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Agius DR, Kapazoglou A, Avramidou E, Baranek M, Carneros E, Caro E, Castiglione S, Cicatelli A, Radanovic A, Ebejer JP, Gackowski D, Guarino F, Gulyás A, Hidvégi N, Hoenicka H, Inácio V, Johannes F, Karalija E, Lieberman-Lazarovich M, Martinelli F, Maury S, Mladenov V, Morais-Cecílio L, Pecinka A, Tani E, Testillano PS, Todorov D, Valledor L, Vassileva V. Exploring the crop epigenome: a comparison of DNA methylation profiling techniques. Front Plant Sci 2023; 14:1181039. [PMID: 37389288 PMCID: PMC10306282 DOI: 10.3389/fpls.2023.1181039] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/27/2023] [Indexed: 07/01/2023]
Abstract
Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.
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Affiliation(s)
- Dolores Rita Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
- Biology Department, Ġ.F.Abela Junior College, Msida, Malta
| | - Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Evangelia Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Miroslav Baranek
- Mendeleum-Insitute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czechia
| | - Elena Carneros
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Stefano Castiglione
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Angela Cicatelli
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Aleksandra Radanovic
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
| | - Jean-Paul Ebejer
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Francesco Guarino
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Andrea Gulyás
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Norbert Hidvégi
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Hans Hoenicka
- Genomic Research Department, Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | - Vera Inácio
- BioISI – BioSystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Frank Johannes
- Plant Epigenomics, Technical University of Munich (TUM), Freising, Germany
| | - Erna Karalija
- Faculty of Science, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Michal Lieberman-Lazarovich
- Department of Vegetables and Field Crops, Agricultural Research Organization, Volcani Center, Institute of Plant Sciences, Rishon LeZion, Israel
| | | | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures EA1207 USC1328, INRAE, Université d’Orléans, Orléans, France
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Pilar S. Testillano
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Dimitar Todorov
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias, University of Oviedo, Oviedo, Spain
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
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González-García MP, Conesa CM, Lozano-Enguita A, Baca-González V, Simancas B, Navarro-Neila S, Sánchez-Bermúdez M, Salas-González I, Caro E, Castrillo G, Del Pozo JC. Temperature changes in the root ecosystem affect plant functionality. Plant Commun 2023; 4:100514. [PMID: 36585788 DOI: 10.1016/j.xplc.2022.100514] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 05/11/2023]
Abstract
Climate change is increasing the frequency of extreme heat events that aggravate its negative impact on plant development and agricultural yield. Most experiments designed to study plant adaption to heat stress apply homogeneous high temperatures to both shoot and root. However, this treatment does not mimic the conditions in natural fields, where roots grow in a dark environment with a descending temperature gradient. Excessively high temperatures severely decrease cell division in the root meristem, compromising root growth, while increasing the division of quiescent center cells, likely in an attempt to maintain the stem cell niche under such harsh conditions. Here, we engineered the TGRooZ, a device that generates a temperature gradient for in vitro or greenhouse growth assays. The root systems of plants exposed to high shoot temperatures but cultivated in the TGRooZ grow efficiently and maintain their functionality to sustain proper shoot growth and development. Furthermore, gene expression and rhizosphere or root microbiome composition are significantly less affected in TGRooZ-grown roots than in high-temperature-grown roots, correlating with higher root functionality. Our data indicate that use of the TGRooZ in heat-stress studies can improve our knowledge of plant response to high temperatures, demonstrating its applicability from laboratory studies to the field.
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Affiliation(s)
- Mary Paz González-García
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Carlos M Conesa
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Alberto Lozano-Enguita
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Victoria Baca-González
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Bárbara Simancas
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Sara Navarro-Neila
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - María Sánchez-Bermúdez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Isai Salas-González
- Undergraduate Program in Genomic Sciences, Center for Genomics Sciences, Universidad Nacional Autonóma de México, Av. Universidad s/n. Col. Chamilpa, Cuernavaca 62210, Morelos, México
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Gabriel Castrillo
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Juan C Del Pozo
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain.
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Garcia-Donas J, Martínez-Urbistondo D, Velázquez Kennedy K, Villares P, Barquin A, Dominguez A, Rodriguez-Moreno JF, Caro E, Suarez del Villar R, Nistal-Villan E, Yagüe M, Ortiz M, Barba M, Ruiz-Llorente S, Quiralte M, Zanin M, Rodríguez C, Navarro P, Berraondo P, Madurga R. Randomized phase II clinical trial of ruxolitinib plus simvastatin in COVID19 clinical outcome and cytokine evolution. Front Immunol 2023; 14:1156603. [PMID: 37143685 PMCID: PMC10151807 DOI: 10.3389/fimmu.2023.1156603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Background Managing the inflammatory response to SARS-Cov-2 could prevent respiratory insufficiency. Cytokine profiles could identify cases at risk of severe disease. Methods We designed a randomized phase II clinical trial to determine whether the combination of ruxolitinib (5 mg twice a day for 7 days followed by 10 mg BID for 7 days) plus simvastatin (40 mg once a day for 14 days), could reduce the incidence of respiratory insufficiency in COVID-19. 48 cytokines were correlated with clinical outcome. Participants Patients admitted due to COVID-19 infection with mild disease. Results Up to 92 were included. Mean age was 64 ± 17, and 28 (30%) were female. 11 (22%) patients in the control arm and 6 (12%) in the experimental arm reached an OSCI grade of 5 or higher (p = 0.29). Unsupervised analysis of cytokines detected two clusters (CL-1 and CL-2). CL-1 presented a higher risk of clinical deterioration vs CL-2 (13 [33%] vs 2 [6%] cases, p = 0.009) and death (5 [11%] vs 0 cases, p = 0.059). Supervised Machine Learning (ML) analysis led to a model that predicted patient deterioration 48h before occurrence with a 85% accuracy. Conclusions Ruxolitinib plus simvastatin did not impact the outcome of COVID-19. Cytokine profiling identified patients at risk of severe COVID-19 and predicted clinical deterioration. Trial registration https://clinicaltrials.gov/, identifier NCT04348695.
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Affiliation(s)
- Jesus Garcia-Donas
- Gynecological, Genitourinary and Skin Cancer Unit HM CIOCC MADRID (Centro Integral Oncológico Clara Campal), Department of Basic Medical Sciences, Hospital Universitario HM Sanchinarro, HM Hospitales, Institute of Applied Molecular Medicine (IMMA), Facultad de Medicina, Universidad San Pablo CEU, CEU Universities, Madrid, Spain
- *Correspondence: Jesus Garcia-Donas, ;
| | | | | | - Paula Villares
- Internal Medicine Service Hospital HM Sanchinarro, Madrid, Spain
| | - Arántzazu Barquin
- Gynecological, Genitourinary and Skin Cancer Unit HM CIOCC MADRID (Centro Integral Oncológico Clara Campal), Department of Basic Medical Sciences, Hospital Universitario HM Sanchinarro, HM Hospitales, Institute of Applied Molecular Medicine (IMMA), Facultad de Medicina, Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Andrea Dominguez
- Internal Medicine Service Hospital HM Sanchinarro, Madrid, Spain
| | - Juan Francisco Rodriguez-Moreno
- Gynecological, Genitourinary and Skin Cancer Unit HM CIOCC MADRID (Centro Integral Oncológico Clara Campal), Department of Basic Medical Sciences, Hospital Universitario HM Sanchinarro, HM Hospitales, Institute of Applied Molecular Medicine (IMMA), Facultad de Medicina, Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Elena Caro
- Internal Medicine Service Hospital HM Sanchinarro, Madrid, Spain
| | | | - Estanislao Nistal-Villan
- Microbiology Section, Dpto. CC, Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, Madrid, Spain
- Facultad de Medicina, Instituto de Medicina Molecular Aplicada (IMMA), Universidad San Pablo-CEU, Madrid, Spain
| | - Monica Yagüe
- Laboratory of Innovation in Oncology HM CIOCC MADRID (Centro Integral Oncológico Clara Campal), Department of Basic Medical Sciences, Facultad de Medicina, Hospital Universitario HM Sanchinarro, HM Hospitales, Institute of Applied Molecular Medicine (IMMA), Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Maria Ortiz
- Clinical Trials Pharmacy, Clara Campal Comprehensive Cancer Center, Hospital Universitario de Sanchinarro, Madrid, Spain
| | - Maria Barba
- Laboratory of Innovation in Oncology HM CIOCC MADRID (Centro Integral Oncológico Clara Campal), Department of Basic Medical Sciences, Facultad de Medicina, Hospital Universitario HM Sanchinarro, HM Hospitales, Institute of Applied Molecular Medicine (IMMA), Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Sergio Ruiz-Llorente
- Laboratory of Innovation in Oncology HM CIOCC MADRID (Centro Integral Oncológico Clara Campal), Department of Basic Medical Sciences, Facultad de Medicina, Hospital Universitario HM Sanchinarro, HM Hospitales, Institute of Applied Molecular Medicine (IMMA), Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Miguel Quiralte
- Laboratory of Innovation in Oncology HM CIOCC MADRID (Centro Integral Oncológico Clara Campal), Department of Basic Medical Sciences, Facultad de Medicina, Hospital Universitario HM Sanchinarro, HM Hospitales, Institute of Applied Molecular Medicine (IMMA), Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Massimiliano Zanin
- Instituto de Física Interdisciplinar y Sistemas Complejos IFISC (CSIC-UIB), Palma de Mallorca, Spain
| | - Cristina Rodríguez
- Grupo de Cáncer Endocirno, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
| | - Paloma Navarro
- Laboratory of Innovation in Oncology HM CIOCC MADRID (Centro Integral Oncológico Clara Campal), Department of Basic Medical Sciences, Facultad de Medicina, Hospital Universitario HM Sanchinarro, HM Hospitales, Institute of Applied Molecular Medicine (IMMA), Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Pedro Berraondo
- Program of Immunology and Immunotherapy, Cima Universidad de Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Rodrigo Madurga
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid, Spain
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Merino E, Gimeno A, Alcalde M, Coy J, Boix V, Molina-Pardines C, Ventero MP, Galiana A, Caro E, Rodríguez JC. Impact of Sepsis Flow Chip, a novelty fast microbiology method, in the treatment of bacteremia caused by Gram-negative bacilli. Rev Esp Quimioter 2021; 34:193-199. [PMID: 33764003 PMCID: PMC8179947 DOI: 10.37201/req/109.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Objective The aim of this study was to assess the impact of the information provided by the new Sepsis Chip Flow system (SFC) and other fast microbiological techniques on the selection of the appropriate antimicrobial treatment by the clinical researchers of an antimicrobial stewardship team. Methods Two experienced clinical researchers performed the theoretical exercise of independently selecting the treatment for patients diagnosed by bacteremia due to bacilli gram negative (BGN). At first, the clinicians had only available the clinical characteristics of 74 real patients. Sequentially, information regarding the Gram stain, MALDI-TOF, and SFC from Vitro were provided. Initially, the researchers prescribed an antimicrobial therapy based on the clinical data, later these data were complementing with information from microbiological techniques, and the clinicians made their decisions again. Results The data provided by the Gram stain reduced the number of patients prescribed with combined treatments (for clinician 1, from 23 to 7, and for clinician 2, from 28 to 12), but the use of carbapenems remained constant. In line with this, the data obtained by the MALDI-TOF also decreased the combined treatment, and the use of carbapenems remained unchanged. By contrast, the data on antimicrobial resistance provided by the SFC reduced the carbapenems treatment. Conclusions From the theoretical model the Gram stain and the MALDI-TOF results achieved a reduction in the combined treatment. However, the new system tested (SFC), due to the resistance mechanism data provided, not only reduced the combined treatment, it also decreased the prescription of the carbapenems.
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Affiliation(s)
| | | | | | | | | | - C Molina-Pardines
- Carmen Molina Pardines, Department of Microbiology, General University Hospital of Alicante-ISABIAL, Spain.
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Montes N, Cobos A, Gil-Valle M, Caro E, Pagán I. Arabidopsis thaliana Genes Associated with Cucumber mosaic virus Virulence and Their Link to Virus Seed Transmission. Microorganisms 2021; 9:692. [PMID: 33801693 PMCID: PMC8067046 DOI: 10.3390/microorganisms9040692] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/27/2022] Open
Abstract
Virulence, the effect of pathogen infection on progeny production, is a major determinant of host and pathogen fitness as it affects host fecundity and pathogen transmission. In plant-virus interactions, ample evidence indicates that virulence is genetically controlled by both partners. However, the host genetic determinants are poorly understood. Through a genome-wide association study (GWAS) of 154 Arabidopsis thaliana genotypes infected by Cucumber mosaic virus (CMV), we identified eight host genes associated with virulence, most of them involved in response to biotic stresses and in cell wall biogenesis in plant reproductive structures. Given that virulence is a main determinant of the efficiency of plant virus seed transmission, we explored the link between this trait and the genetic regulation of virulence. Our results suggest that the same functions that control virulence are also important for CMV transmission through seeds. In sum, this work provides evidence of a novel role for some previously known plant defense genes and for the cell wall metabolism in plant virus interactions.
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Affiliation(s)
- Nuria Montes
- Unidad de Fisiología Vegetal, Departamento Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU Universities, Boadilla del Monte, 28003 Madrid, Spain;
- Servicio de Reumatología, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria (IIS-IP), 28006 Madrid, Spain
| | - Alberto Cobos
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and Departamento de Biotecnología-Biología Vegetal, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28045 Madrid, Spain; (A.C.); (M.G.-V.); (E.C.)
| | - Miriam Gil-Valle
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and Departamento de Biotecnología-Biología Vegetal, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28045 Madrid, Spain; (A.C.); (M.G.-V.); (E.C.)
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and Departamento de Biotecnología-Biología Vegetal, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28045 Madrid, Spain; (A.C.); (M.G.-V.); (E.C.)
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and Departamento de Biotecnología-Biología Vegetal, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28045 Madrid, Spain; (A.C.); (M.G.-V.); (E.C.)
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Eseverri Á, Baysal C, Medina V, Capell T, Christou P, Rubio LM, Caro E. Transit Peptides From Photosynthesis-Related Proteins Mediate Import of a Marker Protein Into Different Plastid Types and Within Different Species. Front Plant Sci 2020; 11:560701. [PMID: 33101328 PMCID: PMC7545105 DOI: 10.3389/fpls.2020.560701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/07/2020] [Indexed: 06/01/2023]
Abstract
Nucleus-encoded plastid proteins are synthesized as precursors with N-terminal targeting signals called transit peptides (TPs), which mediate interactions with the translocon complexes at the outer (TOC) and inner (TIC) plastid membranes. These complexes exist in multiple isoforms in higher plants and show differential specificity and tissue abundance. While some show specificity for photosynthesis-related precursor proteins, others distinctly recognize nonphotosynthetic and housekeeping precursor proteins. Here we used TPs from four Arabidopsis thaliana proteins, three related to photosynthesis (chlorophyll a/b binding protein, Rubisco activase) and photo-protection (tocopherol cyclase) and one involved in the assimilation of ammonium into amino-acids, and whose expression is most abundant in the root (ferredoxin dependent glutamate synthase 2), to determine whether they were able to mediate import of a nuclear-encoded marker protein into plastids of different tissues of a dicot and a monocot species. In A. thaliana, import and processing efficiency was high in all cases, while TP from the rice Rubisco small chain 1, drove very low import in Arabidopsis tissues. Noteworthy, our results show that Arabidopsis photosynthesis TPs also mediate plastid import in rice callus, and in leaf and root tissues with almost a 100% efficiency, providing new biotechnological tools for crop improvement strategies based on recombinant protein accumulation in plastids by the expression of nuclear-encoded transgenes.
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Affiliation(s)
- Álvaro Eseverri
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Can Baysal
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Vicente Medina
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Teresa Capell
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain
| | - Luis M. Rubio
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Elena Caro
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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Eseverri Á, López‐Torrejón G, Jiang X, Burén S, Rubio LM, Caro E. Use of synthetic biology tools to optimize the production of active nitrogenase Fe protein in chloroplasts of tobacco leaf cells. Plant Biotechnol J 2020; 18:1882-1896. [PMID: 31985876 PMCID: PMC7415783 DOI: 10.1111/pbi.13347] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 05/07/2023]
Abstract
The generation of nitrogen fixing crops is considered a challenge that could lead to a new agricultural 'green' revolution. Here, we report the use of synthetic biology tools to achieve and optimize the production of active nitrogenase Fe protein (NifH) in the chloroplasts of tobacco plants. Azotobacter vinelandii nitrogen fixation genes, nifH, M, U and S, were re-designed for protein accumulation in tobacco cells. Targeting to the chloroplast was optimized by screening and identifying minimal length transit peptides performing properly for each specific Nif protein. Putative peptidyl-prolyl cis-trans isomerase NifM proved necessary for NifH solubility in the stroma. Purified NifU, a protein involved in the biogenesis of NifH [4Fe-4S] cluster, was found functional in NifH reconstitution assays. Importantly, NifH purified from tobacco chloroplasts was active in the reduction of acetylene to ethylene, with the requirement of nifU and nifS co-expression. These results support the suitability of chloroplasts to host functional nitrogenase proteins, paving the way for future studies in the engineering of nitrogen fixation in higher plant plastids and describing an optimization pipeline that could also be used in other organisms and in the engineering of new metabolic pathways in plastids.
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Affiliation(s)
- Álvaro Eseverri
- Centre for Plant Biotechnology and GenomicsInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Universidad Politécnica de Madrid (UPM)MadridSpain
| | - Gema López‐Torrejón
- Centre for Plant Biotechnology and GenomicsInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Universidad Politécnica de Madrid (UPM)MadridSpain
- Departamento de Biotecnología-Biología Ve ge talEscuela Técnica Superior de Ingeniería AgronómicaAlimentaría y de BiosistemasUniversidad Politécnica de MadridMadridSpain
| | - Xi Jiang
- Centre for Plant Biotechnology and GenomicsInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Universidad Politécnica de Madrid (UPM)MadridSpain
| | - Stefan Burén
- Centre for Plant Biotechnology and GenomicsInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Universidad Politécnica de Madrid (UPM)MadridSpain
| | - Luis M. Rubio
- Centre for Plant Biotechnology and GenomicsInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Universidad Politécnica de Madrid (UPM)MadridSpain
- Departamento de Biotecnología-Biología Ve ge talEscuela Técnica Superior de Ingeniería AgronómicaAlimentaría y de BiosistemasUniversidad Politécnica de MadridMadridSpain
| | - Elena Caro
- Centre for Plant Biotechnology and GenomicsInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Universidad Politécnica de Madrid (UPM)MadridSpain
- Departamento de Biotecnología-Biología Ve ge talEscuela Técnica Superior de Ingeniería AgronómicaAlimentaría y de BiosistemasUniversidad Politécnica de MadridMadridSpain
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Katsuya-Gaviria K, Caro E, Carrillo-Barral N, Iglesias-Fernández R. Reactive Oxygen Species (ROS) and Nucleic Acid Modifications During Seed Dormancy. Plants (Basel) 2020; 9:E679. [PMID: 32471221 PMCID: PMC7356579 DOI: 10.3390/plants9060679] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/24/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022]
Abstract
The seed is the propagule of higher plants and allows its dissemination and the survival of the species. Seed dormancy prevents premature germination under favourable conditions. Dormant seeds are only able to germinate in a narrow range of conditions. During after-ripening (AR), a mechanism of dormancy release, seeds gradually lose dormancy through a period of dry storage. This review is mainly focused on how chemical modifications of mRNA and genomic DNA, such as oxidation and methylation, affect gene expression during late stages of seed development, especially during dormancy. The oxidation of specific nucleotides produced by reactive oxygen species (ROS) alters the stability of the seed stored mRNAs, being finally degraded or translated into non-functional proteins. DNA methylation is a well-known epigenetic mechanism of controlling gene expression. In Arabidopsis thaliana, while there is a global increase in CHH-context methylation through embryogenesis, global DNA methylation levels remain stable during seed dormancy, decreasing when germination occurs. The biological significance of nucleic acid oxidation and methylation upon seed development is discussed.
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Affiliation(s)
- Kai Katsuya-Gaviria
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223-Pozuelo de Alarcón, Spain; (K.K.-G.); (E.C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040-Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223-Pozuelo de Alarcón, Spain; (K.K.-G.); (E.C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040-Madrid, Spain
| | - Néstor Carrillo-Barral
- Departamento de Fisiología Vegetal, Facultad de Ciencias, Universidad da Coruña (UdC), 15008-A Coruña, Spain;
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223-Pozuelo de Alarcón, Spain; (K.K.-G.); (E.C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040-Madrid, Spain
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Baysal C, Pérez-González A, Eseverri Á, Jiang X, Medina V, Caro E, Rubio L, Christou P, Zhu C. Recognition motifs rather than phylogenetic origin influence the ability of targeting peptides to import nuclear-encoded recombinant proteins into rice mitochondria. Transgenic Res 2020; 29:37-52. [PMID: 31598902 PMCID: PMC7000509 DOI: 10.1007/s11248-019-00176-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/01/2019] [Indexed: 10/30/2022]
Abstract
Mitochondria fulfil essential functions in respiration and metabolism as well as regulating stress responses and apoptosis. Most native mitochondrial proteins are encoded by nuclear genes and are imported into mitochondria via one of several receptors that recognize N-terminal signal peptides. The targeting of recombinant proteins to mitochondria therefore requires the presence of an appropriate N-terminal peptide, but little is known about mitochondrial import in monocotyledonous plants such as rice (Oryza sativa). To gain insight into this phenomenon, we targeted nuclear-encoded enhanced green fluorescent protein (eGFP) to rice mitochondria using six mitochondrial pre-sequences with diverse phylogenetic origins, and investigated their effectiveness by immunoblot analysis as well as confocal and electron microscopy. We found that the ATPA and COX4 (Saccharomyces cerevisiae), SU9 (Neurospora crassa), pFA (Arabidopsis thaliana) and OsSCSb (Oryza sativa) peptides successfully directed most of the eGFP to the mitochondria, whereas the MTS2 peptide (Nicotiana plumbaginifolia) showed little or no evidence of targeting ability even though it is a native plant sequence. Our data therefore indicate that the presence of particular recognition motifs may be required for mitochondrial targeting, whereas the phylogenetic origin of the pre-sequences probably does not play a key role in the success of mitochondrial targeting in dedifferentiated rice callus and plants.
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Affiliation(s)
- Can Baysal
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
| | - Ana Pérez-González
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Álvaro Eseverri
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Xi Jiang
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Vicente Medina
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
| | - Elena Caro
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Luis Rubio
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain.
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Diezma‐Navas L, Pérez‐González A, Artaza H, Alonso L, Caro E, Llave C, Ruiz‐Ferrer V. Crosstalk between epigenetic silencing and infection by tobacco rattle virus in Arabidopsis. Mol Plant Pathol 2019; 20:1439-1452. [PMID: 31274236 PMCID: PMC6792132 DOI: 10.1111/mpp.12850] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
DNA methylation is an important epigenetic mechanism for controlling innate immunity against microbial pathogens in plants. Little is known, however, about the manner in which viral infections interact with DNA methylation pathways. Here we investigate the crosstalk between epigenetic silencing and viral infections in Arabidopsis inflorescences. We found that tobacco rattle virus (TRV) causes changes in the expression of key transcriptional gene silencing factors with RNA-directed DNA methylation activities that coincide with changes in methylation at the whole genome level. Viral susceptibility/resistance was altered in DNA (de)methylation-deficient mutants, suggesting that DNA methylation is an important regulatory system controlling TRV proliferation. We further show that several transposable elements (TEs) underwent transcriptional activation during TRV infection, and that TE regulation likely involved both DNA methylation-dependent and -independent mechanisms. We identified a cluster of disease resistance genes regulated by DNA methylation in infected plants that were enriched for TEs in their promoters. Interestingly, TEs and nearby resistance genes were co-regulated in TRV-infected DNA (de)methylation mutants. Our study shows that DNA methylation contributes to modulate the outcome of viral infections in Arabidopsis, and opens up new possibilities for exploring the role of TE regulation in antiviral defence.
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Affiliation(s)
- Laura Diezma‐Navas
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones BiológicasCSICRamiro de Maeztu 9MadridSpain
- Doctorado en Biotecnología y Recursos Genéticos de Plantas y Microorganismos AsociadosETSI Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid28040MadridSpain
| | - Ana Pérez‐González
- Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Campus de Montegancedo UPM28223Pozuelo de Alarcón, MadridSpain
| | - Haydeé Artaza
- Bionformatic and Statistic Service, Centro de Investigaciones BiológicasCSICRamiro de Maeztu 928040MadridSpain
- Present address:
Department of Clinical ScienceUniversity of Bergen5020BergenNorway
| | - Lola Alonso
- Bionformatic and Statistic Service, Centro de Investigaciones BiológicasCSICRamiro de Maeztu 928040MadridSpain
- Present address:
Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center (CNIO)MadridSpain
| | - Elena Caro
- Centro de Biotecnología y Genómica de PlantasUniversidad Politécnica de Madrid (UPM)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Campus de Montegancedo UPM28223Pozuelo de Alarcón, MadridSpain
| | - César Llave
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones BiológicasCSICRamiro de Maeztu 9MadridSpain
| | - Virginia Ruiz‐Ferrer
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones BiológicasCSICRamiro de Maeztu 9MadridSpain
- Present address:
Department of Plant Physiology, Plant Biotechnology and Molecular Biology Group. Environmental Sciences and Biochemistry SchoolCastilla‐La Mancha UniversityToledoSpain
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Pérez-González A, Caro E. Benefits of using genomic insulators flanking transgenes to increase expression and avoid positional effects. Sci Rep 2019; 9:8474. [PMID: 31186481 PMCID: PMC6560062 DOI: 10.1038/s41598-019-44836-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 11/14/2018] [Accepted: 05/23/2019] [Indexed: 01/03/2023] Open
Abstract
For more than 20 years, plant biologists have tried to achieve complete control of transgene expression. Until the techniques to target transgenes to safe harbor sites in the genome become routine, flanking transgenes with genetic insulators, DNA sequences that create independent domains of gene expression, can help avoid positional effects and stabilize their expression. We have, for the first time, compared the effect of three insulator sequences previously described in the literature and one never tested before. Our results indicate that their use increases transgene expression, but only the last one reduces variability between lines and between individuals. We have analyzed the integration of insulator-flanked T-DNAs using whole genome re-sequencing (to our knowledge, also for the first time) and found data suggesting that chiMARs can shelter transgene insertions from neighboring repressive epigenetic states. Finally, we could also observe a loss of accuracy of the RB insertion in the lines harboring insulators, evidenced by a high frequency of truncation of T-DNAs and of insertion of vector backbone that, however, did not affect transgene expression. Our data supports that the effect of each genetic insulator is different and their use in transgenic constructs should depend on the needs of each specific experiment.
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Affiliation(s)
- Ana Pérez-González
- Centre for Plant Biotechnology and Genomics Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Campus Montegancedo UPM Pozuelo de Alarcón (Madrid), Madrid, Spain
| | - Elena Caro
- Centre for Plant Biotechnology and Genomics Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Campus Montegancedo UPM Pozuelo de Alarcón (Madrid), Madrid, Spain.
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Pérez-González A, Caro E. Effect of transcription terminator usage on the establishment of transgene transcriptional gene silencing. BMC Res Notes 2018; 11:511. [PMID: 30055650 PMCID: PMC6064074 DOI: 10.1186/s13104-018-3649-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/24/2018] [Indexed: 11/10/2022] Open
Abstract
Objective Obtaining high and stable transgene expression is of vital importance for plant genetic engineering. A lot is known about the relationship between terminator efficiency and gene expression, but no studies have addressed the relationship between terminator usage and transgene expression stability or heritable gene silencing. In this paper, we aim to analyze if terminators are a determining factor in the establishment of promoter DNA methylation of plant transgenes. Results Our experiments comparing plants with a LUC reporter under the 35S CaMV promoter and good efficiency terminators (Thsp, T35S) show that the use of efficient terminator sequences does not avoid the accumulation of promoter DNA methylation and transgene silencing. However, Thsp lead to a higher reporter gene expression and lower promoter DNA methylation levels than T35S, supporting that terminator usage is indeed involved in the establishment of TGS by methylation of transgenes’ promoters. In the case of a terminatorless construct, the PTGS initiated by the improperly terminated mRNAs is not followed by the establishment of heritable silencing in the form of strong promoter DNA methylation, like in the case of TAS genes and reactivated TEs (for the transgene DNA methylation levels remained below the 20%). Electronic supplementary material The online version of this article (10.1186/s13104-018-3649-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana Pérez-González
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Elena Caro
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain.
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13
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Pérez-González A, Kniewel R, Veldhuizen M, Verma HK, Navarro-Rodríguez M, Rubio LM, Caro E. Adaptation of the GoldenBraid modular cloning system and creation of a toolkit for the expression of heterologous proteins in yeast mitochondria. BMC Biotechnol 2017; 17:80. [PMID: 29132331 PMCID: PMC5683533 DOI: 10.1186/s12896-017-0393-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [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: 05/12/2017] [Accepted: 10/30/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is a need for the development of synthetic biology methods and tools to facilitate rapid and efficient engineering of yeast that accommodates the needs of specific biotechnology projects. In particular, the manipulation of the mitochondrial proteome has interesting potential applications due to its compartmentalized nature. One of these advantages resides in the fact that metalation occurs after protein import into mitochondria, which contains pools of iron, zinc, copper and manganese ions that can be utilized in recombinant metalloprotein metalation reactions. Another advantage is that mitochondria are suitable organelles to host oxygen sensitive proteins as a low oxygen environment is created within the matrix during cellular respiration. RESULTS Here we describe the adaptation of a modular cloning system, GoldenBraid2.0, for the integration of assembled transcriptional units into two different sites of the yeast genome, yielding a high expression level. We have also generated a toolkit comprising various promoters, terminators and selection markers that facilitate the generation of multigenic constructs and allow the reconstruction of biosynthetic pathways within Saccharomyces cerevisiae. To facilitate the specific expression of recombinant proteins within the mitochondrial matrix, we have also included in the toolkit an array of mitochondrial targeting signals and tested their efficiency at different growth conditions. As a proof of concept, we show here the integration and expression of 14 bacterial nitrogen fixation (nif) genes, some of which are known to require specific metallocluster cofactors that contribute to their stability yet make these proteins highly sensitive to oxygen. For one of these genes, nifU, we show that optimal production of this protein is achieved through the use of the Su9 mitochondrial targeting pre-sequence and glycerol as a carbon source to sustain aerobic respiration. CONCLUSIONS We present here an adapted GoldenBraid2.0 system for modular cloning, genome integration and expression of recombinant proteins in yeast. We have produced a toolkit that includes inducible and constitutive promoters, mitochondrial targeting signals, terminators and selection markers to guarantee versatility in the design of recombinant transcriptional units. By testing the efficiency of the system with nitrogenase Nif proteins and different mitochondrial targeting pre-sequences and growth conditions, we have paved the way for future studies addressing the expression of heterologous proteins in yeast mitochondria.
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Affiliation(s)
- Ana Pérez-González
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Ryan Kniewel
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain.,Present Address: Department of Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CIB-CSIC), 28040, Madrid, Spain
| | - Marcel Veldhuizen
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Hemant K Verma
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain.,Present Address: Mankind Research Centre, IMT Manesar, Gurgaon, Haryana, 122050, India
| | - Mónica Navarro-Rodríguez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain.
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Merino E, Caro E, Ramos JR, Boix V, Gimeno A, Rodríguez JC, Riera G, Más P, Sanchéz-Paya J, Reus S, Torrús D, Portilla J. Impact of a stewardship program on bacteraemia in adult inpatients. Rev Esp Quimioter 2017; 30:257-263. [PMID: 28597623] [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: 06/07/2023]
Abstract
OBJECTIVE Bloodstream infections (BSIs) are associated with considerable morbidity and mortality among inpatients. The aim of this study was to evaluate the impact of a stewardship program on clinical and antimicrobial therapy-related outcomes in patients with bacteraemia. METHODS Single-centre, before-and-after quasi-experimental study in adult inpatients. Over 1 January 2013 to 31 June 2013 all patients aged 18 years or older with a bacteraemia (interven-tion group, N=200) were compared to a historical cohort (1 Janu-ary 2012 to 31 December 2012) (control group, N=200). RESULTS Following blood culture results and adjusting for potential confounders, the stewardship program was associated with more changes to antibiotic regimens (adjusted odds ratio [ORa]: 4.6, 95% CI 2.9, 7.4), more adjustments to antimicrobial therapy (ORa: 2.4, 95% CI 1.5, 3.8), and better source control in the first five days (ORa 1.6, 95% CI: 1.0, 2.7). In the subgroup that initially received inappropriate empiric treatment (n=138), the intervention was associated with more antibiotic changes (OR: 3.9, 95% CI: 1.8, 8.5) and a better choice of definitive antimicrobial therapy (OR 2.3 95% CI: 1.2, 4.6). There were also more antibiotic changes in the subgroups with both Gram-negative (OR: 2.8, 95% CI: 1.6, 4.9; n=217) and Gram-positive (OR: 4.6, 95% CI: 1.8, 9.9; n=135) bacteraemia among those receiving the intervention, while the Gram-positive subgroup also received more appropriate definitive antimicrobial therapy (OR: 3.9, 95% CI: 1.8, 8.8). CONCLUSIONS The stewardship program improved treatment of patients with bacteraemia and appropriateness of therapy.
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Affiliation(s)
| | | | - J R Ramos
- José Manuel Ramos, Department of Internal Medicine, Hospital General Universitario de Alicante e Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL-Fundación FISABIO), Calle Pintor Baeza, 12; 03010 Alicante. Spain.
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Caro E, Francés R, Zapater P, Pascual S, Bellot P, Such J. Grade of soluble inflammatory response is mainly affected by circulating bacterial DNA concentrations in cirrhosis. Liver Int 2016; 36:1473-80. [PMID: 26991936 DOI: 10.1111/liv.13118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/08/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Patients with decompensated cirrhosis show a marked innate immune response that shows a wide variability. The reasons for this fact have not been previously evaluated. This investigation was undertaken to study factors influencing the immune response intensity in both serum and ascitic fluid in patients with cirrhosis and ascites with presence of bactDNA. METHODS 77 patients with cirrhosis and presence of bactDNA fragments in blood and ascitic fluid were included. Identification of bactDNA was evaluated by 16SrRNA gene PCR followed by nucleotide sequencing and by species-specific PCR. Concentration of amplified bacterial-DNA, bacteria identification, LPS, TNF-alpha, IFN-gamma, Interleukin 12 and nitric oxide in serum and ascitic fluid were evaluated as factors related to intensity of the immune response. RESULTS Serum and AF levels of bactDNA, TNF-α, IFN-γ and nitric oxide concentration were higher in patients with presence of bactDNA from gram negative bacteria. Serum TNF-α levels showed a significant correlation with concentrations of bactDNA (r = 0.88; P = 0.001) and LPS (r = 0.28; P = 0.016). Serum nitric oxide levels were also significantly correlated with concentrations of bactDNA (r = 0.761; P = 0.001) but not with LPS levels. Levels of INF-γ and IL-12 were not significantly correlated with either bactDNA nor LPS levels. Plasmatic concentration of bactDNA was the most accurately correlated factor with the inflammatory response (ancova model included only levels of bactDNA (r(2) = 0.87, P = 0.047 for TNF-α; r(2) = 0.45, P = 0.03 for NOx). CONCLUSIONS Bacterial-DNA concentration is the most influencing variable associated with serum TNF-α and nitric oxide response.
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Affiliation(s)
- Elena Caro
- Unidad Hepática, Hospital General Universitario de Alicante, Alicante, Spain
| | - Rubén Francés
- Departamento de Medicina Clínica, Universidad Miguel Hernández, Alicante, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro Zapater
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.,Unidad de Farmacología Clínica, Hospital General Universitario de Alicante y Universidad Miguel Hernández, Alicante, Spain
| | - Sonia Pascual
- Unidad Hepática, Hospital General Universitario de Alicante, Alicante, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Pablo Bellot
- Unidad Hepática, Hospital General Universitario de Alicante, Alicante, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - José Such
- Digestive Disease Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, UAE, Lerner School of medicine, Case Western Reserve University, Cleveland, OH, US.
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Griesheimer D, Gill D, Nease B, Sutton T, Stedry M, Dobreff P, Carpenter D, Trumbull T, Caro E, Joo H, Millman D. MC21 v.6.0 – A continuous-energy Monte Carlo particle transport code with integrated reactor feedback capabilities. ANN NUCL ENERGY 2015. [DOI: 10.1016/j.anucene.2014.08.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Jolliffe R, Seers H, Jackson S, Caro E, Weeks L, Polley MJ. The Responsiveness, Content Validity, and Convergent Validity of the Measure Yourself Concerns and Wellbeing (MYCaW) Patient-Reported Outcome Measure. Integr Cancer Ther 2014; 14:26-34. [DOI: 10.1177/1534735414555809] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Objective. Measure Yourself Concerns and Wellbeing (MYCaW) is a patient-centered questionnaire that allows cancer patients to identify and quantify the severity of their “concerns” and “wellbeing,” as opposed to using a predetermined list. MYCaW administration is brief and aids in prioritizing treatment approaches. Our goal was to assess the convergent validity and responsiveness of MYCaW scores over time, the generalizability of the existing qualitative coding framework in different complementary and integrative oncology settings and content validity. Methods. Baseline and 6-week follow-up data (n = 82) from MYCaW and FACIT-SpEx questionnaires were collected for a service evaluation of the Living Well with the Impact of Cancer course at Penny Brohn Cance Care. MYCaW convergent validity was determined using Spearman’s rank correlation test, and responsiveness indices assessed score changes over time. The existing qualitative coding framework was reviewed using a new data set (n = 158) and coverage of concern categories compared with items of existing outcome measures. Results. Good correlation between MYCaW and FACIT-SpEx score changes were achieved ( r = −0.57, P ≥ .01). MYCaW Profile and Concern scores were highly responsive to change: standardized response mean = 1.02 and 1.08; effect size = 1.26 and 1.22. MYCaW change scores showed the anticipated gradient of change according to clinically relevant degrees of change. Categories, including “spirituality,” “weight change,” and “practical concerns” were added to the coding framework to improve generalizability. Conclusions. MYCaW scores were highly responsive to change, allowing personalized patient outcomes to be quantified; the qualitative coding framework appears generalizable across different integrative oncology settings and has broader coverage of patient-identified concerns compared with existing cancer-related patient-reported outcome measures.
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Affiliation(s)
| | | | | | | | - Laura Weeks
- Ottawa Integrative Cancer Centre, Ottawa, Ontario, Canada
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Ramos JM, Torrús D, Amador C, Jover F, Pérez-Chacón F, Ponce Y, Arjona FJ, Caro E, Martínez-Peinado C, Gallegos I, Cuadrado JM, Tello A, Gutiérrez F. Multicenter epidemiological and clinical study on imported Chagas diseases in Alicante, Spain. Pathog Glob Health 2013. [PMID: 23182138 DOI: 10.1179/2047773212y.0000000039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Recently, there has been an increase in the number of patients with Chagas disease outside of areas that are generally considered endemic. The aim of this investigation is to describe the clinical profile of a series of patients with Chagas disease in Alicante, Spain, which is a province located on the coast of the Mediterranean Sea. This study was performed at four general hospitals in Alicante between January 2002 and May 2011. A total of 128 patients from seven countries were diagnosed with Trypanosoma cruzi. The main country of origin of these patients was Bolivia (n5101; 78.9%), and the median of age of these patients was 35 years (range: 0–72 years). Four (3.3%) patients were children under 14 years of age, and 81 (63.3%) were female. Polymerase chain reaction (PCR) was used to analyze 106 patients, 66.0% of whom demonstrated positive PCR results. Visceral involvement was diagnosed in 26.8%: 24.1% demonstrated cardiac involvement, 0.9% demonstrated gastrointestinal involvement, 0.9% demonstrated cardiac and gastrointestinal involvement, and 0.9% demonstrated involvement of the central nervous system. Syncope was found to be associated with cardiomyopathy (28.0% versus 5.2%) (odds ratio: 6.5; 95% confidence interval: 1.5–27.1). Seventy-six patients received treatment with benznidazole, of whom 57 (75.0%) completed the treatment course without significant adverse events and 17.1% discontinued benznidazole due to adverse events. In total, 50% of patients experienced documented adverse reactions. Among patients with positive PCR results before treatment, all demonstrated negative PCR results following treatment. In conclusion, majority of our patients were female Bolivians immigrants, one of four of our patients demonstrated cardiac involvement, and treatment tolerance was poor. It is important to improve the clinical and epidemiological knowledge of Chagas disease in nonendemic with additional multicenter studies in order to determine the magnitude of this problem and provide improved public health and health resource planning.
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Affiliation(s)
- José M Ramos
- Department of Internal Medicine, Hospital General Universitario de Alicante, C/Pintor Baeza 10, Alicante, Spain.
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Affiliation(s)
- Elena Caro
- Centro de Biologia Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera 1, Cantoblanco, Madrid, Spain
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Caro E, Stroud H, Greenberg MVC, Bernatavichute YV, Feng S, Groth M, Vashisht AA, Wohlschlegel J, Jacobsen SE. The SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation-independent manner. PLoS Genet 2012; 8:e1002995. [PMID: 23071452 PMCID: PMC3469426 DOI: 10.1371/journal.pgen.1002995] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [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: 05/01/2012] [Accepted: 08/14/2012] [Indexed: 12/28/2022] Open
Abstract
In eukaryotic cells, environmental and developmental signals alter chromatin structure and modulate gene expression. Heterochromatin constitutes the transcriptionally inactive state of the genome and in plants and mammals is generally characterized by DNA methylation and histone modifications such as histone H3 lysine 9 (H3K9) methylation. In Arabidopsis thaliana, DNA methylation and H3K9 methylation are usually colocated and set up a mutually self-reinforcing and stable state. Here, in contrast, we found that SUVR5, a plant Su(var)3-9 homolog with a SET histone methyltransferase domain, mediates H3K9me2 deposition and regulates gene expression in a DNA methylation-independent manner. SUVR5 binds DNA through its zinc fingers and represses the expression of a subset of stimulus response genes. This represents a novel mechanism for plants to regulate their chromatin and transcriptional state, which may allow for the adaptability and modulation necessary to rapidly respond to extracellular cues.
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Affiliation(s)
- Elena Caro
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Hume Stroud
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Maxim V. C. Greenberg
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Yana V. Bernatavichute
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Suhua Feng
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Martin Groth
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Ajay A. Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Steve E. Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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Du J, Zhong X, Bernatavichute YV, Stroud H, Feng S, Caro E, Vashisht AA, Terragni J, Chin HG, Tu A, Hetzel J, Wohlschlegel JA, Pradhan S, Patel DJ, Jacobsen SE. Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell 2012. [PMID: 23021223 DOI: 10.1016/j.cell.2012.07.034.dual] [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] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT3 interacts with H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated with H3K9me2, and CMT3 stably associated with H3K9me2-containing nucleosomes. Crystal structures of maize CMT3 homolog ZMET2, in complex with H3K9me2 peptides, showed that ZMET2 binds H3K9me2 via both bromo adjacent homology (BAH) and chromo domains. The structures reveal an aromatic cage within both BAH and chromo domains as interaction interfaces that capture H3K9me2. Mutations that abolish either interaction disrupt CMT3 binding to nucleosomes and show a complete loss of CMT3 activity in vivo. Our study establishes dual recognition of H3K9me2 marks by BAH and chromo domains and reveals a distinct mechanism of interplay between DNA methylation and histone modification.
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Affiliation(s)
- Jiamu Du
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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Stroud H, Hale CJ, Feng S, Caro E, Jacob Y, Michaels SD, Jacobsen SE. DNA methyltransferases are required to induce heterochromatic re-replication in Arabidopsis. PLoS Genet 2012; 8:e1002808. [PMID: 22792077 PMCID: PMC3390372 DOI: 10.1371/journal.pgen.1002808] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [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: 03/26/2012] [Accepted: 05/18/2012] [Indexed: 12/17/2022] Open
Abstract
The relationship between epigenetic marks on chromatin and the regulation of DNA replication is poorly understood. Mutations of the H3K27 methyltransferase genes, ARABIDOPSIS TRITHORAX-RELATED PROTEIN5 (ATXR5) and ATXR6, result in re-replication (repeated origin firing within the same cell cycle). Here we show that mutations that reduce DNA methylation act to suppress the re-replication phenotype of atxr5 atxr6 mutants. This suggests that DNA methylation, a mark enriched at the same heterochromatic regions that re-replicate in atxr5/6 mutants, is required for aberrant re-replication. In contrast, RNA sequencing analyses suggest that ATXR5/6 and DNA methylation cooperatively transcriptionally silence transposable elements (TEs). Hence our results suggest a complex relationship between ATXR5/6 and DNA methylation in the regulation of DNA replication and transcription of TEs. Before cell division the genome is required to replicate once to ensure that each daughter cell inherits a full copy of genomic DNA. Eukaryotic DNA is wrapped around histones to form nucleosomes. Chemical modifications of DNA and histones are known to regulate gene expression. There is growing evidence that these modifications also regulate DNA replication, however very little is understood. Two histone methyltransferases, ARABIDOPSIS TRITHORAX-RELATED PROTEIN5 (ATXR5) and ATXR6, are required to prevent over-replication of normally silent regions of the genome called heterochromatin. Heterochromatin is enriched with transposable elements (TEs) that are silenced by modifications such as DNA methylation. We find that losses of DNA methylation suppress the over-replication defect in an atxr5 atxr6 mutant background. This suggests that DNA methylation positively regulates DNA replication in the absence of ATXR5/6. We further study the relationship between ATXR5/6 and DNA methylation in regulating the expression of TEs and find that they cooperatively silence TEs. Together these findings reveal relationships between DNA and histone modifications in regulating basic biological processes such as DNA replication and gene expression.
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Affiliation(s)
- Hume Stroud
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Christopher J. Hale
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Suhua Feng
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Elena Caro
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Yannick Jacob
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Scott D. Michaels
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Steven E. Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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López-Siguero JP, López-Canti LF, Espino R, Caro E, Fernández-García JM, Gutiérrez-Macías A, Rial JM, Lechuga JL, Macías F, Martínez-Aedo MJ, Rico S, Rodríguez I, Guillén J, Arroyo FJ, Bernal S, Espigares R, Núñez M, Escribano A, Barrionuevo JL, Gentil J, Barrios V, Fernández-Nistal A, Martos-Moreno GA, Martínez V, Argente J. Effect of recombinant growth hormone on leptin, adiponectin, resistin, interleukin-6, tumor necrosis factor-α and ghrelin levels in growth hormone-deficient children. J Endocrinol Invest 2011; 34:300-6. [PMID: 20634639 DOI: 10.1007/bf03347090] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Treatment with GH promotes linear growth and decreases body fat in patients with isolated GH deficiency (GHD). However, few studies have analyzed how GH replacement modifies ghrelin levels and the adipokine profile and the relationship of these modifications with the metabolic changes. AIMS To analyze the eventual differences between serum levels of leptin, leptin soluble receptor (sOBR), resistin, adiponectin, interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), total (TG) and acylated ghrelin (AG) and lipid and glycemic profiles in children with GHD, as well as to determine the effect of GH replacement on these parameters during the first year of therapy. SUBJECTS AND METHODS Thirty pre-pubertal (Tanner stage I) GHD children and 30 matched controls were enrolled. Children with GHD were studied before and after 6 and 12 months of GH treatment. Weight, height, BMI, fasting glucose, insulin, lipid profile and serum levels of adipokines and ghrelin were studied at every visit. Adi - pokines, insulin and ghrelin levels were determined by using commercial radio- and enzymoimmunoassays. RESULTS At baseline children with GHD had significantly higher sOBR (p<0.01) and adiponectin (p<0.01) levels than controls. Treatment with GH resulted in a decline in leptin (p<0.05) and TG (p<0.001) levels, an increase of homeostasis model assessment index and restored IGF-I levels (p<0.001). CONCLUSIONS These data indicate that GH replacement has a negative effect on leptin levels and may also produce a slight unfavorable effect on carbohydrate metabolism. In addition, the changes observed in the adipokine profile appear to be independent of body mass index.
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Caro E, Reus SJ, García A, Piñar D. [Curing a case of a pacemaker infection without removing it completely]. Enferm Infecc Microbiol Clin 2011; 29:157-8. [PMID: 21334113 DOI: 10.1016/j.eimc.2010.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 08/18/2010] [Accepted: 08/31/2010] [Indexed: 11/17/2022]
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Jacob Y, Stroud H, Leblanc C, Feng S, Zhuo L, Caro E, Hassel C, Gutierrez C, Michaels SD, Jacobsen SE. Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases. Nature 2010; 466:987-91. [PMID: 20631708 PMCID: PMC2964344 DOI: 10.1038/nature09290] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 06/24/2010] [Indexed: 12/15/2022]
Abstract
Multiple pathways prevent DNA replication from occurring more than once per cell cycle. These pathways block re-replication by strictly controlling the activity of pre-replication complexes, which assemble at specific sites in the genome called origins. Here we show that mutations in the homologous histone 3 lysine 27 (H3K27) monomethyltransferases, ARABIDOPSIS TRITHORAX-RELATED PROTEIN5 (ATXR5) and ATXR6, lead to re-replication of specific genomic locations. Most of these locations correspond to transposons and other repetitive and silent elements of the Arabidopsis genome. These sites also correspond to high levels of H3K27 monomethylation, and mutation of the catalytic SET domain is sufficient to cause the re-replication defect. Mutation of ATXR5 and ATXR6 also causes upregulation of transposon expression and has pleiotropic effects on plant development. These results uncover a novel pathway that prevents over-replication of heterochromatin in Arabidopsis.
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Affiliation(s)
- Yannick Jacob
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, Indiana 47405, USA
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Caro E, Montilla S, Castañeda C, León J, Quintana P, Saez L. 24. Neurophysiological changes in coeliac disease: A case study. Clin Neurophysiol 2009. [DOI: 10.1016/j.clinph.2008.09.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Castañeda C, Botella L, Caro E, León J, Montilla S, Paradinas F, Escobar-Morreale H, Galan J. 16. Evoked potentials in patients with differentiated thyroid carcinoma before and during levothyroxine withdrawal. Clin Neurophysiol 2009. [DOI: 10.1016/j.clinph.2008.09.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Sanchez MDLP, Caro E, Desvoyes B, Ramirez-Parra E, Gutierrez C. Chromatin dynamics during the plant cell cycle. Semin Cell Dev Biol 2008; 19:537-46. [PMID: 18707013 DOI: 10.1016/j.semcdb.2008.07.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Revised: 07/23/2008] [Accepted: 07/24/2008] [Indexed: 11/30/2022]
Abstract
Cell cycle progression depends on a highly regulated series of events of which transcriptional control plays a major role. In addition, during the S-phase not only DNA but chromatin as a whole needs to be faithfully duplicated. Therefore, both nucleosome dynamics as well as local changes in chromatin organization, including introduction and/or removal of covalent DNA and histone modifications, at genes with a key role in cell proliferation, are of primary relevance. Chromatin duplication during the S-phase and the chromosome segregation during mitosis are cell cycle stages critical for maintenance of epigenetic marks or for allowing the daughter products to acquire a distinct epigenetic landscape and, consequently, a unique cell fate decision. These aspects of chromatin dynamics together with the strict coupling of cell proliferation, cell differentiation and post-embryonic organogenesis have a profound impact on plant growth, development and response to external signals.
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Affiliation(s)
- María de la Paz Sanchez
- Centro de Biologia Molecular "Severo Ochoa", Consejo Superior de Investigaciones Cientificas, Universidad Autonoma de Madrid, Nicolas Cabrera 1, Cantoblanco, Madrid, Spain
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Caro E, Desvoyes B, Ramirez-Parra E, Sanchez MDLP, Gutierrez C. Endoreduplication control during plant development. SEB Exp Biol Ser 2008; 59:167-187. [PMID: 18368923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Elena Caro
- CMBSO, Universidad Autonoma de Madrid, Cantoblanco, Spain
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Caro E, Gutierrez C. A green GEM: intriguing analogies with animal geminin. Trends Cell Biol 2007; 17:580-5. [PMID: 17997094 DOI: 10.1016/j.tcb.2007.09.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Revised: 09/21/2007] [Accepted: 09/24/2007] [Indexed: 01/16/2023]
Abstract
The transition of precursor cells from an undifferentiated proliferative state to differentiated cells with specific fates is of primary importance for multicellular organisms. Animals and plants have evolved two unrelated proteins, geminin and GEM, respectively, that play analogous roles in regulating this transition. These proteins are involved, probably in early G1 phase of the cell cycle, in regulating the expression of genes involved in cell fate and initiation of differentiation. They also interact with Cdt1, a component of the pre-replication complexes involved in DNA replication licensing in early G1 phase. The interaction of geminin and GEM with Cdt1 and transcriptional regulators is competitive, suggesting that these interactions can play a pivotal role in coordinating DNA replication, cell division and cell fate decisions.
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Affiliation(s)
- Elena Caro
- Centro de Biologia Molecular "Severo Ochoa", Consejo Superior de Investigaciones Cientificas, Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Caro E, Castellano MM, Gutierrez C. GEM, a Novel Factor in the Coordination of Cell Division to Cell Fate Decisions in the Arabidopsis Epidermis. Plant Signal Behav 2007; 2:494-495. [PMID: 19704596 PMCID: PMC2634346 DOI: 10.4161/psb.2.6.4579] [Citation(s) in RCA: 8] [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] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Accepted: 06/12/2007] [Indexed: 05/28/2023]
Abstract
Cell division and cell fate decisions are highly regulated processes that need to be coordinated both spatially and temporally for correct plant growth and development. Gaining a deeper molecular and cellular understanding of these links is especially relevant for plant biology since, unlike in animals, formation of new organs is a process that takes place after embryogenesis and continues throughout the entire plant lifespan. The recent identification of a novel factor, GEM, has provided a molecular framework that coordinates cell division to cell fate in the Arabidopsis epidermis. GEM is an inhibitor of cell division through interacting with CDT1, a DNA replication protein. It also inhibits the expression of the homeobox GLABRA2 (GL2) gene that determines the hair/non-hair fate and the pavement/trichome fate in the root and leaf epidermis, respectively. GEM seems to be crucial in controlling the balance of activating/repressing histone modifications at its target promoters.
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Affiliation(s)
- Elena Caro
- Centro de Biología Molecular "Severo Ochoa"; Consejo Superior de Investigaciones Científicas; Universidad Autónoma de Madrid; Madrid, Spain
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Beltran A, Caro E, Marcé RM, Cormack PAG, Sherrington DC, Borrull F. Synthesis and application of a carbamazepine-imprinted polymer for solid-phase extraction from urine and wastewater. Anal Chim Acta 2007; 597:6-11. [PMID: 17658306 DOI: 10.1016/j.aca.2007.06.040] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 06/18/2007] [Accepted: 06/19/2007] [Indexed: 11/30/2022]
Abstract
A molecularly imprinted polymer (MIP) designed to enable the selective extraction of carbamazepine (CBZ) from effluent wastewater and urine samples has been synthesised using a non-covalent molecular imprinting approach. The MIP was evaluated chromatographically in the first instance and its affinity for CBZ also confirmed by solid-phase extraction (SPE). The optimal conditions for SPE consisted of conditioning of the cartridge using acidified water purified from a Milli-Q system, loading of the sample under basic aqueous conditions, clean-up using acetonitrile and elution with methanol. The attractive molecular recognition properties of the MIP gave rise to good CBZ recoveries (80%) when 100 mL of effluent water spiked with 1 microg L(-1) was percolated through the polymer. For urine samples, 2 mL samples spiked with 2.5 microg L(-1) CBZ were extracted with a recovery of 65%. For urine, the linear range was 0.05-24 mg L(-1), the limit of detection was 25 microg L(-1) and precision, expressed as relative standard deviation at 0.5 mg L(-1) (n=3), was 3.1% and 12.6% for repeatability and reproducibility between days, respectively.
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Affiliation(s)
- A Beltran
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili, Marcel.lí Domingo s/n, Campus Sescelades, 43007 Tarragona, Spain
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Caro E, Castellano MM, Gutierrez C. A chromatin link that couples cell division to root epidermis patterning in Arabidopsis. Nature 2007; 447:213-7. [PMID: 17450124 DOI: 10.1038/nature05763] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 03/21/2007] [Indexed: 12/11/2022]
Abstract
Cell proliferation and cell fate decisions are strictly coupled processes during plant embryogenesis and organogenesis. In the Arabidopsis thaliana root epidermis, expression of the homeobox GLABRA2 (GL2) gene determines hair/non-hair cell fate. This requires signalling of positional information from the underlying cortical layer, complex transcriptional regulation and a change in chromatin accessibility. However, the molecular connections among these factors and with cell division are not known. Here we have identified a GL2-expression modulator, GEM, as an interactor of CDT1, a DNA replication protein. GEM also interacts with TTG1 (TRANSPARENT TESTA GLABRA1), a WD40-repeat protein involved in GL2-dependent cell fate decision, and modulates both cell division and GL2 expression. Here we show that GEM participates in the maintenance of the repressor histone H3K9 methylation status of root patterning genes, providing a link between cell division, fate and differentiation during Arabidopsis root development.
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Affiliation(s)
- Elena Caro
- Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Caro E, Marcé R, Cormack P, Sherrington D, Borrull F. Synthesis and application of an oxytetracycline imprinted polymer for the solid-phase extraction of tetracycline antibiotics. Anal Chim Acta 2005. [DOI: 10.1016/j.aca.2005.07.047] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Castellano MDM, Boniotti MB, Caro E, Schnittger A, Gutierrez C. DNA replication licensing affects cell proliferation or endoreplication in a cell type-specific manner. Plant Cell 2004; 16:2380-93. [PMID: 15316110 PMCID: PMC520940 DOI: 10.1105/tpc.104.022400] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2004] [Accepted: 06/23/2004] [Indexed: 05/17/2023]
Abstract
In eukaryotic cells, the function of DNA replication licensing components (Cdc6 and Cdt1, among others) is crucial for cell proliferation and genome stability. However, little is known about their role in whole organisms and whether licensing control interfaces with differentiation and developmental programs. Here, we study Arabidopsis thaliana CDT1, its regulation, and the consequences of overriding licensing control. The availability of AtCDT1 is strictly regulated at two levels: (1) at the transcription level, by E2F and growth-arresting signals, and (2) posttranscriptionally, by CDK phosphorylation, a step that is required for its proteasome-mediated degradation. We also show that CDC6 and CDT1 are key targets for the coordination of cell proliferation, differentiation, and development. Indeed, altered CDT1 or CDC6 levels have cell type-specific effects in developing Arabidopsis plants: in leaf cells competent to divide, cell proliferation is stimulated, whereas in cells programmed to undergo differentiation-associated endoreplication rounds, extra endocycles are triggered. Thus, we propose that DNA replication licensing control is critical for the proper maintenance of proliferative potential, developmental programs, and morphogenetic patterns.
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Affiliation(s)
- María del Mar Castellano
- Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Sifontes S, Infante JF, Pérez P, Caro E, Sierra G, Campa C. The hyperferremic mouse model for the evaluation of the effectiveness of VA-MENGOC-BC against Neisseria meningitidis B clinical isolates. Arch Med Res 1997; 28:41-5. [PMID: 9078586] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
VA-MENGOC-BC is a vaccine against B and C serogroups of Neisseria meningitidis. Its effectiveness at population level has been shown after the application of the vaccine in Cuba, Brazil, Argentina and Colombia. In vitro assays are not always able to reproduce the microorganism-host relationships and this makes it necessary to compile and standardize results obtained in animal models to extrapolate them with a greater degree of safety for humans. We evaluated the effectiveness of VA-MENGOC-BC against Neisseria meningitidis group B isolates from clinically ill patients in Latin America (Argentina, B not typeable: P1; Chile, not typed; Colombia, B4:P1.15 and Cuba B4:P1.15) using Balb/cJ mice treated with iron to make them susceptible to Neisseria meningitidis. The lethal median dose of each strain and of two others that were not included in challenge assays (Brazil: P1.15 and Argentina, B2b:P1.10) were determined. Results were 2.68 x 10(6), 3.16 x 10(7), 1.98 x 10(8), 1.28 x 10(9), 6.42 x 10(6) and 3.88 x 10(7) colony forming units (CFU), respectively. Non-immunized animals and mice treated with one and two doses of VA-MENGOC-BC were challenged with 10(3)-(10) CFU. Protection ranged from 30 to 100% with one dose and was equal to or higher than 70% with the two-dose immunization schedule. A significant protection could not be observed against the Colombian isolate from the lethality point of view, but the mean time of survival lengthened in immunized animals in relation to the controls. The applied inoculum of this strain was much higher (505 x LD50) than the remaining ones. The protection conferred was evident; nevertheless, more data are needed to determine how relevant the results are to humans.
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Affiliation(s)
- S Sifontes
- Centro de Bioactivos Químicos, Universidad Central, Las Villas, Habana, Cuba
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Girón F, Caro E, Domínguez J. A conjugate family for ar(1) processes with exponential errors. COMMUN STAT-THEOR M 1994. [DOI: 10.1080/03610929408831353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Díaz Colodrero G, Altclas J, Jasovich A, Mikaelian G, Fiks G, Caro E. [Microbiology and conservative surgery of serious infections of the diabetic foot]. Enferm Infecc Microbiol Clin 1992; 10:451-5. [PMID: 1489772] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Between June of 1987 and August 1988 we evaluated 31 diabetic patients hospitalized for severe foot infections to determine the etiologic agents, the value of the bacteriologic samples obtained, the benefits of conservative surgery and variable predictors of a major amputation. Sixteen patients suffered from necrosis, 16 osteomyelitis, 14 ulcers, 5 cellulitis, and/or abscesses and 22 had vascular compromise. Samples were taken from these infections excluding necrotic material. We isolate 76 microorganisms (2.4/pt), 57% Gram-positive cocci (predominantly S. aureus and enterococci), and 43% Gram-negative bacilli. Anaerobes were not isolated probably secondary to the exclusion of necrotic samples. There was high incidence of skin and soft tissue sampling (79%) bone (13/16) and surgical curettage (11/11). In 9 patients the correlation of soft tissue sampling and bone sampling was assessed with a positive correlation with respect to Gram-positive cocci. Twenty-one patients required conservative surgeries of the foot (9 underwent revascularization), 67% of which avoided a mayor amputation. However no significant variables predictive of a major amputation were detected in this study. In summary, the conservative surgery allowed to 2 out of 3 patients to preserve the foot.
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