start site of the repABC operon was determined; (ii) the promoter region was identified by site-directed mutagenesis of the putative -35 and -10 hexameric elements; and (iii) RepA was recognized as a negative regulator of the transcription of the repABC operon.
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Affiliation(s)
- M A Ramírez-Romero
- Programa de Evolución Molecular, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apartado Postal 565-A, Cuernavaca, Morelos, México
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Ramírez-Romero MA, Soberón N, Pérez-Oseguera A, Téllez-Sosa J, Cevallos MA. Structural elements required for replication and incompatibility of the Rhizobium etli symbiotic plasmid. J Bacteriol 2000; 182:3117-24. [PMID: 10809690 PMCID: PMC94497 DOI: 10.1128/jb.182.11.3117-3124.2000] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/1999] [Accepted: 02/25/2000] [Indexed: 11/20/2022] Open
Abstract
The symbiotic plasmid of Rhizobium etli CE3 belongs to the RepABC family of plasmid replicons. This family is characterized by the presence of three conserved genes, repA, repB, and repC, encoded by the same DNA strand. A long intergenic sequence (igs) between repB and repC is also conserved in all members of the plasmid family. In this paper we demonstrate that (i) the repABC genes are organized in an operon; (ii) the RepC product is essential for replication; (iii) RepA and RepB products participate in plasmid segregation and in the regulation of plasmid copy number; (iv) there are two cis-acting incompatibility regions, one located in the igs (incalpha) and the other downstream of repC (incbeta) (the former is essential for replication); and (v) RepA is a trans-acting incompatibility factor. We suggest that incalpha is a cis-acting site required for plasmid partitioning and that the origin of replication lies within incbeta.
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Affiliation(s)
- M A Ramírez-Romero
- Programa de Evolución Molecular, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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