1
|
López-Luis MA, Soriano-Pérez EE, Parada-Fabián JC, Torres J, Maldonado-Rodríguez R, Méndez-Tenorio A. A Proposal for a Consolidated Structural Model of the CagY Protein of Helicobacter pylori. Int J Mol Sci 2023; 24:16781. [PMID: 38069104 PMCID: PMC10706595 DOI: 10.3390/ijms242316781] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
CagY is the largest and most complex protein from Helicobacter pylori's (Hp) type IV secretion system (T4SS), playing a critical role in the modulation of gastric inflammation and risk for gastric cancer. CagY spans from the inner to the outer membrane, forming a channel through which Hp molecules are injected into human gastric cells. Yet, a tridimensional structure has been reported for only short segments of the protein. This intricate protein was modeled using different approaches, including homology modeling, ab initio, and deep learning techniques. The challengingly long middle repeat region (MRR) was modeled using deep learning and optimized using equilibrium molecular dynamics. The previously modeled segments were assembled into a 1595 aa chain and a 14-chain CagY multimer structure was assembled by structural alignment. The final structure correlated with published structures and allowed to show how the multimer may form the T4SS channel through which CagA and other molecules are translocated to gastric cells. The model confirmed that MRR, the most polymorphic and complex region of CagY, presents numerous cysteine residues forming disulfide bonds that stabilize the protein and suggest this domain may function as a contractile region playing an essential role in the modulating activity of CagY on tissue inflammation.
Collapse
Affiliation(s)
- Mario Angel López-Luis
- Laboratorio de Biotecnología y Bioinformática Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Lázaro Cárdenas, Mexico City 11340, Mexico; (M.A.L.-L.); (E.E.S.-P.); (J.C.P.-F.); (R.M.-R.)
| | - Eva Elda Soriano-Pérez
- Laboratorio de Biotecnología y Bioinformática Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Lázaro Cárdenas, Mexico City 11340, Mexico; (M.A.L.-L.); (E.E.S.-P.); (J.C.P.-F.); (R.M.-R.)
| | - José Carlos Parada-Fabián
- Laboratorio de Biotecnología y Bioinformática Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Lázaro Cárdenas, Mexico City 11340, Mexico; (M.A.L.-L.); (E.E.S.-P.); (J.C.P.-F.); (R.M.-R.)
| | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico;
| | - Rogelio Maldonado-Rodríguez
- Laboratorio de Biotecnología y Bioinformática Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Lázaro Cárdenas, Mexico City 11340, Mexico; (M.A.L.-L.); (E.E.S.-P.); (J.C.P.-F.); (R.M.-R.)
| | - Alfonso Méndez-Tenorio
- Laboratorio de Biotecnología y Bioinformática Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Lázaro Cárdenas, Mexico City 11340, Mexico; (M.A.L.-L.); (E.E.S.-P.); (J.C.P.-F.); (R.M.-R.)
| |
Collapse
|
2
|
Fragoso-Fonseca DE, Ruiz-Hernández UE, Trujillo-Salgado BB, Manuell-Barrios RT, Garcés-Ayala F, Del Mazo-López JC, Méndez-Tenorio A, Hernández-Rivas L, Ramírez-González JE, Escobar-Escamilla N. Analysis of the genomic diversity of human papillomavirus type 31 in cervical samples reveals the presence of novel sublineages in clade C. Arch Virol 2022; 167:2795-2800. [PMID: 36085531 DOI: 10.1007/s00705-022-05589-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/04/2022] [Accepted: 07/22/2022] [Indexed: 12/14/2022]
Abstract
Human papillomavirus 31 (HPV31) is the fourth most frequent high-risk HPV (HR-HPV) genotype identified in cervical cancer (CC) worldwide and in Mexico. It has been recently classified into three lineages (A, B, and C) and eight sublineages (A1, A2, B1, B2, and C1 - C4). Here, we report the complete genomic sequences of 14 HPV31 isolates from cervical samples, and these were compared with viral genome sequences from the GenBank database for phylogenetic and genetic distance analysis. The formation of two novel clades within the C lineage (proposed as C5 and C6) was observed, with a well-defined variant-specific mutational pattern. The smallest average pairwise distance was 0.71% for lineages A and B, 0.94% for lineages A and C, and 1.01% for lineages B and C, and between sublineages, these values were 0.21% for clade A, 0.29% for clade B, and 0.24% for clade C. The isolates were grouped into the sublineages A1, B2, C1-C3, and C6. This is the first report on the whole-genome diversity of HPV31 in Mexico.
Collapse
Affiliation(s)
- David Esaú Fragoso-Fonseca
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
- Laboratorio de Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | | | - Brenda Berenice Trujillo-Salgado
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
- Facultad de Ciencia y Tecnología, Universidad Simón Bolívar, Mexico City, Mexico
| | - Rita Teresita Manuell-Barrios
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
| | - Fabiola Garcés-Ayala
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
| | - Juan Carlos Del Mazo-López
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
| | - Alfonso Méndez-Tenorio
- Laboratorio de Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Lucía Hernández-Rivas
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
| | - José Ernesto Ramírez-González
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
- Facultad de Ciencia y Tecnología, Universidad Simón Bolívar, Mexico City, Mexico
| | - Noé Escobar-Escamilla
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico.
- Facultad de Ciencia y Tecnología, Universidad Simón Bolívar, Mexico City, Mexico.
| |
Collapse
|
3
|
García-Morales L, Del Portillo P, Anzola JM, Ares MA, Helguera-Repetto AC, Cerna-Cortes JF, Méndez-Tenorio A, García MJ, Otal I, Martín C, Gonzalez-y-Merchand JA, Rivera-Gutiérrez S. The Lack of the TetR-Like Repressor Gene BCG_2177c (Rv2160A) May Help Mycobacteria Overcome Intracellular Redox Stress and Survive Longer Inside Macrophages When Surrounded by a Lipid Environment. Front Cell Infect Microbiol 2022; 12:907890. [PMID: 35873160 PMCID: PMC9301340 DOI: 10.3389/fcimb.2022.907890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/30/2022] [Accepted: 06/06/2022] [Indexed: 11/23/2022] Open
Abstract
Mycobacteria, like other microorganisms, survive under different environmental variations by expressing an efficient adaptive response, oriented by regulatory elements, such as transcriptional repressors of the TetR family. These repressors in mycobacteria also appear to be related to cholesterol metabolism. In this study, we have evaluated the effect of a fatty acid (oleic–palmitic–stearic)/cholesterol mixture on some phenotypic and genotypic characteristics of a tetR-mutant strain (BCG_2177c mutated gene) of M. bovis BCG, a homologous of Rv2160A of M. tuberculosis. In order to accomplish this, we have analyzed the global gene expression of this strain by RNA-seq and evaluated its neutral-lipid storage capacity and potential to infect macrophages. We have also determined the macrophage response by measuring some pro- and anti-inflammatory cytokine expressions. In comparison with wild-type microorganisms, we showed that the mutation in the BCG_2177c gene did not affect the growth of M. bovis BCG in the presence of lipids but it probably modified the structure/composition of its cell envelope. Compared to with dextrose, an overexpression of the transcriptome of the wild-type and mutant strains was observed when these mycobacteria were cultured in lipids, mainly at the exponential phase. Twelve putative intracellular redox balance maintenance genes and four others coding for putative transcriptional factors (including WhiB6 and three TetR-like) were the main elements repeatedly overexpressed when cultured in the presence of lipids. These genes belonged to the central part of what we called the “genetic lipid signature” for M. bovis BCG. We have also found that all these mycobacteria genotypic changes affected the outcome of BCG-infected macrophages, being the mutant strain most adapted to persist longer inside the host. This high persistence result was also confirmed when mutant-infected macrophages showed overexpression of the anti-inflammatory cytokine TGF-β versus pro-inflammatory cytokines. In summary, the lack of this TetR-like repressor expression, within a lipid environment, may help mycobacteria overcome intracellular redox stress and survive longer inside their host.
Collapse
Affiliation(s)
- Lázaro García-Morales
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Patricia Del Portillo
- Grupo de Biotecnología Molecular, Grupo de Bioinformática y Biología Computacional, Corporación CorpoGen, Bogotá, Colombia
| | - Juan M. Anzola
- Grupo de Biotecnología Molecular, Grupo de Bioinformática y Biología Computacional, Corporación CorpoGen, Bogotá, Colombia
- Facultad de Ingeniería y Ciencias Básicas, Universidad Central, Bogotá, D.C., Colombia
| | - Miguel A. Ares
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Addy C. Helguera-Repetto
- Departamento de Inmuno-Bioquímica, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Ciudad de México, Mexico
| | - Jorge F. Cerna-Cortes
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Alfonso Méndez-Tenorio
- Laboratorio de Bioinformática y Biotecnología Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María J. García
- Departamento de Medicina Preventiva, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Isabel Otal
- Grupo de Genética de Micobacterias, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- Centro de Investigación Biomédica en Red (CIBER) Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Martín
- Grupo de Genética de Micobacterias, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- Centro de Investigación Biomédica en Red (CIBER) Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Jorge A. Gonzalez-y-Merchand
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
- *Correspondence: Jorge A. Gonzalez-y-Merchand, ; Sandra Rivera-Gutiérrez,
| | - Sandra Rivera-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
- *Correspondence: Jorge A. Gonzalez-y-Merchand, ; Sandra Rivera-Gutiérrez,
| |
Collapse
|
4
|
Moran-Garcia N, Lopez-Saucedo C, Becerra A, Meza-Segura M, Hernandez-Cazares F, Guerrero-Baez J, Galindo-Gómez S, Tsutsumi V, Schnoor M, Méndez-Tenorio A, Nataro JP, Estrada-Garcia T. A Novel Adult Murine Model of Typical Enteroaggregative Escherichia coli Infection Reveals Microbiota Dysbiosis, Mucus Secretion, and AAF/II-Mediated Expression and Localization of β-Catenin and Expression of MUC1 in Ileum. Front Cell Infect Microbiol 2022; 12:885191. [PMID: 35706909 PMCID: PMC9190437 DOI: 10.3389/fcimb.2022.885191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 02/27/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Typical enteroaggregative Escherichia coli (tEAEC) is a diarrheagenic E. coli pathotype associated with pediatric and traveler’s diarrhea. Even without diarrhea, EAEC infections in children also lead to increased gut inflammation and growth shortfalls. EAEC strain’s defining phenotype is the aggregative adherence pattern on epithelial cells attributable to the aggregative adherence fimbriae (AAF). EAEC only causes diarrhea in humans; therefore, not much is known of the exact intestinal region of infection and damage or its interactions with intestinal enterocytes in vivo and in situ. This study aimed to develop a new tEAEC mouse model of infection, characterize the microbiota of infected mice, and evaluate in situ the expression of host adherence and surface molecules triggering EAEC infection and the role of the EAEC AAF-II in adherence. Six-week-old C57BL/6 mice, without previous antibiotic treatment, were orally challenged with EAEC 042 strain or EAEC 042 AAF-II mutant (ΔAAF/II) strain, or DAEC-MXR strain (diffusely adherent E. coli clinical isolate), and with saline solution (control group). Paraffin sections of the colon and ileum were stained with H&E and periodic acid-Schiff. ZO-1, β-catenin, MUC1, and bacteria were analyzed by immunofluorescence. EAEC-infected mice, in comparison with DAEC-MXR-infected and control mice, significantly lost weight during the first 3 days. After 7 days post-infection, mucus production was increased in the colon and ileum, ZO-1 localization remained unaltered, and morphological alterations were more pronounced in the ileum since increased expression and apical localization of β-catenin in ileal enterocytes were observed. EAEC-infected mice developed dysbiosis 21 days post-infection. At 4 days post-infection, EAEC strain 042 formed a biofilm on ileal villi and increased the expression and apical localization of β-catenin in ileal enterocytes; these effects were not seen in animals infected with the 042 ΔAAF/II strain. At 3 days post-infection, MUC1 expression on ileal enterocytes was mainly detectable among infected mice and colocalized with 042 strains on the enterocyte surface. We developed a novel mouse model of EAEC infection, which mimics human infection, not an illness, revealing that EAEC 042 exerts its pathogenic effects in the mouse ileum and causes dysbiosis. This model is a unique tool to unveil early molecular mechanisms of EAEC infection in vivo and in situ.
Collapse
Affiliation(s)
| | | | - Adriana Becerra
- Department of Molecular Biomedicine, CINVESTAV-IPN, Mexico City, Mexico
| | - Mario Meza-Segura
- Department of Molecular Biomedicine, CINVESTAV-IPN, Mexico City, Mexico
| | | | | | - Silvia Galindo-Gómez
- Department of Infectomics and Molecular Pathogenesis, CINVESTAV-IPN, Mexico City, Mexico
| | - Víctor Tsutsumi
- Department of Infectomics and Molecular Pathogenesis, CINVESTAV-IPN, Mexico City, Mexico
| | - Michael Schnoor
- Department of Molecular Biomedicine, CINVESTAV-IPN, Mexico City, Mexico
| | - Alfonso Méndez-Tenorio
- Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - James P. Nataro
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Teresa Estrada-Garcia
- Department of Molecular Biomedicine, CINVESTAV-IPN, Mexico City, Mexico
- *Correspondence: Teresa Estrada-Garcia,
| |
Collapse
|
5
|
Murcia-Garzón J, Méndez-Tenorio A. Promiscuous Domains in Eukaryotes and HAT Proteins in FUNGI Have Followed Different Evolutionary Paths. J Mol Evol 2022; 90:124-138. [PMID: 35084521 DOI: 10.1007/s00239-021-10046-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/27/2021] [Indexed: 10/19/2022]
Abstract
Diverse studies have shown that the content of genes present in sequenced genomes does not seem to correlate with the complexity of the organisms. However, various studies have shown that organism complexity and the size of the proteome has, indeed, a significant correlation. This characteristic allows us to postulate that some molecular mechanisms have permitted a greater functional diversity to some proteins to increase their participation in developing organisms with higher complexity. Among those mechanisms, the domain promiscuity, defined as the ability of the domains to organize in combination with other distinct domains, is of great importance for the evolution of organisms. Previous works have analyzed the degree of domain promiscuity of the proteomes showing how it seems to have paralleled the evolution of eukaryotic organisms. The latter has motivated the present study, where we analyzed the domain promiscuity in a collection of 84 eukaryotic proteomes representative of all the taxonomy groups of the tree of life. Using a grammar definition approach, we determined the architecture of 1,223,227 proteins, conformed by 2,296,371 domains, which established 839,184 bigram types. The phylogenetic reconstructions based on differences in the content of information from measures of proteome promiscuity confirm that the evolution of the promiscuity of domains in eukaryotic organisms resembles the evolutionary history of the species. However, a close analysis of the PHD and RING domains, the most promiscuous domains found in fungi and functional components of chromatin remodeling enzymes and important expression regulators, suggests an evolution according to their function.
Collapse
Affiliation(s)
- Jazmín Murcia-Garzón
- Laboratorio de Biotecnología Vegetal, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Boulevard del Maestro S/N esq. Elías Piña, Col. Narciso Mendoza, 88710, Reynosa, Tamaulipas, Mexico
| | - Alfonso Méndez-Tenorio
- Laboratorio de Biotecnología y Bioinformática Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala s/n, Col. Santo Tomás, 11340, Mexico City, Mexico.
| |
Collapse
|
6
|
Torres-Longoria B, Fragoso-Fonseca DE, Núñez-León A, de la Luz Torres M, Vázquez-Pichardo M, Escobar-Escamilla N, Wong-Arámbula C, Ramírez-González JE, Méndez-Tenorio A, Castro-Mussot ME, Moreno-Altamirano MMB, Membrillo-Hernández J, López-Martínez I, Díaz-Quiñónez JA. Epidemiological surveillance of chikungunya fever in Mexico since its introduction in 2014-2016 and identification of circulating genotypes. Mol Biol Rep 2021; 48:1967-1975. [PMID: 33523371 DOI: 10.1007/s11033-021-06151-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 01/12/2021] [Indexed: 11/28/2022]
Abstract
In 2014, the chikungunya virus (CHIKV) was detected for the first time in Mexico, the identified strain was the one corresponding to the Asian genotype which was phylogenetically grouped with the strains that circulated in the British Virgin Islands outbreak and was later classified with lineages of Caribbean strains. In three years, 13,569 cases of chikungunya were registered in Mexico. Although the transmission and spread of the virus are now considered a moderate risk, the danger that the virus reemerges is not ruled out due to the infestation of Aedes mosquitoes. In this study, we reviewed the chikungunya fever (CHIKF) cases reported between 2014 and 2016 to reanalyze the data. Seventeen cases were selected from different states where the circulation of the virus had been reported. Statistical data were analyzed and a retrospective analysis was carried out. Nucleic acid sequences were determined of these 17 samples. 2015 was the year with the highest number of cases (92.8%) and they were detected in 28 states of the country. There is a predominance of females, and the most affected age group was between 25 and 44 years. In 2016, CHIKV genotypes were not known, in this study the presence of the Asian genotype of Caribbean lineage was confirmed. The presence of the West African and ECSA genotypes was phylogenetically ruled out. The sequences obtained were deposited in GeneBank.
Collapse
Affiliation(s)
- Belem Torres-Longoria
- Laboratorio de Inmunorregulación, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico.,Departamento de Virología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - David Esaú Fragoso-Fonseca
- Unidad de Desarrollo Tecnológico e Investigación Molecular, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr, Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - Alma Núñez-León
- Departamento de Virología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - María de la Luz Torres
- Departamento de Virología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - Mauricio Vázquez-Pichardo
- Departamento de Virología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - Noé Escobar-Escamilla
- Unidad de Desarrollo Tecnológico e Investigación Molecular, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr, Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - Claudia Wong-Arámbula
- Unidad de Desarrollo Tecnológico e Investigación Molecular, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr, Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - José Ernesto Ramírez-González
- Unidad de Desarrollo Tecnológico e Investigación Molecular, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr, Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - Alfonso Méndez-Tenorio
- Laboratorio Biotecnología y Bioinformática Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - María Eugenia Castro-Mussot
- Laboratorio de Inmunología Celular e Inmunopatogénesis, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - María M B Moreno-Altamirano
- Laboratorio de Inmunorregulación, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | - Irma López-Martínez
- Unidad de Desarrollo Tecnológico e Investigación Molecular, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr, Manuel Martínez Báez" (InDRE), Secretaria de Salud, Mexico City, Mexico
| | - José Alberto Díaz-Quiñónez
- División de Estudios de Posgrado, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico.
| |
Collapse
|
7
|
Hernández-Ochoa B, Gómez-Manzo S, Sánchez-Carrillo A, Marcial-Quino J, Rocha-Ramírez LM, Santos-Segura A, Ramírez-Nava EJ, Arreguin-Espinosa R, Cuevas-Cruz M, Méndez-Tenorio A, Calderón-Jaimes E. Enhanced Antigiardial Effect of Omeprazole Analog Benzimidazole Compounds. Molecules 2020; 25:molecules25173979. [PMID: 32882836 PMCID: PMC7504735 DOI: 10.3390/molecules25173979] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 11/22/2022] Open
Abstract
Giardiasis is a diarrheal disease that is highly prevalent in developing countries. Several drugs are available for the treatment of this parasitosis; however, failures in drug therapy are common, and have adverse effects and increased resistance of the parasite to the drug, generating the need to find new alternative treatments. In this study, we synthesized a series of 2-mercaptobenzimidazoles that are derivatives of omeprazole, and the chemical structures were confirmed through mass, 1H NMR, and 13C NMR techniques. The in vitro efficacy compounds against Giardia, as well as its effect on the inhibition of triosephosphate isomerase (TPI) recombinant, were investigated, the inactivation assays were performed with 0.2 mg/mL of the enzyme incubating for 2 h at 37 °C in TE buffer, pH 7.4 with increasing concentrations of the compounds. Among the target compounds, H-BZM2, O2N-BZM7, and O2N-BZM9 had greater antigiardial activity (IC50: 36, 14, and 17 µM on trophozoites), and inhibited the TPI enzyme (K2: 2.3, 3.2, and 2.8 M−1 s−1) respectively, loading alterations on the secondary structure, global stability, and tertiary structure of the TPI protein. Finally, we demonstrated that it had low toxicity on Caco-2 and HT29 cells. This finding makes it an attractive potential starting point for new antigiardial drugs.
Collapse
Affiliation(s)
- Beatriz Hernández-Ochoa
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Ciudad de Mexico 06720, Mexico; (A.S.-C.); (A.S.-S.)
- Correspondence: (B.H.-O.); (E.C.-J.); Tel.: +52-5228917 (ext. 2000) (B.H.-O.)
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (S.G.-M.); (E.J.R.-N.)
| | - Adrián Sánchez-Carrillo
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Ciudad de Mexico 06720, Mexico; (A.S.-C.); (A.S.-S.)
| | - Jaime Marcial-Quino
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de Mexico 04530, Mexico;
| | - Luz María Rocha-Ramírez
- Unidad de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Secretaría de Salud Dr. Márquez No. 162, Col Doctores, Delegación Cuauhtémoc, Ciudad de México 06720, Mexico;
| | - Araceli Santos-Segura
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Ciudad de Mexico 06720, Mexico; (A.S.-C.); (A.S.-S.)
| | - Edson Jiovany Ramírez-Nava
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico; (S.G.-M.); (E.J.R.-N.)
| | - Roberto Arreguin-Espinosa
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico 04510, Mexico; (R.A.-E.); (M.C.-C.)
| | - Miguel Cuevas-Cruz
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico 04510, Mexico; (R.A.-E.); (M.C.-C.)
| | - Alfonso Méndez-Tenorio
- Laboratorio de Biotecnología y Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico;
| | - Ernesto Calderón-Jaimes
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Ciudad de Mexico 06720, Mexico; (A.S.-C.); (A.S.-S.)
- Correspondence: (B.H.-O.); (E.C.-J.); Tel.: +52-5228917 (ext. 2000) (B.H.-O.)
| |
Collapse
|
8
|
Zapi-Colín L, Gutiérrez-González G, Rodríguez-Martínez S, Cancino-Diaz J, Méndez-Tenorio A, Pérez-Tapia S, Gómez-Chávez F, Cedillo-Peláez C, Cancino-Diaz M. A peptide derived from phage-display limits psoriasis-like lesions in mice. Heliyon 2020; 6:e04162. [PMID: 32577560 PMCID: PMC7304002 DOI: 10.1016/j.heliyon.2020.e04162] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/31/2020] [Accepted: 06/04/2020] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Psoriasis is a pro-inflammatory disease with unknown etiology, that is characterized by skin inflammation and keratinocytes hyperproliferation. Specific inhibition of inflammation has shown positive effects avoiding the progression of the psoriatic lesions in different animal models of the disease, turning this strategy as a remarkable therapeutic alternative. OBJECTIVE To screen the effectiveness of a novel IFN-α/β signalling inhibitor in the development reduction of skin lesions in IMQ and TPA mice models of psoriasis. METHODS We used a Phage-peptide library for the screening of a peptide with inhibitory effects on the development of psoriasis-like lesions in mice. To evaluate the in vivo effect of the phage-peptides (Phpep3D) and the derived peptide (Pep3D), we administered Phpep3D or Pep3D intradermally in mice with imiquimod (IMQ)-induced psoriasis and 12-O-tetradecanoyl phorbol-13-acetate (TPA)-induced psoriasis. We scored the lesions, and we determined the number of neutrophils and the production of some pro-inflammatory cytokines in the lesions. RESULTS In this work, we describe how the Ph3pepD and Pep3D reduced skin thickness, redness, and acanthosis despite the presence of the psoriasis inducers, IMQ or TPA. We also found that Pep3D reduced the number of GR1+ infiltrated cells and decreased the production of IL-17A and TNFα in the psoriatic skin of mice. In-silico, docking analysis showed that Pep3D may interact with the interferon-alpha receptor, but further analyses should be performed to uncover the mechanism of action of this peptide. CONCLUSION Our results suggest that Pep3D could be used as a new treatment for psoriasis.
Collapse
Affiliation(s)
- L.A. Zapi-Colín
- Laboratorio de Inmunología Innata, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomas 11340 Miguel Hidalgo, Mexico City, Mexico
| | - G. Gutiérrez-González
- Laboratorio de Inmunología Innata, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomas 11340 Miguel Hidalgo, Mexico City, Mexico
| | - S. Rodríguez-Martínez
- Laboratorio de Inmunología Innata, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomas 11340 Miguel Hidalgo, Mexico City, Mexico
| | - J.C. Cancino-Diaz
- Laboratorio de Inmunomicrobiología, Departmento de Microbiología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomas 11340 Miguel Hidalgo, Mexico City, Mexico
| | - A. Méndez-Tenorio
- Laboratorio de Biotecnología y Bioinformática, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomas 11340 Miguel Hidalgo, Mexico City, Mexico
| | - S.M. Pérez-Tapia
- Laboratorio Nacional para Servicios Especializados de Investigación, Desarrollo e Innovación (I+D+i) para Farmoquímicos y Biotecnológicos (LANSEIDI-FarBiotec-CONACyT), Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomas 11340 Miguel Hidalgo, Mexico City, Mexico
- Unidad de Desarrollo e Investigación en Bioprocesos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomas 11340 Miguel Hidalgo, Mexico City, Mexico
| | - F. Gómez-Chávez
- Cátedras CONACyT-Instituto Nacional de Pediatría, Secretaría de Salud, 04530 CDMX, Mexico
- Laboratorio de Inmunología Experimental, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Mexico City, Mexico
- Departmento de Formación Básica Disciplinaria. Escuela Nacional de Medicina y Homeopatía– IPN, 07320 Mexico City, Mexico
| | - C. Cedillo-Peláez
- Laboratorio de Inmunología Experimental, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Mexico City, Mexico
| | - M.E. Cancino-Diaz
- Laboratorio de Inmunología Innata, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Prolongación de Carpio y Plan de Ayala s/n, Colonia Santo Tomas 11340 Miguel Hidalgo, Mexico City, Mexico
| |
Collapse
|
9
|
Ramírez-González EA, Moreno-Lafont MC, Méndez-Tenorio A, Cancino-Díaz ME, Estrada-García I, López-Santiago R. Prediction of Structure and Molecular Interaction with DNA of BvrR, a Virulence-Associated Regulatory Protein of Brucella. Molecules 2019; 24:E3137. [PMID: 31470504 PMCID: PMC6749498 DOI: 10.3390/molecules24173137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 06/24/2019] [Revised: 08/10/2019] [Accepted: 08/23/2019] [Indexed: 11/28/2022] Open
Abstract
Brucellosis, also known as "undulant fever" is a zoonotic disease caused by Brucella, which is a facultative intracellular bacterium. Despite efforts to eradicate this disease, infection in uncontrolled domestic animals persists in several countries and therefore transmission to humans is common. Brucella evasion of the innate immune system depends on its ability to evade the mechanisms of intracellular death in phagocytic cells. The BvrR-BvrS two-component system allows the bacterium to detect adverse conditions in the environment. The BvrS protein has been associated with genes of virulence factors, metabolism, and membrane transport. In this study, we predicted the DNA sequence recognized by BvrR with Gibbs Recursive Sampling and identified the three-dimensional structure of BvrR using I-TASSER suite, and the interaction mechanism between BvrR and DNA with Protein-DNA docking and molecular dynamics (MD) simulation. Based on the Gibbs recursive Sampling analysis, we found the motif AAHTGC (H represents A, C, and T nucleotides) as a possible sequence recognized by BvrR. The docking and EMD simulation results showed that C-terminal effector domain of BvrR protein is likely to interact with AAHTGC sequence. In conclusion, we predicted the structure, recognition motif, and interaction of BvrR with DNA.
Collapse
Affiliation(s)
- Edgar A Ramírez-González
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
| | - Martha C Moreno-Lafont
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
| | - Alfonso Méndez-Tenorio
- Laboratorio de Biotecnología y Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
| | - Mario E Cancino-Díaz
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
| | - Iris Estrada-García
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
| | - Rubén López-Santiago
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico.
| |
Collapse
|
10
|
Merida-Vieyra J, De Colsa-Ranero A, Arzate-Barbosa P, Arias-de la Garza E, Méndez-Tenorio A, Murcia-Garzón J, Aquino-Andrade A. First clinical isolate of Escherichia coli harboring mcr-1 gene in Mexico. PLoS One 2019; 14:e0214648. [PMID: 30947268 PMCID: PMC6448934 DOI: 10.1371/journal.pone.0214648] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 09/12/2018] [Accepted: 03/17/2019] [Indexed: 11/19/2022] Open
Abstract
Our aim in this report was to describe the characteristics of the first clinical isolate of Escherichia coli (EC-PAG-733) harboring the mcr-1 gene found in Mexico. This isolate was obtained from a fecal sample from a young child with an oncological condition. We obtained the whole-genome sequence using next-generation sequencing and analyzed the sequence by bioinformatics tools. EC-PAG-733 was resistant to third- and fourth-generation cephalosporins and was susceptible to all carbapenems and amikacin; it was also resistant to ciprofloxacin, levofloxacin, gentamicin and colistin at a minimum inhibitory concentration (MIC) of 4 μg/mL. This isolate was classified as O11:H25-ST457. EC-PAG-733 harbored an ESBL type CTX-M-55 as well as several virulence factors that have been associated with Enteroaggregative Escherichia coli (EAEC). The mcr-1 gene was located within an IncI2 plasmid. The results of this whole genome shotgun project were deposited in DDBJ/ENA/GenBank under the accession number QKXE00000000.
Collapse
Affiliation(s)
- Jocelin Merida-Vieyra
- Molecular Microbiology Laboratory, Instituto Nacional de Pediatria (National Institute of Pediatrics INP), Mexico City, Mexico
| | - Agustín De Colsa-Ranero
- Molecular Microbiology Laboratory, Instituto Nacional de Pediatria (National Institute of Pediatrics INP), Mexico City, Mexico.,Pediatric Infectious Diseases Department, INP, Mexico City, Mexico
| | | | | | - Alfonso Méndez-Tenorio
- Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional (National School of Biological Sciences, National Polytechnic Institute), Mexico City, Mexico
| | - Jazmin Murcia-Garzón
- Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional (National School of Biological Sciences, National Polytechnic Institute), Mexico City, Mexico
| | - Alejandra Aquino-Andrade
- Molecular Microbiology Laboratory, Instituto Nacional de Pediatria (National Institute of Pediatrics INP), Mexico City, Mexico
| |
Collapse
|
11
|
Gómez-García O, Andrade-Pavón D, Campos-Aldrete E, Ballinas-Indilí R, Méndez-Tenorio A, Villa-Tanaca L, Álvarez-Toledano C. Synthesis, Molecular Docking, and Antimycotic Evaluation of Some 3-Acyl Imidazo[1,2-a]pyrimidines. Molecules 2018. [PMID: 29518930 PMCID: PMC6017402 DOI: 10.3390/molecules23030599] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A series of 3-benzoyl imidazo[1,2-a]pyrimidines, obtained from N-heteroarylformamidines in good yields, was tested in silico and in vitro for binding and inhibition of seven Candida species (Candida albicans (ATCC 10231), Candida dubliniensis (CD36), Candida glabrata (CBS138), Candida guilliermondii (ATCC 6260), Candida kefyr, Candida krusei (ATCC 6358) and Candida tropicalis (MYA-3404)). To predict binding mode and energy, each compound was docked in the active site of the lanosterol 14α-demethylase enzyme (CYP51), essential for fungal growth of Candida species. Antimycotic activity was evaluated as the 50% minimum inhibitory concentration (MIC50) for the test compounds and two reference drugs, ketoconazole and fluconazole. All test compounds had a better binding energy (range: -6.11 to -9.43 kcal/mol) than that found for the reference drugs (range: 48.93 to -6.16 kcal/mol). In general, the test compounds showed greater inhibitory activity of yeast growth than the reference drugs. Compounds 4j and 4f were the most active, indicating an important role in biological activity for the benzene ring with electron-withdrawing substituents. These compounds show the best MIC50 against C. guilliermondii and C. glabrata, respectively. The current findings suggest that the 3-benzoyl imidazo[1,2-a]pyrimidine derivatives, herein synthesized by an accessible methodology, are potential antifungal drugs.
Collapse
Affiliation(s)
- Omar Gómez-García
- Departamento de Química Orgánica-Laboratorio de Síntesis de Fármacos Heterocíclicos, Escuela Nacional de Ciencias Biológicas-IPN, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, C.P. 11340 Ciudad de México, Mexico.
| | - Dulce Andrade-Pavón
- Departamento de Microbiología-Laboratorio de Biología Molecular de Bacterias y Levaduras, Escuela Nacional de Ciencias Biológicas-IPN, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, C.P. 11340 Ciudad de México, Mexico.
| | - Elena Campos-Aldrete
- Departamento de Química Orgánica-Laboratorio de Síntesis de Fármacos Heterocíclicos, Escuela Nacional de Ciencias Biológicas-IPN, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, C.P. 11340 Ciudad de México, Mexico.
| | - Ricardo Ballinas-Indilí
- Instituto de Química-UNAM, Circuito Exterior, Ciudad Universitaria, Coyoacán, C.P. 04510 Ciudad de México, Mexico.
| | - Alfonso Méndez-Tenorio
- Departamento de Bioquímica-Laboratorio de Biotecnología y Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas-IPN, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, C.P. 11340 Ciudad de México, Mexico.
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología-Laboratorio de Biología Molecular de Bacterias y Levaduras, Escuela Nacional de Ciencias Biológicas-IPN, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, C.P. 11340 Ciudad de México, Mexico.
| | - Cecilio Álvarez-Toledano
- Instituto de Química-UNAM, Circuito Exterior, Ciudad Universitaria, Coyoacán, C.P. 04510 Ciudad de México, Mexico.
| |
Collapse
|
12
|
González-Durán E, Vázquez-Pichardo M, Torres-Flores JM, Garcés-Ayala F, Méndez-Tenorio A, Curiel-Quesada E, Ortiz-Alcántara JM, Castelán-Sánchez HG, Salas-Benito JS, Torres-Longoria B, López-Martínez I, Hernández-Rivas L, Membrillo-Hernández J, Díaz-Quiñonez JA, Ramírez-González JE. Genotypic variability analysis of DENV-1 in Mexico reveals the presence of a novel Mexican lineage. Arch Virol 2018; 163:1643-1647. [PMID: 29426993 DOI: 10.1007/s00705-018-3759-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/16/2018] [Indexed: 10/18/2022]
Abstract
Here, we report for the first time the circulation of dengue virus type 1 (DENV-1) belonging to the lineage IV of genotype V (African American genotype) based on phylogenetic analysis of nucleotide sequences from 10 DENV-1-positive samples obtained in Mexico between 2012 and 2014. Our data revealed that the lineages III and IV of DENV-1 genotype V were found circulating during the same period, probably explaining the rise in the number of cases of severe dengue during that period.
Collapse
Affiliation(s)
- Elizabeth González-Durán
- Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Mexico, CDMX, Mexico
| | - Mauricio Vázquez-Pichardo
- Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Mexico, CDMX, Mexico
| | - Jesús Miguel Torres-Flores
- Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional, 11340, Mexico, CDMX, Mexico
| | - Fabiola Garcés-Ayala
- Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Mexico, CDMX, Mexico
| | - Alfonso Méndez-Tenorio
- Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional, 11340, Mexico, CDMX, Mexico
| | - Everardo Curiel-Quesada
- Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional, 11340, Mexico, CDMX, Mexico
| | - Joanna María Ortiz-Alcántara
- Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Mexico, CDMX, Mexico
| | - Hugo Gildardo Castelán-Sánchez
- Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Mexico, CDMX, Mexico
| | - Juan Santiago Salas-Benito
- Escuela Nacional de Medicina y Homeopatía (ENMyH), Instituto Politécnico Nacional, 07320, Mexico, CDMX, Mexico
| | - Belem Torres-Longoria
- Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Mexico, CDMX, Mexico
| | - Irma López-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Mexico, CDMX, Mexico
| | - Lucía Hernández-Rivas
- Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Mexico, CDMX, Mexico
| | - Jorge Membrillo-Hernández
- Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Mexico, CDMX, Mexico
| | - José Alberto Díaz-Quiñonez
- Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Mexico, CDMX, Mexico. .,División de Estudios de Posgrado, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510, Mexico, CDMX, Mexico.
| | - José Ernesto Ramírez-González
- Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez" (InDRE), Secretaría de Salud, Francisco de P. Miranda 177, Lomas de Plateros, 01480, Mexico, CDMX, Mexico
| |
Collapse
|
13
|
Cetina-Corona A, López-Sánchez U, Salinas-Trujano J, Méndez-Tenorio A, Barrón BL, Torres-Flores J. Peptides Derived from Glycoproteins H and B of Herpes Simplex Virus Type 1 and Herpes Simplex Virus Type 2 Are Capable of Blocking Herpetic Infection in vitro. Intervirology 2017; 59:235-242. [PMID: 28329739 DOI: 10.1159/000464134] [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] [Received: 11/23/2016] [Accepted: 02/08/2017] [Indexed: 11/19/2022] Open
Abstract
AIMS The aim of this study was to design peptides derived from glycoproteins H (gH) and B (gB) of herpes simplex viruses type 1 (HSV-1) and type 2 (HSV-2) with the potential to block herpetic infection and to evaluate their ability to inhibit HSV-1 and HSV-2 infection in vitro. METHODS A library of continuous 15-25 residue stretches (CRSs) located at the surface of gH and gB from HSV-1 and HSV-2 was created. These CRSs were analyzed, and only those that were highly flexible and rich in charged residues were selected for the design of the antiviral peptides (AVPs). The toxicity of the AVPs was evaluated by MTT reduction assays. Virucidal activity of the AVPs was determined by a plaque reduction assay, and their antiviral effect was measured by cell viability assays. RESULTS AND CONCLUSION Four AVPs (CB-1, CB-2, U-1, and U-2) derived from gB and gH were designed and synthetized, none of which showed high levels of toxicity in Vero cells. The U-1 and U-2 gB-derived AVPs showed high virucidal and antiviral activities against both HSV-1 and HSV-2. The gH-derived peptide CB-1 showed high virucidal and antiviral activities against HSV-2, while CB-2 showed similar results against HSV-1. The peptides CB-1 and CB-2 showed higher IC50 values than the U-1 and U-2 peptides.
Collapse
Affiliation(s)
- Abraham Cetina-Corona
- Laboratorio de Virología, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | | | | | | | | |
Collapse
|
14
|
Bello M, Torres MJ, Méndez-Tenorio A, Correa-Basurto J. Conformational changes associated with L16P and T118M mutations in the membrane-embedded PMP22 protein, consequential in CMT-1A. J Biomol Struct Dyn 2016; 35:2880-2894. [PMID: 27609586 DOI: 10.1080/07391102.2016.1234415] [Citation(s) in RCA: 3] [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: 01/09/2023]
Abstract
Peripheral myelin protein 22 (PMP22) resides in the plasma membrane and is required for myelin formation in the peripheral nervous system. Excess PMP22 mutants accumulate in the endoplasmic reticulum (ER) resulting in the inherited neuropathies of Charcot-Marie-Tooth disease. However, there was no evidence of the structure of PMP22 or how mutations affect its folding. Therefore, in this study, we combined bioinformatics and homology modeling approaches to obtain three-dimensional native and mutated PMP22 models and its anchoring to a POPC membrane, submitted to .5-μs MD simulations, to determine how the L16P and T118M mutations affect the conformational behavior of PMP22. In addition, we investigated the ability of the native and mutated species to accumulate in the ER, via interaction with RER1, by combining protein-protein docking and MD simulations, taking the conformations that were most representative of the native and mutated PMP22 systems and RER1 conformations. Principal component analysis over MD simulations revealed that L16P and T118M mutations resulted in increased structural instability compared to the native form, which is consistent with previous experimental findings of increased structural fluctuations along a loop connecting transmembrane α-helix1 and α-helix2. Docking and MD simulations coupled with the MMGBSA approach allowed the identification that the binding interface for the PMP22-RER1 complex takes place through transmembrane α-helix1 and α-helix2, with higher effective binding free energy values between the mutated PMP22 systems and RER1 than for the native PMP22, mainly through van der Waals interactions.
Collapse
Affiliation(s)
- Martiniano Bello
- a Laboratorio de Modelado Molecular y Bioinformática de la Escuela Superior de Medicina , Instituto Politécnico Nacional , Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Ciudad de México C.P. 11340 , México
| | - Mixtli J Torres
- b Laboratorio de biotecnología y bioinformática genómica de la Escuela Nacional de Ciencias Biológicas , Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n , Col. Santo Tomás, Ciudad de México C.P. 11340 , México
| | - Alfonso Méndez-Tenorio
- b Laboratorio de biotecnología y bioinformática genómica de la Escuela Nacional de Ciencias Biológicas , Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n , Col. Santo Tomás, Ciudad de México C.P. 11340 , México
| | - José Correa-Basurto
- a Laboratorio de Modelado Molecular y Bioinformática de la Escuela Superior de Medicina , Instituto Politécnico Nacional , Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Ciudad de México C.P. 11340 , México
| |
Collapse
|
15
|
García-Chequer AJ, Méndez-Tenorio A, Olguín-López G, Sánchez-Vallejo C, Isa P, Arias CF, Torres J, Hernández-Angeles A, Ramírez-Ortiz MA, Lara C, Cabrera-Muñoz MDL, Sadowinski-Pine S, Bravo-Ortiz JC, Ramón-García G, Diegopérez-Ramírez J, Ramírez-Reyes G, Casarrubias-Islas R, Ramírez J, Orjuela M, Ponce-Castañeda MV. Illumina next generation sequencing data and expression microarrays data from retinoblastoma and medulloblastoma tissues. Data Brief 2016; 6:908-16. [PMID: 26937470 PMCID: PMC4753385 DOI: 10.1016/j.dib.2015.12.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 12/15/2015] [Accepted: 12/31/2015] [Indexed: 12/01/2022] Open
Abstract
Retinoblastoma (Rb) is a pediatric intraocular malignancy and probably the most robust clinical model on which genetic predisposition to develop cancer has been demonstrated. Since deletions in chromosome 13 have been described in this tumor, we performed next generation sequencing to test whether recurrent losses could be detected in low coverage data. We used Illumina platform for 13 tumor tissue samples: two pools of 4 retinoblastoma cases each and one pool of 5 medulloblastoma cases (raw data can be found at http://www.ebi.ac.uk/ena/data/view/PRJEB6630). We first created an in silico reference profile generated from a human sequenced genome (GRCh37p5). From this data we calculated an integrity score to get an overview of gains and losses in all chromosomes; we next analyzed each chromosome in windows of 40 kb length, calculating for each window the log2 ratio between reads from tumor pool and in silico reference. Finally we generated panoramic maps with all the windows whether lost or gained along each chromosome associated to its cytogenetic bands to facilitate interpretation. Expression microarrays was done for the same samples and a list of over and under expressed genes is presented here. For this detection a significance analysis was done and a log2 fold change was chosen as significant (raw data can be found at http://www.ncbi.nlm.nih.gov/geo/accession number GSE11488). The complete research article can be found at Cancer Genetics journal (Garcia-Chequer et al., in press) [1]. In summary here we provide an overview with visual graphics of gains and losses chromosome by chromosome in retinoblastoma and medulloblastoma, also the integrity score analysis and a list of genes with relevant expression associated. This material can be useful to researchers that may want to explore gains and losses in other malignant tumors with this approach or compare their data with retinoblastoma.
Collapse
Affiliation(s)
- A J García-Chequer
- Unidad de Investigación Médica en Enfermedades Infecciosas, Hospital de Pediatría, Instituto Mexicano del Seguro Social, Centro Médico Nacional SXXI, México D.F., Mexico
| | - A Méndez-Tenorio
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D.F., Mexico
| | - G Olguín-López
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D.F., Mexico
| | - C Sánchez-Vallejo
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D.F., Mexico
| | - P Isa
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - C F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - J Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas, Hospital de Pediatría, Instituto Mexicano del Seguro Social, Centro Médico Nacional SXXI, México D.F., Mexico
| | - A Hernández-Angeles
- Unidad de Investigación Médica en Enfermedades Infecciosas, Hospital de Pediatría, Instituto Mexicano del Seguro Social, Centro Médico Nacional SXXI, México D.F., Mexico
| | | | - C Lara
- Hospital Infantil de México Federico Gómez, México D.F., Mexico
| | | | | | | | | | | | | | | | - J Ramírez
- Unidad de Microarreglos, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México D.F., Mexico
| | | | - M V Ponce-Castañeda
- Unidad de Investigación Médica en Enfermedades Infecciosas, Hospital de Pediatría, Instituto Mexicano del Seguro Social, Centro Médico Nacional SXXI, México D.F., Mexico
| |
Collapse
|
16
|
Fuentes-Pananá EM, Larios-Serrato V, Méndez-Tenorio A, Morales-Sánchez A, Arias CF, Torres J. Assessment of Epstein-Barr virus nucleic acids in gastric but not in breast cancer by next-generation sequencing of pooled Mexican samples. Mem Inst Oswaldo Cruz 2016; 111:200-8. [PMID: 26910355 PMCID: PMC4804503 DOI: 10.1590/0074-02760150405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 10/22/2015] [Accepted: 01/12/2016] [Indexed: 12/21/2022] Open
Abstract
Gastric (GC) and breast (BrC) cancer are two of the most common and deadly tumours.
Different lines of evidence suggest a possible causative role of viral infections for
both GC and BrC. Wide genome sequencing (WGS) technologies allow searching for viral
agents in tissues of patients with cancer. These technologies have already
contributed to establish virus-cancer associations as well as to discovery new tumour
viruses. The objective of this study was to document possible associations of viral
infection with GC and BrC in Mexican patients. In order to gain idea about cost
effective conditions of experimental sequencing, we first carried out an in
silico simulation of WGS. The next-generation-platform IlluminaGallx was
then used to sequence GC and BrC tumour samples. While we did not find viral
sequences in tissues from BrC patients, multiple reads matching Epstein-Barr virus
(EBV) sequences were found in GC tissues. An end-point polymerase chain reaction
confirmed an enrichment of EBV sequences in one of the GC samples sequenced,
validating the next-generation sequencing-bioinformatics pipeline.
Collapse
Affiliation(s)
- Ezequiel M Fuentes-Pananá
- Unidad de Investigación en Virología y Cáncer, Hospital Infantil de México Federico Gómez, México, DF, México
| | - Violeta Larios-Serrato
- Laboratorio de Biotecnología y Bioinformática Genómica, Unidad Profesional Lázaro Cárdenas, Escuela Nacional de Ciencias Biológicas, México, DF, México
| | - Alfonso Méndez-Tenorio
- Laboratorio de Biotecnología y Bioinformática Genómica, Unidad Profesional Lázaro Cárdenas, Escuela Nacional de Ciencias Biológicas, México, DF, México
| | - Abigail Morales-Sánchez
- Unidad de Investigación en Virología y Cáncer, Hospital Infantil de México Federico Gómez, México, DF, México
| | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, México
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, México, DF, México
| |
Collapse
|
17
|
García-Chequer AJ, Méndez-Tenorio A, Olguín-Ruiz G, Sánchez-Vallejo C, Isa P, Arias CF, Torres J, Hernández-Angeles A, Ramírez-Ortiz MA, Lara C, Cabrera-Muñoz ML, Sadowinski-Pine S, Bravo-Ortiz JC, Ramón-García G, Diegopérez-Ramírez J, Ramírez-Reyes G, Casarrubias-Islas R, Ramírez J, Orjuela MA, Ponce-Castañeda MV. Overview of recurrent chromosomal losses in retinoblastoma detected by low coverage next generation sequencing. Cancer Genet 2015; 209:57-69. [PMID: 26883451 DOI: 10.1016/j.cancergen.2015.12.001] [Citation(s) in RCA: 6] [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] [Received: 06/25/2015] [Revised: 09/01/2015] [Accepted: 12/03/2015] [Indexed: 12/12/2022]
Abstract
Genes are frequently lost or gained in malignant tumors and the analysis of these changes can be informative about the underlying tumor biology. Retinoblastoma is a pediatric intraocular malignancy, and since deletions in chromosome 13 have been described in this tumor, we performed genome wide sequencing with the Illumina platform to test whether recurrent losses could be detected in low coverage data from DNA pools of Rb cases. An in silico reference profile for each pool was created from the human genome sequence GRCh37p5; a chromosome integrity score and a graphics 40 Kb window analysis approach, allowed us to identify with high resolution previously reported non random recurrent losses in all chromosomes of these tumors. We also found a pattern of gains and losses associated to clear and dark cytogenetic bands respectively. We further analyze a pool of medulloblastoma and found a more stable genomic profile and previously reported losses in this tumor. This approach facilitates identification of recurrent deletions from many patients that may be biological relevant for tumor development.
Collapse
Affiliation(s)
- A J García-Chequer
- Unidad de Investigación Médica en Enfermedades Infecciosas, Centro Médico Nacional SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico
| | - A Méndez-Tenorio
- Lab. Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D.F., Mexico
| | - G Olguín-Ruiz
- Lab. Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D.F., Mexico
| | - C Sánchez-Vallejo
- Lab. Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D.F., Mexico
| | - P Isa
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - C F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - J Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas, Centro Médico Nacional SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico
| | - A Hernández-Angeles
- Unidad de Investigación Médica en Enfermedades Infecciosas, Centro Médico Nacional SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico
| | | | - C Lara
- Hospital Infantil de México Federico Gómez, México D.F., Mexico
| | | | | | - J C Bravo-Ortiz
- Hospital de Pediatría, CMN SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico
| | - G Ramón-García
- Hospital de Pediatría, CMN SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico
| | - J Diegopérez-Ramírez
- Hospital de Pediatría, CMN SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico
| | - G Ramírez-Reyes
- Hospital de Pediatría, CMN SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico
| | - R Casarrubias-Islas
- Hospital de Pediatría, CMN SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico
| | - J Ramírez
- Unidad de Microarreglos, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México D.F., Mexico
| | | | - M V Ponce-Castañeda
- Unidad de Investigación Médica en Enfermedades Infecciosas, Centro Médico Nacional SXXI, Instituto Mexicano del Seguro Social, México D.F., Mexico.
| |
Collapse
|
18
|
Avilés-Jiménez F, Guitron A, Segura-López F, Méndez-Tenorio A, Iwai S, Hernández-Guerrero A, Torres J. Microbiota studies in the bile duct strongly suggest a role for Helicobacter pylori in extrahepatic cholangiocarcinoma. Clin Microbiol Infect 2015; 22:178.e11-178.e22. [PMID: 26493848 DOI: 10.1016/j.cmi.2015.10.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [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: 08/27/2015] [Revised: 10/01/2015] [Accepted: 10/05/2015] [Indexed: 02/07/2023]
Abstract
Biliary tract cancer or extrahepatic cholangiocarcinoma (ECCA) represents the sixth commonest cause of cancer in the gastrointestinal tract in western countries. We aimed to characterize the microbiota and its predicted associated functions in the biliary tract of ECCA and benign biliary pathology (BBP). Samples were taken from 100 patients with ECCA and 100 patients with BBP by endoscopic cholangio-pancreatography for DNA extraction. Ten patients with ECCA and ten with BBP were selected for microbiota studies using the V4-16S rRNA gene and sequenced in Illumina platform. Microbiota analyses included sample-to-sample distance metrics, ordination/clustering and prediction of functions. Presence of Nesterenkonia sp. and Helicobacter pylori cagA and vacA genes were tested in the 100 ECCA and 100 BBP samples. Phylum Proteobacteria dominated all samples (60.4% average). Ordination multicomponent analyses showed significant microbiota separation between ECCA and BBP (p 0.010). Analyses of 4002 operational taxonomic units with presence variation in at least one category probed a separation of ECCA from BBP. Among these, Nesterenkonia decreased, whereas Methylophilaceae, Fusobacterium, Prevotella, Actinomyces, Novosphingobium and H. pylori increased in ECCA. Predicted associated functions showed increased abundance of H. pylori virulence genes in ECCA. cagA and vacA genes were confirmed by PCR in ECCA and BBP samples. This is the first microbiota report in ECCA and BBP to show significant changes in microbial composition. Bacterial species unusual for human flora were found: Methylophilaceae and Nesterenkonia are reported in hypersaline soils, and Mesorhizobium is a nitrogen-fixing bacterium. Enrichment of virulence genes confirms previous studies suggesting that H. pylori might be associated with ECCA.
Collapse
Affiliation(s)
- F Avilés-Jiménez
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, IMSS, Mexico
| | - A Guitron
- Departamento de Endoscopía Digestiva, UMAE 71 IMSS, Coahuila, Mexico
| | - F Segura-López
- Departamento de Anestesiología, UMAE 71 IMSS, Coahuila, Mexico
| | - A Méndez-Tenorio
- Laboratorio de Biotecnología y Bioinformática Genómica, ENCB, Instituto Politécnico Nacional, Mexico
| | - S Iwai
- Second Genome, South San Francisco, CA, USA
| | | | - J Torres
- Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatría, IMSS, Mexico.
| |
Collapse
|
19
|
Castillo P, Cetina AF, Méndez-Tenorio A, Espinoza-Fonseca LM, Barrón BL. Papillomavirus binding factor (PBF) is an intrinsically disordered protein with potential participation in osteosarcoma genesis, in silico evidence. Theor Biol Med Model 2014; 11:51. [PMID: 25471943 PMCID: PMC4265421 DOI: 10.1186/1742-4682-11-51] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 08/12/2014] [Accepted: 10/21/2014] [Indexed: 11/17/2022] Open
Abstract
Background Papillomavirus binding factor (PBF) or zinc finger protein 395 is a transcription factor associated to a poor prognosis in patients with osteosarcoma, an aggressive bone cancer that predominantly affects adolescents. To investigate the role of the PBF protein in the osteosarcoma genesis, in this paper we present the bioinformatics analysis of physicochemical properties of PBF and its probable interactions with several key cellular targets. Results The physicochemical characteristics determined to PBF, disorder-promoting amino acids, flexibility, hydrophobicity, prediction of secondary and tertiary structures and probability to be crystallized, supported that this protein can be considered as an intrinsically disordered protein (IDP), with a zinc finger-like domain. The in silico analysis to find out PBF interactions with cellular factors, confirmed the experimentally demonstrated interaction of PBF with two key cellular proteins involved in regulation of cellular apoptosis, 14-3-3β and Scythe/BAT3 proteins. Furthermore, other interactions were found with proteins like HDAC1 and TPR which are known to be deregulated in several cancers. Experimental confirmation of specific interactions will contribute to understand the osteosarcoma process and might lead to the identification of new targets for diagnosis and treatments. Conclusions According to the in silico PBF analyses, this protein can be considered as an IDP capable to bind several key cellular factors, and these interactions might play an important role in the osteosarcoma process.
Collapse
Affiliation(s)
| | | | | | | | - Blanca L Barrón
- Department of Microbiology, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Casco de Santo Tomás, México, DF 11340, México.
| |
Collapse
|
20
|
Valencia-Hipόlito A, Hernández-Atenógenes M, Vega GG, Maldonado-Valenzuela A, Ramon G, Mayani H, Peña Alonso Y, Martinez-Maza O, Méndez-Tenorio A, Huerta-Yepez S, Bonavida B, Vega MI. Expression of KLF4 is a predictive marker for survival in pediatric Burkitt lymphoma. Leuk Lymphoma 2014; 55:1806-14. [PMID: 24067139 DOI: 10.3109/10428194.2013.848437] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [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: 02/03/2023]
Abstract
Krüppel-like factor 4 (KLF4) is expressed in a variety of tissues with diverse physiological functions and activities. KLF4 can also function as a tumor suppressor or an oncogene, depending on the cellular context. Its role in hematological malignancies is controversial. This study examined the expression levels of KLF4 by immunohistochemistry in 73 pediatric non-Hodgkin lymphomas (NHLs) in a tissue microarray and also on several B-NHL cell lines. Elevated levels of KLF4 expression were detected in 66% of lymphoma cases and were more frequent in the Burkitt lymphoma (p = 0.05) subtype. There was a significant predictive power for outcome with low KLF4 expression, predicting a favorable overall survival compared to high levels. Multivariate analyses confirmed the association of KLF4 expression with unfavorable overall survival (p < 0.005). These findings were consistent with analyses in existing NHL microarray datasets. The present findings revealed that KLF4 is overexpressed in Burkitt pediatric lymphoma and is a potential biomarker for inferior overall survival.
Collapse
Affiliation(s)
- Alberto Valencia-Hipόlito
- Oncology Research Unit, Oncology Hospital, Siglo XXI National Medical Center , IMSS, Mexico City , Mexico
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Carreño-Durán LR, Larios-Serrato V, Jaimes-Díaz H, Pérez-Cervantes H, Zepeda-López H, Sánchez-Vallejo CJ, Olguín-Ruiz GE, Maldonado-Rodríguez R, Méndez-Tenorio A. Design of a set of probes with high potential for influenza virus epidemiological surveillance. Bioinformation 2013; 9:414-20. [PMID: 23750091 PMCID: PMC3670124 DOI: 10.6026/97320630009414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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] [Received: 04/09/2013] [Accepted: 04/10/2013] [Indexed: 11/23/2022] Open
Abstract
An Influenza Probe Set (IPS) consisting in 1,249 9-mer probes for genomic fingerprinting of closely and distantly related Influenza Virus strains was designed and tested in silico. The IPS was derived from alignments of Influenza genomes. The RNA segments of 5,133 influenza strains having diverse degree of relatedness were concatenated and aligned. After alignment, 9-mer sites having high Shannon entropy were searched. Additional criteria such as: G+C content between 35 to 65%, absence of dimer or trimer consecutive repeats, a minimum of 2 differences between 9mers and selecting only sequences with Tm values between 34.5 and 36.5oC were applied for selecting probes with high sequential entropy. Virtual Hybridization was used to predict Genomic Fingerprints to assess the capability of the IPS to discriminate between influenza and related strains. Distance scores between pairs of Influenza Genomic Fingerprints were calculated, and used for estimating Taxonomic Trees. Visual examination of both Genomic Fingerprints and Taxonomic Trees suggest that the IPS is able to discriminate between distant and closely related Influenza strains. It is proposed that the IPS can be used to investigate, by virtual or experimental hybridization, any new, and potentially virulent, strain.
Collapse
Affiliation(s)
- Luis R Carreño-Durán
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, Escuela Nacional de Ciencias Biológicas,
Instituto Politécnico Nacional, México City, Méxic
| | - V Larios-Serrato
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, Escuela Nacional de Ciencias Biológicas,
Instituto Politécnico Nacional, México City, Méxic
| | - Hueman Jaimes-Díaz
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, Escuela Nacional de Ciencias Biológicas,
Instituto Politécnico Nacional, México City, Méxic
| | - Hilda Pérez-Cervantes
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, Escuela Nacional de Ciencias Biológicas,
Instituto Politécnico Nacional, México City, Méxic
| | - Héctor Zepeda-López
- Laboratory of Conservation Medicine, Escuela Superior de Medicina, Instituto
Politécnico Nacional, México City, México
| | - Carlos Javier Sánchez-Vallejo
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, Escuela Nacional de Ciencias Biológicas,
Instituto Politécnico Nacional, México City, Méxic
| | - Gabriela Edith Olguín-Ruiz
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, Escuela Nacional de Ciencias Biológicas,
Instituto Politécnico Nacional, México City, Méxic
| | - Rogelio Maldonado-Rodríguez
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, Escuela Nacional de Ciencias Biológicas,
Instituto Politécnico Nacional, México City, Méxic
| | - Alfonso Méndez-Tenorio
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, Escuela Nacional de Ciencias Biológicas,
Instituto Politécnico Nacional, México City, Méxic
| |
Collapse
|
22
|
Cruz-Laguna EY, Gámez-Méndez AM, Vargas-Robles H, Ríos A, Méndez-Tenorio A, Escalante B. Renin-angiotensin system blockade: Effect on renal mRNA expression in 5/6 nephrectomized rats. Health (London) 2013. [DOI: 10.4236/health.2013.54a002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
23
|
Mancilla-Herrera I, Méndez-Tenorio A, Wong-Baeza I, Jiménez-Uribe AP, Alcántara-Hernández M, Ocadiz-Ruiz R, Moreno-Eutimio MA, Arriaga-Pizano LA, López-Macías C, González-y-Merchand J, Isibasi A. A Toll/IL-1R/resistance domain-containing thioredoxin regulates phagocytosis in Entamoeba histolytica. Parasit Vectors 2012; 5:224. [PMID: 23043976 PMCID: PMC3481431 DOI: 10.1186/1756-3305-5-224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 02/22/2012] [Accepted: 09/22/2012] [Indexed: 11/22/2022] Open
Abstract
Background Entamoeba histolytica is a protozoan parasite that infects humans and causes amebiasis affecting developing countries. Phagocytosis of epithelial cells, erythrocytes, leucocytes, and commensal microbiota bacteria is a major pathogenic mechanism used by this parasite. A Toll/IL-1R/Resistance (TIR) domain-containing protein is required in phagocytosis in the social ameba Dictyostelium discoideum, an ameba closely related to Entamoeba histolytica in phylogeny. In insects and vertebrates, TIR domain-containing proteins regulate phagocytic and cell activation. Therefore, we investigated whether E. histolytica expresses TIR domain-containing molecules that may be involved in the phagocytosis of erythrocytes and bacteria. Methods Using in silico analysis we explored in Entamoeba histolytica databases for TIR domain containing sequences. After silencing TIR domain containing sequences in trophozoites by siRNA we evaluated phagocytosis of erythrocytes and bacteria. Results We identified an E. histolytica thioredoxin containing a TIR-like domain. The secondary and tertiary structure of this sequence exhibited structural similarity to TIR domain family. Thioredoxin transcripts silenced in E. histolytica trophozoites decreased erythrocytes and E. coli phagocytosis. Conclusion TIR domain-containing thioredoxin of E. histolytica could be an important element in erythrocytes and bacteria phagocytosis.
Collapse
Affiliation(s)
- Ismael Mancilla-Herrera
- Medical Research Unit on Immunochemistry, Specialties Hospital, National Medical Centre Siglo XXI, Mexican Social Security Institute, Mexico City, Mexico
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Casique-Almazán J, Larios-Serrato V, Olguín-Ruíz GE, Sánchez-Vallejo CJ, Maldonado-Rodríguez R, Méndez-Tenorio A. Universal fingerprinting chip server. Bioinformation 2012; 8:586-8. [PMID: 22829736 PMCID: PMC3398781 DOI: 10.6026/97320630008586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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] [Received: 05/23/2012] [Accepted: 06/16/2012] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED The Virtual Hybridization approach predicts the most probable hybridization sites across a target nucleic acid of known sequence, including both perfect and mismatched pairings. Potential hybridization sites, having a user-defined minimum number of bases that are paired with the oligonucleotide probe, are first identified. Then free energy values are evaluated for each potential hybridization site, and if it has a calculated free energy of equal or higher negative value than a user-defined free energy cut-off value, it is considered as a site of high probability of hybridization. The Universal Fingerprinting Chip Applications Server contains the software for visualizing predicted hybridization patterns, which yields a simulated hybridization fingerprint that can be compared with experimentally derived fingerprints or with a virtual fingerprint arising from a different sample. AVAILABILITY The database is available for free at http://bioinformatica.homelinux.org/UFCVH/
Collapse
Affiliation(s)
- Janet Casique-Almazán
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences,
National Polytechnic Institute, CP 11340, Mexico City, Mexico
| | - Violeta Larios-Serrato
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences,
National Polytechnic Institute, CP 11340, Mexico City, Mexico
| | - Gabriela Edith Olguín-Ruíz
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences,
National Polytechnic Institute, CP 11340, Mexico City, Mexico
| | - Carlos Javier Sánchez-Vallejo
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences,
National Polytechnic Institute, CP 11340, Mexico City, Mexico
| | - Rogelio Maldonado-Rodríguez
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences,
National Polytechnic Institute, CP 11340, Mexico City, Mexico
| | - Alfonso Méndez-Tenorio
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences,
National Polytechnic Institute, CP 11340, Mexico City, Mexico
| |
Collapse
|
25
|
Villegas-Rosales PM, Méndez-Tenorio A, Ortega-Soto E, Barrón BL. Bioinformatics prediction of siRNAs as potential antiviral agents against dengue viruses. Bioinformation 2012; 8:519-22. [PMID: 22829722 PMCID: PMC3398769 DOI: 10.6026/97320630008519] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 06/08/2012] [Indexed: 01/30/2023] Open
Abstract
Dengue virus (DENV 1-4) represents the major emerging arthropod-borne viral infection in the world. Currently, there is neither an available vaccine nor a specific treatment. Hence, there is a need of antiviral drugs for these viral infections; we describe the prediction of short interfering RNA (siRNA) as potential therapeutic agents against the four DENV serotypes. Our strategy was to carry out a series of multiple alignments using ClustalX program to find conserved sequences among the four DENV serotype genomes to obtain a consensus sequence for siRNAs design. A highly conserved sequence among the four DENV serotypes, located in the encoding sequence for NS4B and NS5 proteins was found. A total of 2,893 complete DENV genomes were downloaded from the NCBI, and after a depuration procedure to identify identical sequences, 220 complete DENV genomes were left. They were edited to select the NS4B and NS5 sequences, which were aligned to obtain a consensus sequence. Three different servers were used for siRNA design, and the resulting siRNAs were aligned to identify the most prevalent sequences. Three siRNAs were chosen, one targeted the genome region that codifies for NS4B protein and the other two; the region for NS5 protein. Predicted secondary structure for DENV genomes was used to demonstrate that the siRNAs were able to target the viral genome forming double stranded structures, necessary to activate the RNA silencing machinery.
Collapse
|
26
|
Reyes-Prieto F, García-Chéquer AJ, Jaimes-Díaz H, Casique-Almazán J, Espinosa-Lara JM, Palma-Orozco R, Méndez-Tenorio A, Maldonado-Rodríguez R, Beattie KL. LifePrint: a novel k-tuple distance method for construction of phylogenetic trees. Adv Appl Bioinform Chem 2011; 4:13-27. [PMID: 21918634 PMCID: PMC3169951 DOI: 10.2147/aabc.s15021] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Here we describe LifePrint, a sequence alignment-independent k-tuple distance method to estimate relatedness between complete genomes. METHODS We designed a representative sample of all possible DNA tuples of length 9 (9-tuples). The final sample comprises 1878 tuples (called the LifePrint set of 9-tuples; LPS9) that are distinct from each other by at least two internal and noncontiguous nucleotide differences. For validation of our k-tuple distance method, we analyzed several real and simulated viroid genomes. Using different distance metrics, we scrutinized diverse viroid genomes to estimate the k-tuple distances between these genomic sequences. Then we used the estimated genomic k-tuple distances to construct phylogenetic trees using the neighbor-joining algorithm. A comparison of the accuracy of LPS9 and the previously reported 5-tuple method was made using symmetric differences between the trees estimated from each method and a simulated "true" phylogenetic tree. RESULTS The identified optimal search scheme for LPS9 allows only up to two nucleotide differences between each 9-tuple and the scrutinized genome. Similarity search results of simulated viroid genomes indicate that, in most cases, LPS9 is able to detect single-base substitutions between genomes efficiently. Analysis of simulated genomic variants with a high proportion of base substitutions indicates that LPS9 is able to discern relationships between genomic variants with up to 40% of nucleotide substitution. CONCLUSION Our LPS9 method generates more accurate phylogenetic reconstructions than the previously proposed 5-tuples strategy. LPS9-reconstructed trees show higher bootstrap proportion values than distance trees derived from the 5-tuple method.
Collapse
Affiliation(s)
- Fabián Reyes-Prieto
- Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences, Mexico City, Mexico
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Orozco-Colín A, Carrillo-García A, Méndez-Tenorio A, Ponce-de-León S, Mohar A, Maldonado-Rodríguez R, Guerra-Arias R, Flores-Gil O, Sotelo-Regil R, Lizano M. Geographical variation in human papillomavirus prevalence in Mexican women with normal cytology. Int J Infect Dis 2010; 14:e1082-7. [DOI: 10.1016/j.ijid.2010.07.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Revised: 07/27/2010] [Accepted: 07/29/2010] [Indexed: 10/18/2022] Open
|
28
|
Rangel-López A, Méndez-Tenorio A, Beattie KL, Maldonado R, Mendoza P, Vázquez G, Pérez-Plasencia C, Sánchez M, Navarro G, Salcedo M. Specific mutation screening of TP53 gene by low-density DNA microarray. Nanotechnol Sci Appl 2009; 2:1-12. [PMID: 24198462 PMCID: PMC3781765] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Abstract
TP53 is the most commonly mutated gene in human cancers. Approximately 90% of mutations in this gene are localized between domains encoding exons 5 to 8. The aim of this investigation was to examine the ability of the low density DNA microarray with the assistance of double tandem hybridization platform to characterize TP53 mutational hotspots in exons 5, 7, and 8 of the TP53. Nineteen capture probes specific to each potential mutation site were designed to hybridize to specific site. Virtual hybridization was used to predict the stability of hybridization of each capture probe with the target. Thirty-three DNA samples from different sources were analyzed for mutants in these exons. A total of 32 codon substitutions were found by DNA sequencing. 24 of them a showed a perfect correlation with the hybridization pattern system and DNA sequencing analysis of the regions scanned. Although in this work we directed our attention to some of the most representative mutations of the TP53 gene, the results suggest that this microarray system proved to be a rapid, reliable, and effective method for screening all the mutations in TP53 gene.
Collapse
Affiliation(s)
- Angélica Rangel-López
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN Siglo XXI-IMSS, Mexico City, Mexico
- Unidad de Investigación Médica en Enfermedades Nefrológicas, Hospital de Especialidades, CMN Siglo XXI-IMSS, Mexico City; Mexico
- Laboratorio de Biotecnología y Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas, IPN Mexico City, Mexico
| | - Alfonso Méndez-Tenorio
- Laboratorio de Biotecnología y Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas, IPN Mexico City, Mexico
| | | | - Rogelio Maldonado
- Laboratorio de Biotecnología y Bioinformática Genómica, Escuela Nacional de Ciencias Biológicas, IPN Mexico City, Mexico
| | - Patricia Mendoza
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN Siglo XXI-IMSS, Mexico City, Mexico
| | - Guelaguetza Vázquez
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN Siglo XXI-IMSS, Mexico City, Mexico
| | - Carlos Pérez-Plasencia
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México UNAM, Instituto Nacional de Cancerología INCAN, Mexico City, Mexico
| | - Martha Sánchez
- Unidad de Investigación Médica en Enfermedades Nefrológicas, Hospital de Especialidades, CMN Siglo XXI-IMSS, Mexico City; Mexico
| | | | - Mauricio Salcedo
- Laboratorio de Oncología Genómica, Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, CMN Siglo XXI-IMSS, Mexico City, Mexico
| |
Collapse
|
29
|
Méndez-Tenorio A, Flores-Cortés P, Guerra-Trejo A, Jaimes-Díaz H, Reyes-Rosales E, Maldonado-Rodríguez A, Espinosa-Lara M, Maldonado-Rodríguez R, Kenneth LB. In silico evaluation of a novel DNA chip based fingerprinting technology for viral identification. Rev Latinoam Microbiol 2006; 48:56-65. [PMID: 17578073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The identification of microorganisms by whole genome DNA fingerprinting was tested "in silico". 94 HPV genome sequences were submitted to virtual hybridization analysis on a DNA chip with 342 probes. This Universal Fingerprinting Chip (UFC) constitutes a representative set of probes of all the possible 8-mer sequences having at least two internal and non contiguous sequence differences between all them. A virtual hybridization analysis was performed in order to find the fingerprinting pattern that represents the signals produced for the hybridization of the probes allowing at most a single mismatch. All the fingerprints for each virus were compared against each other in order to obtain all the pairwise distances measures. A match-extension strategy was applied to identify only the shared signals corresponding to the hybridization of the probes with homologous sequences between two HPV genomes. A phylogenetic tree was constructed from the fingerprint distances using the Neighbor-Joining algorithm implemented in the program Phylip 3.61. This tree was compared with that produced from the alignment of whole genome HPV sequences calculated with the program Clustal_X 1.83. The similarities between both trees are suggesting that the UFC-8 is able to discriminate accurately between viral genomes. A fingerprint comparative analysis suggests that the UFC-8 can differentiate between HPV types and sub-types.
Collapse
Affiliation(s)
- Alfonso Méndez-Tenorio
- Laboratorio de Tecnología del DNA, Escuela Nacional de Ciencias Biológicas. IPN. Prol. de Carpio y Plan de Ayala s/n, Col. Santo Tomás, 11340, Mexico DF
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Rangel-López A, Maldonado-Rodríguez R, Salcedo-Vargas M, Espinosa-Lara JM, Méndez-Tenorio A, Beattie KL. Low density DNA microarray for detection of most frequent TP53 missense point mutations. BMC Biotechnol 2005; 5:8. [PMID: 15713227 PMCID: PMC553977 DOI: 10.1186/1472-6750-5-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [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: 07/01/2004] [Accepted: 02/15/2005] [Indexed: 11/13/2022] Open
Abstract
Background We have developed an oligonucleotide microarray (genosensor) utilizing a double tandem hybridization technique to search for 9 point mutations located in the most frequently altered codons of the TP53 gene. Isolated and multiplexed PCR products, 108 and 92 bp long, from exons 7 and 8, respectively, were obtained from 24 different samples. Single-stranded target DNA was then prepared from isolated or multiplexed PCR products, through cyclic DNA synthesis. Independent ssDNA's were annealed with the corresponding pairs of labeled stacking oligonucleotides to create partially duplex DNA having a 7-nt gap, which contains the sequence that will be interrogated by the capture probes forming double tandem hybridization. In the case of multiplexed ssPCR products, only two stacking oligonucleotides were added per target, therefore the gap for the PCR products having two consecutive codons to be interrogated in exon 7 was 12 nt long, so only single tandem hybridization was produced with these respective probes. Results 18 codon substitutions were found by DNA sequencing. In 13 of them a perfect correlation with the pattern of hybridization was seen (In 5 no signal was seen with the wt probe while a new signal was seen with the appropriate mutant probe, and in 8 more, as expected, no signal was seen with any probe due to the absence of the corresponding probe in the array). In 3 other cases a mutation was falsely suggested by the combination of the absence of the wild type signal along with a false signal in the other probe. In the other 2 cases the presence of the mutation was not detected due to the production of a false hybridization signal with the wild type probe. In both cases (false mutation or no mutation detected) relatively stable mismatched target/probe duplexes should be formed. These problems could be avoided by the addition of probes to improve the performance of the array. Conclusion Our results demonstrate that a simple TP53 microarray employing short (7-mer) probes, used in combination with single or double tandem hybridization approach and a simple or multiplex target preparation method, can identify common TP53 missense mutations from a variety of DNA sources with good specificity.
Collapse
Affiliation(s)
- Angélica Rangel-López
- Escuela Nacional de Ciencias Biológicas IPN, México, 11340, D. F., México, 11340, D. F., México
- Unidad de Investigación Médica en Enfermedades Oncológicas. Hospital de Oncología. Centro Médico Nacional S XXI. IMSS, México, D. F., México
| | | | - Mauricio Salcedo-Vargas
- Unidad de Investigación Médica en Enfermedades Oncológicas. Hospital de Oncología. Centro Médico Nacional S XXI. IMSS, México, D. F., México
| | | | - Alfonso Méndez-Tenorio
- Escuela Nacional de Ciencias Biológicas IPN, México, 11340, D. F., México, 11340, D. F., México
| | | |
Collapse
|
31
|
Reyes-López MA, Méndez-Tenorio A, Maldonado-Rodríguez R, Doktycz MJ, Fleming JT, Beattie KL. Fingerprinting of prokaryotic 16S rRNA genes using oligodeoxyribonucleotide microarrays and virtual hybridization. Nucleic Acids Res 2003; 31:779-89. [PMID: 12527788 PMCID: PMC140498 DOI: 10.1093/nar/gkg132] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [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: 06/19/2002] [Revised: 11/01/2002] [Accepted: 11/01/2002] [Indexed: 11/14/2022] Open
Abstract
An oligonucleotide microarray hybridization system to differentiate microbial species was designed and tested. Seven microbial species were studied, including one Bacillus and six Pseudomonas strains. DNA sequences near the 5' end of 16S rRNA genes were aligned and two contiguous regions of high variability, flanked by highly conserved sequences, were found. The conserved sequences were used to design PCR primers which efficiently amplified these polymorphic regions from all seven species. The amplicon sequences were used to design 88 9mer hybridization probes which were arrayed onto glass slides. Single-stranded, fluorescence-tagged PCR products were hybridized to the microarrays at 15 degrees C. The experimental results were compared with the DeltaG(0) values for all matched and mismatched duplexes possible between the synthetic probes and the 16S target sequences of the seven test species, calculated using a 'virtual hybridization' software program. Although the observed hybridization patterns differed significantly from patterns predicted solely on the basis of perfect sequence matches, a unique hybridization fingerprint was obtained for each of the species, including closely related Pseudomonas species, and there was a reasonable correlation between the intensity of observed hybridization signals and the calculated DeltaG(0) values. The results suggest that both perfect and mismatched pairings can contribute to microbial identification by hybridization fingerprinting.
Collapse
Affiliation(s)
- Miguel Angel Reyes-López
- Life Sciences Division, Oak Ridge National Laboratory, Building 4500-S, MS 6123, Bethel Valley Road, PO Box 2008, Oak Ridge, TN 37831, USA
| | | | | | | | | | | |
Collapse
|
32
|
Maldonado-Rodríguez R, Espinosa-Lara M, Barrera-León O, Colin-Tovar C, González-Yebra B, Salcedo-Vargas M, Santiago-Hernández JC, Méndez-Tenorio A, Beattie KL. Detection of Mutations in RET Proto-Oncogene Codon 634 Through Double Tandem Hybridization. Mol Biotechnol 2003; 25:113-29. [PMID: 14526122 DOI: 10.1385/mb:25:2:113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We developed a procedure to detect the 7 point mutations at Cys634 of the proto-oncogene RET, which is responsible for medullary thyroid carcinoma (MTC). Genomic DNA was prepared from blood samples obtained from normal and MTC-affected individuals belonging to a family with a history of the disease. The RET genotype for each individual was first established by performing restriction and sequencing analyses. Single-stranded target DNA was prepared by asymmetric polymerase chain reaction (PCR) amplification of a 93-bp fragment containing Cys634. The target was annealed with pairs of prelabeled stacking oligonucleotides designed to create appropriate 7-nucleotide gaps, which served as the sites of subsequent hybridization with glass-immobilized 7-mer probes. The target-stacking oligonucleotide duplexes were hybridized with DNA chips containing a set of eight 7-mer probes designed to detect the wild-type sequence and the seven point mutations described. We tested two sets of immobilized probes containing internal or 5'-terminal codon-634 single-base variations. Both groups of probes were able to discriminatively identify the mutations. The hybridization patterns indicated that the disease in this family was due to the C634Y mutation, in accord with the original sequence analysis. The hybridization-based mutation assignment was additionally supported by determination of the control homozygous and heterozygous hybridization patterns produced with synthetic targets having the normal or codon 634 mutant sequences. The effects of mismatch type and nearest-neighbor sequences on the occurrence of false-positive (mismatched) hybridizations are discussed.
Collapse
|