154 results on '"Agudelo-Romero, Patricia"'
Search Results
2. Transcriptomic analysis of primary nasal epithelial cells reveals altered interferon signalling in preterm birth survivors at one year of age.
- Author
-
Evans, Denby J., Hillas, Jessica K., Iosifidis, Thomas, Simpson, Shannon J., Kicic, Anthony, and Agudelo-Romero, Patricia
- Subjects
PRIMARY cell culture ,GENE expression ,RNA analysis ,NASAL mucosa ,PREMATURE labor - Abstract
Introduction: Many survivors of preterm birth (<37 weeks gestation) have lifelong respiratory deficits, the drivers of which remain unknown. Influencers of pathophysiological outcomes are often detectable at the gene level and pinpointing these differences can help guide targeted research and interventions. This study provides the first transcriptomic analysis of primary nasal airway epithelial cells in survivors of preterm birth at approximately 1 year of age. Methods: Nasal airway epithelial brushings were collected, and primary cell cultures established from term (>37 weeks gestation) and very preterm participants (≤32 weeks gestation). Ex vivo RNA was collected from brushings with sufficient cell numbers and in vitro RNA was extracted from cultured cells, with bulk RNA sequencing performed on both the sample types. Differential gene expression was assessed using the limma-trend pipeline and pathway enrichment identified using Reactome andGOanalysis. To corroborate gene expression data, cytokine concentrations were measured in cell culture supernatant. Results: Transcriptomic analysis to compare term and preterm cells revealed 2,321 genes differentially expressed in ex vivo samples and 865 genes differentially expressed in cultured basal cell samples. Over one third of differentially expressed genes were related to host immunity, with interferon signalling pathways dominating the pathway enrichment analysis and IRF1 identified as a hub gene. Corroboration of disrupted interferon release showed that concentrations of IFN-α2 were below measurable limits in term samples but elevated in preterm samples [19.4 (76.7) pg/ml/μg protein, p = 0.03]. IFN-γ production was significantly higher in preterm samples [3.3 (1.5) vs. 9.4 (17.7) pg/ml/μg protein; p = 0.01] as was IFN-β [7.8 (2.5) vs. 13.6 (19.5) pg/ml/μg protein, p = 0.01]. Conclusion: Host immunity may be compromised in the preterm nasal airway epithelium in early life. Altered immune responses may lead to cycles of repeated infections, causing persistent inflammation and tissue damage which can have significant impacts on long-term respiratory function. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
3. Airway epithelium respiratory illnesses and allergy (AERIAL) birth cohort: study protocol
- Author
-
Kicic-Starcevich, Elizabeth, primary, Hancock, David G., additional, Iosifidis, Thomas, additional, Agudelo-Romero, Patricia, additional, Caparros-Martin, Jose A., additional, Karpievitch, Yuliya V., additional, Silva, Desiree, additional, Turkovic, Lidija, additional, Le Souef, Peter N., additional, Bosco, Anthony, additional, Martino, David J., additional, Kicic, Anthony, additional, Prescott, Susan L., additional, and Stick, Stephen M., additional
- Published
- 2024
- Full Text
- View/download PDF
4. Nasal and Amnion Methylomes: Biomarkers for Smoke Exposure and Maternal Asthma
- Author
-
Agudelo-Romero, Patricia, primary, Iosifidis, Thomas, additional, Kicic-Starcevich, Elizabeth, additional, Hancock, David, additional, Caparros-Martin, Jose, additional, Martino, David, additional, and Stick, Stephen, additional
- Published
- 2024
- Full Text
- View/download PDF
5. Evolutionary insights into FYVE and PHOX effector proteins from the moss Physcomitrella patens
- Author
-
Agudelo-Romero, Patricia, Fortes, Ana Margarida, Suárez, Trinidad, Lascano, Hernán Ramiro, and Saavedra, Laura
- Published
- 2020
6. Airway epithelium respiratory illnesses and allergy (AERIAL) birth cohort: Study protocol
- Author
-
Kicic-Starcevich, Elizabeth, Hancock, David G., Iosifidis, Thomas, Agudelo-Romero, Patricia, Caparros-Martin, Jose A., Karpievitch, Yuliya V., Silva, Desiree, Turkovic, Lidija, Le Souef, Peter N., Bosco, Anthony, Martino, David J., Kicic, Anthony, Prescott, Susan L., Stick, Stephen M., Kicic-Starcevich, Elizabeth, Hancock, David G., Iosifidis, Thomas, Agudelo-Romero, Patricia, Caparros-Martin, Jose A., Karpievitch, Yuliya V., Silva, Desiree, Turkovic, Lidija, Le Souef, Peter N., Bosco, Anthony, Martino, David J., Kicic, Anthony, Prescott, Susan L., and Stick, Stephen M.
- Abstract
Introduction: Recurrent wheezing disorders including asthma are complex and heterogeneous diseases that affect up to 30% of all children, contributing to a major burden on children, their families, and global healthcare systems. It is now recognized that a dysfunctional airway epithelium plays a central role in the pathogenesis of recurrent wheeze, although the underlying mechanisms are still not fully understood. This prospective birth cohort aims to bridge this knowledge gap by investigating the influence of intrinsic epithelial dysfunction on the risk for developing respiratory disorders and the modulation of this risk by maternal morbidities, in utero exposures, and respiratory exposures in the first year of life. Methods: The Airway Epithelium Respiratory Illnesses and Allergy (AERIAL) study is nested within the ORIGINS Project and will monitor 400 infants from birth to 5 years. The primary outcome of the AERIAL study will be the identification of epithelial endotypes and exposure variables that influence the development of recurrent wheezing, asthma, and allergic sensitisation. Nasal respiratory epithelium at birth to 6 weeks, 1, 3, and 5 years will be analysed by bulk RNA-seq and DNA methylation sequencing. Maternal morbidities and in utero exposures will be identified on maternal history and their effects measured through transcriptomic and epigenetic analyses of the amnion and newborn epithelium. Exposures within the first year of life will be identified based on infant medical history as well as on background and symptomatic nasal sampling for viral PCR and microbiome analysis. Daily temperatures and symptoms recorded in a study-specific Smartphone App will be used to identify symptomatic respiratory illnesses. Discussion: The AERIAL study will provide a comprehensive longitudinal assessment of factors influencing the association between epithelial dysfunction and respiratory morbidity in early life, and hopefully identify novel targets for diagnosis and e
- Published
- 2024
7. Exploring the Complexity of the Human Respiratory Virome through an In Silico Analysis of Shotgun Metagenomic Data Retrieved from Public Repositories.
- Author
-
Conradie, Talya, Caparros-Martin, Jose A., Egan, Siobhon, Kicic, Anthony, Koks, Sulev, Stick, Stephen M., and Agudelo-Romero, Patricia
- Subjects
METAGENOMICS ,DATA libraries ,VIRAL genomes ,INSTITUTIONAL repositories ,HUMAN body ,DNA viruses ,RNA viruses - Abstract
Background: Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases' pathogenesis. Nevertheless, our understanding of respiratory microbiota is limited by technical constraints, predominantly focusing on bacteria and neglecting crucial populations like viruses. Despite recent efforts to improve our understanding of viral diversity in the human body, our knowledge of viral diversity associated with the human respiratory tract remains limited. Methods: Following a comprehensive search in bibliographic and sequencing data repositories using keyword terms, we retrieved shotgun metagenomic data from public repositories (n = 85). After manual curation, sequencing data files from 43 studies were analyzed using EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Complete and high-quality contigs were further assessed for genomic and taxonomic characterization. Results: Viral contigs were obtained from 194 out of the 868 FASTQ files processed through EVEREST. Of the 1842 contigs that were quality assessed, 8% (n = 146) were classified as complete/high-quality genomes. Most of the identified viral contigs were taxonomically classified as bacteriophages, with taxonomic resolution ranging from the superkingdom level down to the species level. Captured contigs were spread across 25 putative families and varied between RNA and DNA viruses, including previously uncharacterized viral genomes. Of note, airway samples also contained virus(es) characteristic of the human gastrointestinal tract, which have not been previously described as part of the lung virome. Additionally, by performing a meta-analysis of the integrated datasets, ecological trends within viral populations linked to human disease states and their biogeographical distribution along the respiratory tract were observed. Conclusion: By leveraging publicly available repositories of shotgun metagenomic data, the present study provides new insights into viral genomes associated with specimens from the human respiratory tract across different disease spectra. Further studies are required to validate our findings and evaluate the potential impact of these viral communities on respiratory tract physiology. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
8. An Analysis of the Gut Microbiota and Related Metabolites following PCSK9 Inhibition in Statin-Treated Patients with Elevated Levels of Lipoprotein(a)
- Author
-
Caparrós-Martín, Jose A., primary, Maher, Patrice, additional, Ward, Natalie C., additional, Saladié, Montserrat, additional, Agudelo-Romero, Patricia, additional, Stick, Stephen M., additional, Chan, Dick C., additional, Watts, Gerald F., additional, and O’Gara, Fergal, additional
- Published
- 2024
- Full Text
- View/download PDF
9. Roles for Light, Energy, and Oxygen in the Fate of Quiescent Axillary Buds
- Author
-
Signorelli, Santiago, Agudelo-Romero, Patricia, Meitha, Karlia, Foyer, Christine H., and Considine, Michael J.
- Published
- 2018
10. Airway Epithelium Respiratory Illnesses and Allergy (AERIAL) birth cohort: study protocol
- Author
-
Kicic-Starcevich, Elizabeth, primary, Hancock, David G, additional, Iosifidis, Thomas, additional, Agudelo-Romero, Patricia, additional, Caparros-Martin, Jose A, additional, Silva, Desiree, additional, Turkovic, Lidija, additional, Le Souef, Peter N, additional, Bosco, Anthony, additional, Martino, David J, additional, Kicic, Anthony, additional, Prescott, Susan L, additional, and Stick, Stephen M, additional
- Published
- 2023
- Full Text
- View/download PDF
11. Transcriptomic analyses reveal regional signatures in lung allograft recipients
- Author
-
Agudelo-Romero, Patricia, primary, Ling, Kak-Ming, additional, Lavander, Melani A, additional, Wrobel, Jeremy P, additional, Musk, Michael, additional, Stick, Stephen S, additional, and Kicic, Anthony, additional
- Published
- 2023
- Full Text
- View/download PDF
12. Women in the European Virus Bioinformatics Center
- Author
-
Hufsky, Franziska, Abecasis, Ana, Agudelo-Romero, Patricia, Bletsa, Magda, Brown, Katherine, Claus, Claudia, Deinhardt-Emmer, Stefanie, Deng, Li, Friedel, Caroline C, Gismondi, María Inés, Kostaki, Evangelia Georgia, Kühnert, Denise, Kulkarni-Kale, Urmila, Metzner, Karin J, Meyer, Irmtraud M, Miozzi, Laura, Nishimura, Luca, Paraskevopoulou, Sofia, Pérez-Cataluña, Alba, Rahlff, Janina, Thomson, Emma, Tumescheit, Charlotte, van der Hoek, Lia, Van Espen, Lore, Vandamme, Anne-Mieke, Zaheri, Maryam, Zuckerman, Neta, Marz, Manja, Hufsky, Franziska [0000-0002-9489-3182], Abecasis, Ana [0000-0002-3903-5265], Agudelo-Romero, Patricia [0000-0002-3703-4111], Bletsa, Magda [0000-0003-3184-6618], Brown, Katherine [0000-0002-8400-6922], Claus, Claudia [0000-0003-4962-6568], Deinhardt-Emmer, Stefanie [0000-0003-4495-4052], Deng, Li [0000-0003-0225-0663], Friedel, Caroline C [0000-0003-3569-4877], Gismondi, María Inés [0000-0002-2566-1169], Kostaki, Evangelia Georgia [0000-0002-3346-0930], Kühnert, Denise [0000-0002-5657-018X], Kulkarni-Kale, Urmila [0000-0002-1168-2479], Metzner, Karin J [0000-0003-4862-1503], Meyer, Irmtraud M [0000-0002-4048-3479], Miozzi, Laura [0000-0003-0410-8230], Nishimura, Luca [0000-0003-2144-7867], Paraskevopoulou, Sofia [0000-0003-2608-2596], Pérez-Cataluña, Alba [0000-0002-4784-8346], Rahlff, Janina [0000-0002-2132-2709], Thomson, Emma [0000-0003-1482-0889], Tumescheit, Charlotte [0000-0002-7563-5575], van der Hoek, Lia [0000-0003-2803-642X], Van Espen, Lore [0000-0002-3870-4551], Vandamme, Anne-Mieke [0000-0002-6594-2766], Zaheri, Maryam [0000-0003-2777-835X], Zuckerman, Neta [0000-0001-6074-2100], Marz, Manja [0000-0003-4783-8823], Apollo - University of Cambridge Repository, Medical Microbiology and Infection Prevention, AII - Infectious diseases, University of Zurich, Hufsky, Franziska, and Marz, Manja
- Subjects
10028 Institute of Medical Virology ,virus evolution ,virus discovery ,Cancer Research ,viral ecology ,Virus Bioinformatics ,Big Data ,Networking ,Virus Discovery ,Virus Evolution ,Viral Infection ,Transcriptomics ,Emerging Viruses ,Epidemiology ,Viral Ecology ,networking ,virus bioinformatics ,Computational Biology ,610 Medicine & health ,2725 Infectious Diseases ,Research Personnel ,Europe ,emerging viruses ,transcriptomics ,big data ,Viruses ,2406 Virology ,570 Life sciences ,biology ,Humans ,epidemiology ,Female ,viral infection - Abstract
Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics. ispartof: VIRUSES-BASEL vol:14 issue:7 ispartof: location:Switzerland status: published
- Published
- 2022
13. Autophagy modulates growth and development in the moss Physcomitrium patens
- Author
-
Pettinari, Georgina, primary, Finello, Juan, additional, Plaza Rojas, Macarena, additional, Liberatore, Franco, additional, Robert, Germán, additional, Otaiza-González, Santiago, additional, Velez, Pilar, additional, Theumer, Martin, additional, Agudelo-Romero, Patricia, additional, Enet, Alejandro, additional, González, Claudio, additional, Lascano, Ramiro, additional, and Saavedra, Laura, additional
- Published
- 2022
- Full Text
- View/download PDF
14. Transcriptome and metabolome reprogramming in Vitis vinifera cv. Trincadeira berries upon infection with Botrytis cinerea
- Author
-
Agudelo-Romero, Patricia, Erban, Alexander, Rego, Cecília, Carbonell-Bejerano, Pablo, Nascimento, Teresa, Sousa, Lisete, Martínez-Zapater, José M., Kopka, Joachim, and Fortes, Ana Margarida
- Published
- 2015
15. Polyamine Metabolism in Climacteric and Non-Climacteric Fruit Ripening
- Author
-
Fortes, Ana Margarida, primary and Agudelo-Romero, Patricia, additional
- Published
- 2017
- Full Text
- View/download PDF
16. Women in the European Virus Bioinformatics Center
- Author
-
Hufsky, Franziska; https://orcid.org/0000-0002-9489-3182, Abecasis, Ana; https://orcid.org/0000-0002-3903-5265, Agudelo-Romero, Patricia; https://orcid.org/0000-0002-3703-4111, Bletsa, Magda; https://orcid.org/0000-0003-3184-6618, Brown, Katherine; https://orcid.org/0000-0002-8400-6922, Claus, Claudia; https://orcid.org/0000-0003-4962-6568, Deinhardt-Emmer, Stefanie; https://orcid.org/0000-0003-4495-4052, Deng, Li; https://orcid.org/0000-0003-0225-0663, Friedel, Caroline C; https://orcid.org/0000-0003-3569-4877, Gismondi, María Inés; https://orcid.org/0000-0002-2566-1169, Kostaki, Evangelia Georgia; https://orcid.org/0000-0002-3346-0930, Kühnert, Denise; https://orcid.org/0000-0002-5657-018X, Kulkarni-Kale, Urmila; https://orcid.org/0000-0002-1168-2479, Metzner, Karin J; https://orcid.org/0000-0003-4862-1503, Meyer, Irmtraud M; https://orcid.org/0000-0002-4048-3479, Miozzi, Laura; https://orcid.org/0000-0003-0410-8230, Nishimura, Luca; https://orcid.org/0000-0003-2144-7867, Paraskevopoulou, Sofia; https://orcid.org/0000-0003-2608-2596, Pérez-Cataluña, Alba; https://orcid.org/0000-0002-4784-8346, Rahlff, Janina; https://orcid.org/0000-0002-2132-2709, Thomson, Emma; https://orcid.org/0000-0003-1482-0889, Tumescheit, Charlotte; https://orcid.org/0000-0002-7563-5575, van der Hoek, Lia; https://orcid.org/0000-0003-2803-642X, Van Espen, Lore; https://orcid.org/0000-0002-3870-4551, Vandamme, Anne-Mieke; https://orcid.org/0000-0002-6594-2766, Zaheri, Maryam; https://orcid.org/0000-0003-2777-835X, Zuckerman, Neta; https://orcid.org/0000-0001-6074-2100, Marz, Manja; https://orcid.org/0000-0003-4783-8823, Hufsky, Franziska; https://orcid.org/0000-0002-9489-3182, Abecasis, Ana; https://orcid.org/0000-0002-3903-5265, Agudelo-Romero, Patricia; https://orcid.org/0000-0002-3703-4111, Bletsa, Magda; https://orcid.org/0000-0003-3184-6618, Brown, Katherine; https://orcid.org/0000-0002-8400-6922, Claus, Claudia; https://orcid.org/0000-0003-4962-6568, Deinhardt-Emmer, Stefanie; https://orcid.org/0000-0003-4495-4052, Deng, Li; https://orcid.org/0000-0003-0225-0663, Friedel, Caroline C; https://orcid.org/0000-0003-3569-4877, Gismondi, María Inés; https://orcid.org/0000-0002-2566-1169, Kostaki, Evangelia Georgia; https://orcid.org/0000-0002-3346-0930, Kühnert, Denise; https://orcid.org/0000-0002-5657-018X, Kulkarni-Kale, Urmila; https://orcid.org/0000-0002-1168-2479, Metzner, Karin J; https://orcid.org/0000-0003-4862-1503, Meyer, Irmtraud M; https://orcid.org/0000-0002-4048-3479, Miozzi, Laura; https://orcid.org/0000-0003-0410-8230, Nishimura, Luca; https://orcid.org/0000-0003-2144-7867, Paraskevopoulou, Sofia; https://orcid.org/0000-0003-2608-2596, Pérez-Cataluña, Alba; https://orcid.org/0000-0002-4784-8346, Rahlff, Janina; https://orcid.org/0000-0002-2132-2709, Thomson, Emma; https://orcid.org/0000-0003-1482-0889, Tumescheit, Charlotte; https://orcid.org/0000-0002-7563-5575, van der Hoek, Lia; https://orcid.org/0000-0003-2803-642X, Van Espen, Lore; https://orcid.org/0000-0002-3870-4551, Vandamme, Anne-Mieke; https://orcid.org/0000-0002-6594-2766, Zaheri, Maryam; https://orcid.org/0000-0003-2777-835X, Zuckerman, Neta; https://orcid.org/0000-0001-6074-2100, and Marz, Manja; https://orcid.org/0000-0003-4783-8823
- Abstract
Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.
- Published
- 2022
17. Autophagy modulates apical growth and development in the moss Physcomitrium patens
- Author
-
Pettinari, Georgina, primary, Finello, Juan, additional, Rojas, Macarena Plaza, additional, Liberatore, Franco, additional, Robert, Germán, additional, Otaiza-González, Santiago, additional, Velez, Pilar, additional, Theumer, Martin, additional, Agudelo-Romero, Patricia, additional, Gonzalez, Claudio, additional, Lascano, Ramiro, additional, and Saavedra, Laura, additional
- Published
- 2022
- Full Text
- View/download PDF
18. Epithelial and neutrophil responses to microbes in cystic fibrosis airways
- Author
-
Laucirica, Daniel, primary, Schofield, Craig, additional, Mclean, Samantha, additional, Margaroli, Camilla, additional, Agudelo-Romero, Patricia, additional, Stick, Stephen, additional, Tirouvanziam, Rabindra, additional, Riley, Thomas, additional, Kicic, Anthony, additional, and Garratt, Luke, additional
- Published
- 2022
- Full Text
- View/download PDF
19. Adaptation of tobacco etch potyvirus to a susceptible ecotype of Arabidopsis thaliana capacitates it for systemic infection of resistant ecotypes
- Author
-
Lalić, Jasna, Agudelo-Romero, Patricia, Carrasco, Purificación, and Elena, Santiago F.
- Published
- 2010
20. Women in the European Virus Bioinformatics Center
- Author
-
Hufsky, Franziska, Abecasis, Ana, Agudelo-Romero, Patricia, Bletsa, Magda, Brown, Katherine, Claus, Claudia, Deinhardt-Emmer, Stefanie, Deng, Li, Friedel, Caroline C., Gismondi, María Inés, Kostaki, Evangelia Georgia, Kühnert, Denise, Kulkarni-Kale, Urmila, Metzner, Karin J., Meyer, Irmtraud M., Miozzi, Laura, Nishimura, Luca, Paraskevopoulou, Sofia, Pérez-Cataluña, Alba, Rahlff, Janina, Thomson, Emma, Tumescheit, Charlotte, van der Hoek, Lia, Van Espen, Lore, Vandamme, Anne-Mieke, Zaheri, Maryam, Zuckerman, Neta, and Marz, Manja
- Subjects
Commentary ,virus bioinformatics ,big data ,networking ,virus discovery ,virus evolution ,viral infection ,transcriptomics ,emerging viruses ,epidemiology ,viral ecology ,ddc - Published
- 2021
21. The bud dormancy disconnect: latent buds of grapevine are dormant during summer despite a high metabolic rate
- Author
-
Velappan, Yazhini, primary, Chabikwa, Tinashe G, additional, Considine, John A, additional, Agudelo-Romero, Patricia, additional, Foyer, Christine H, additional, Signorelli, Santiago, additional, and Considine, Michael J, additional
- Published
- 2022
- Full Text
- View/download PDF
22. Detection of Bile Acids in Bronchoalveolar Lavage Fluid Defines Early Pathobiological Events in Infants with Cystic Fibrosis
- Author
-
Caparrós-Martín, José Antonio, primary, Saladié, Montserrat, additional, Agudelo-Romero, Patricia, additional, Reen, Jerry, additional, Ware, Robert S., additional, Sly, Peter D., additional, Stick, Stephen M., additional, O’Gara, Fergal, additional, and Group, COMBAT Study, additional
- Published
- 2022
- Full Text
- View/download PDF
23. Dysregulated Notch Signaling in the Airway Epithelium of Children with Wheeze
- Author
-
Iosifidis, Thomas, primary, Sutanto, Erika N., additional, Montgomery, Samuel T., additional, Agudelo-Romero, Patricia, additional, Looi, Kevin, additional, Ling, Kak-Ming, additional, Shaw, Nicole C., additional, Garratt, Luke W., additional, Hillas, Jessica, additional, Martinovich, Kelly M., additional, Kicic-Starcevich, Elizabeth, additional, Vijayasekaran, Shyan, additional, Lannigan, Francis J., additional, Rigby, Paul J., additional, Knight, Darryl A., additional, Stick, Stephen M., additional, and Kicic, Anthony, additional
- Published
- 2021
- Full Text
- View/download PDF
24. Development and validation of a miniaturized bacteriophage host range screening assay against antibiotic resistant Pseudomonas aeruginosa
- Author
-
Ng, Renee Nicole, primary, Grey, Lucinda Jane, additional, Vaitekenas, Andrew, additional, McLean, Samantha Abagail, additional, Rudrum, Jack Dylan, additional, Laucirica, Daniel Rodolfo, additional, Poh, Matthew Wee-Peng, additional, Hillas, Jessica, additional, Winslow, Scott Glenn, additional, Iszatt, Joshua James, additional, Iosifidis, Thomas, additional, Tai, Anna Sze, additional, Agudelo-Romero, Patricia, additional, Chang, Barbara Jane, additional, Stick, Stephen Michael, additional, and Kicic, Anthony, additional
- Published
- 2021
- Full Text
- View/download PDF
25. Pseudomonas aeruginosa modulates neutrophil granule exocytosis in an in vitro model of airway infection.
- Author
-
Laucirica, Daniel R, Schofield, Craig J, McLean, Samantha A, Margaroli, Camilla, Agudelo‐Romero, Patricia, Stick, Stephen M, Tirouvanziam, Rabindra, Kicic, Anthony, and Garratt, Luke W
- Subjects
RHINOVIRUSES ,PSEUDOMONAS aeruginosa ,PSEUDOMONAS aeruginosa infections ,EPITHELIAL cell culture ,NEUTROPHILS ,AIRWAY (Anatomy) ,EXOCYTOSIS - Abstract
A population of neutrophils recruited into cystic fibrosis (CF) airways is associated with proteolytic lung damage, exhibiting high expression of primary granule exocytosis marker CD63 and reduced phagocytic receptor CD16. Causative factors for this population are unknown, limiting intervention. Here we present a laboratory model to characterize responses of differentiated airway epithelium and neutrophils following respiratory infection. Pediatric primary airway epithelial cells were cultured at the air–liquid interface, challenged individually or in combination with rhinovirus (RV) and Pseudomonas aeruginosa, then apically washed with medical saline to sample epithelial infection milieus. Cytokine multiplex analysis revealed epithelial antiviral signals, including IP‐10 and RANTES, increased with exclusive RV infection but were diminished if P. aeruginosa was also present. Proinflammatory signals interleukin‐1α and β were dominant in P. aeruginosa infection milieus. Infection washes were also applied to a published model of neutrophil transmigration into the airways. Neutrophils migrating into bacterial and viral–bacterial co‐infection milieus exhibited the in vivo CF phenotype of increased CD63 expression and reduced CD16 expression, while neutrophils migrating into milieus of RV‐infected or uninfected cultures did not. Individually, bacterial products lipopolysaccharide and N‐formylmethionyl‐leucyl‐phenylalanine and isolated cytokine signals only partially activated this phenotype, suggesting that additional soluble factors in the infection microenvironment trigger primary granule release. Findings identify P. aeruginosa as a trigger of acute airway inflammation and neutrophil primary granule exocytosis, underscoring potential roles of airway microbes in prompting this neutrophil subset. Further studies are required to characterize microbes implicated in primary granule release, and identify potential therapeutic targets. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
26. Development and validation of a miniaturized host range screening assay for bacteriophages
- Author
-
Ng, Renee Nicole, primary, Grey, Lucinda Jean, additional, Vaitekenas, Andrew, additional, McLean, Samantha Abagail, additional, Laucirica, Daniel Rodolfo, additional, Poh, Matthew Wee-Peng, additional, Hillas, Jessica, additional, Winslow, Scott Glenn, additional, Iszatt, Joshua James, additional, Iosifidis, Thomas, additional, Tai, Anna Sze, additional, Agudelo-Romero, Patricia, additional, Chang, Barbara Jane, additional, Stick, Stephen Michael, additional, and Kicic, Anthony, additional
- Published
- 2021
- Full Text
- View/download PDF
27. The seasonal dynamics of bud dormancy in grapevine suggest a regulated checkpoint prior to acclimation
- Author
-
Velappan, Yazhini, primary, Chabikwa, Tinashe G, additional, Considine, John A, additional, Agudelo-Romero, Patricia, additional, Foyer, Christine H, additional, Signorelli, Santiago, additional, and Considine, Michael J, additional
- Published
- 2021
- Full Text
- View/download PDF
28. bud dormancy disconnect: latent buds of grapevine are dormant during summer despite a high metabolic rate.
- Author
-
Velappan, Yazhini, Chabikwa, Tinashe G, Considine, John A, Agudelo-Romero, Patricia, Foyer, Christine H, Signorelli, Santiago, and Considine, Michael J
- Subjects
ABSCISIC acid ,GRAPES ,VITIS vinifera ,SEASONAL temperature variations ,SUMMER ,PHYSIOLOGICAL oxidation ,DORMANCY in plants ,BUDS ,PLANT phenology - Abstract
Grapevine (Vitis vinifera L.) displays wide plasticity to climate; however, the physiology of dormancy along a seasonal continuum is poorly understood. Here we investigated the apparent disconnect between dormancy and the underlying respiratory physiology and transcriptome of grapevine buds, from bud set in summer to bud burst in spring. The establishment of dormancy in summer was pronounced and reproducible; however, this was coupled with little or no change in physiology, indicated by respiration, hydration, and tissue oxygen tension. The release of dormancy was biphasic; the depth of dormancy declined substantially by mid-autumn, while the subsequent decline towards spring was moderate. Observed changes in physiology failed to explain the first phase of dormancy decline, in particular. Transcriptome data contrasting development from summer through to spring also indicated that dormancy was poorly reflected by metabolic quiescence during summer and autumn. Gene Ontology and enrichment data revealed the prevailing influence of abscisic acid (ABA)-related gene expression during the transition from summer to autumn, and promoter motif analysis suggested that photoperiod may play an important role in regulating ABA functions during the establishment of dormancy. Transcriptomic data from later transitions reinforced the importance of oxidation and hypoxia as physiological cues to regulate the maintenance of quiescence and resumption of growth. Collectively these data reveal a novel disconnect between growth and metabolic quiescence in grapevine following bud set, which requires further experimentation to explain the phenology and dormancy relationships. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
29. Microbiomic Analysis on Low Abundant Respiratory Biomass Samples; Improved Recovery of Microbial DNA From Bronchoalveolar Lavage Fluid
- Author
-
Saladié, Montserrat, primary, Caparrós-Martín, Jose Antonio, additional, Agudelo-Romero, Patricia, additional, Wark, Peter A. B., additional, Stick, Stephen M., additional, and O’Gara, Fergal, additional
- Published
- 2020
- Full Text
- View/download PDF
30. Using integrated omics to assess the effects of rhinovirus infection in children with Cystic Fibrosis (CF)
- Author
-
Agudelo-Romero, Patricia, primary, Martinovich, Kelly, additional, Chandler, Joshua D, additional, Ling, Kak-Ming, additional, Sutanto, Erika N, additional, Jones, Dean P, additional, Tirouvanzium, Rabindra M, additional, Stick, Stephen M, additional, Garratt, Luke W, additional, Kicic, Anthony, additional, Erp, Wa, additional, and Cf, Arest, additional
- Published
- 2020
- Full Text
- View/download PDF
31. Rhinovirus Infection Drives Complex Host Airway Molecular Responses in Children With Cystic Fibrosis
- Author
-
Ling, Kak-Ming, primary, Garratt, Luke W., additional, Gill, Erin E., additional, Lee, Amy H. Y., additional, Agudelo-Romero, Patricia, additional, Sutanto, Erika N., additional, Iosifidis, Thomas, additional, Rosenow, Tim, additional, Turvey, Stuart E., additional, Lassmann, Timo, additional, Hancock, Robert E. W., additional, Kicic, Anthony, additional, and Stick, Stephen M., additional
- Published
- 2020
- Full Text
- View/download PDF
32. The Detection of Bile Acids in the Lungs of Paediatric Cystic Fibrosis Patients Is Associated with Altered Inflammatory Patterns
- Author
-
Caparrós-Martín, Jose A., primary, Flynn, Stephanie, additional, Reen, F. Jerry, additional, Woods, David F., additional, Agudelo-Romero, Patricia, additional, Ranganathan, Sarath C., additional, Stick, Stephen M., additional, and O’Gara, Fergal, additional
- Published
- 2020
- Full Text
- View/download PDF
33. Evolutionary insights into PtdIns3P signaling through FYVE and PHOX effector proteins from the moss Physcomitrella patens
- Author
-
Agudelo-Romero, Patricia, primary, Fortes, Ana Margarida, additional, Suárez, Trinidad, additional, Lascano, Hernán Ramiro, additional, and Saavedra, Laura, additional
- Published
- 2019
- Full Text
- View/download PDF
34. Transcriptional Modulation of Polyamine Metabolism in Fruit Species Under Abiotic and Biotic Stress
- Author
-
Fortes, Ana Margarida, primary, Agudelo-Romero, Patricia, additional, Pimentel, Diana, additional, and Alkan, Noam, additional
- Published
- 2019
- Full Text
- View/download PDF
35. Transcript and metabolite analysis in Trincadeira cultivar reveals novel information regarding the dynamics of grape ripening
- Author
-
Martinez- Zapater José M, Grimplet Jerome, Choi Young H, Maltese Federica, Sousa Lisete, Ali Kashif, Silva Marta S, Agudelo-Romero Patricia, Fortes Ana M, Verpoorte Robert, and Pais Maria S
- Subjects
Botany ,QK1-989 - Abstract
Abstract Background Grapes (Vitis vinifera L.) are economically the most important fruit crop worldwide. However, the complexity of molecular and biochemical events that lead to the onset of ripening of nonclimacteric fruits is not fully understood which is further complicated in grapes due to seasonal and cultivar specific variation. The Portuguese wine variety Trincadeira gives rise to high quality wines but presents extremely irregular berry ripening among seasons probably due to high susceptibility to abiotic and biotic stresses. Results Ripening of Trincadeira grapes was studied taking into account the transcriptional and metabolic profilings complemented with biochemical data. The mRNA expression profiles of four time points spanning developmental stages from pea size green berries, through véraison and mature berries (EL 32, EL 34, EL 35 and EL 36) and in two seasons (2007 and 2008) were compared using the Affymetrix GrapeGen® genome array containing 23096 probesets corresponding to 18726 unique sequences. Over 50% of these probesets were significantly differentially expressed (1.5 fold) between at least two developmental stages. A common set of modulated transcripts corresponding to 5877 unigenes indicates the activation of common pathways between years despite the irregular development of Trincadeira grapes. These unigenes were assigned to the functional categories of "metabolism", "development", "cellular process", "diverse/miscellanenous functions", "regulation overview", "response to stimulus, stress", "signaling", "transport overview", "xenoprotein, transposable element" and "unknown". Quantitative RT-PCR validated microarrays results being carried out for eight selected genes and five developmental stages (EL 32, EL 34, EL 35, EL 36 and EL 38). Metabolic profiling using 1H NMR spectroscopy associated to two-dimensional techniques showed the importance of metabolites related to oxidative stress response, amino acid and sugar metabolism as well as secondary metabolism. These results were integrated with transcriptional profiling obtained using genome array to provide new information regarding the network of events leading to grape ripening. Conclusions Altogether the data obtained provides the most extensive survey obtained so far for gene expression and metabolites accumulated during grape ripening. Moreover, it highlighted information obtained in a poorly known variety exhibiting particular characteristics that may be cultivar specific or dependent upon climatic conditions. Several genes were identified that had not been previously reported in the context of grape ripening namely genes involved in carbohydrate and amino acid metabolisms as well as in growth regulators; metabolism, epigenetic factors and signaling pathways. Some of these genes were annotated as receptors, transcription factors, and kinases and constitute good candidates for functional analysis in order to establish a model for ripening control of a non-climacteric fruit.
- Published
- 2011
- Full Text
- View/download PDF
36. Roles for Light, Energy, and Oxygen in the Fate of Quiescent Axillary Buds1[OPEN]
- Author
-
Signorelli, Santiago, Agudelo-Romero, Patricia, Meitha, Karlia, Foyer, Christine H., and Considine, Michael J.
- Subjects
Oxygen ,Plant Leaves ,Chloroplasts ,Light ,Gene Expression Regulation, Plant ,Meristem ,Vitis ,Plastids ,Energy Metabolism ,UPDATES - FOCUS ISSUE ,Plant Shoots ,Signal Transduction - Abstract
The decision of a quiescent axillary bud to commit to regrowth is governed by both metabolic and signaling functions, driven by light, energy, and oxygen availability.
- Published
- 2017
37. Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus
- Author
-
Jaramillo Alfonso, Pérez-Amador Miguel A, Rodrigo Guillermo, Carrera Javier, de la Iglesia Francisca, Carbonell Pablo, Agudelo-Romero Patricia, and Elena Santiago F
- Subjects
Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background Tobacco etch potyvirus (TEV) has been extensively used as model system for the study of positive-sense RNA virus infecting plants. TEV ability to infect Arabidopsis thaliana varies among ecotypes. In this study, changes in gene expression of A. thaliana ecotype Ler infected with TEV have been explored using long-oligonucleotide arrays. A. thaliana Ler is a susceptible host that allows systemic movement, although the viral load is low and syndrome induced ranges from asymptomatic to mild. Gene expression profiles were monitored in whole plants 21 days post-inoculation (dpi). Microarrays contained 26,173 protein-coding genes and 87 miRNAs. Results Expression analysis identified 1727 genes that displayed significant and consistent changes in expression levels either up or down, in infected plants. Identified TEV-responsive genes encode a diverse array of functional categories that include responses to biotic (such as the systemic acquired resistance pathway and hypersensitive responses) and abiotic stresses (droughtness, salinity, temperature, and wounding). The expression of many different transcription factors was also significantly affected, including members of the R2R3-MYB family and ABA-inducible TFs. In concordance with several other plant and animal viruses, the expression of heat-shock proteins (HSP) was also increased. Finally, we have associated functional GO categories with KEGG biochemical pathways, and found that many of the altered biological functions are controlled by changes in basal metabolism. Conclusion TEV infection significantly impacts a wide array of cellular processes, in particular, stress-response pathways, including the systemic acquired resistance and hypersensitive responses. However, many of the observed alterations may represent a global response to viral infection rather than being specific of TEV.
- Published
- 2008
- Full Text
- View/download PDF
38. Developmental control of hypoxia during bud burst in grapevine
- Author
-
Meitha, Karlia, primary, Agudelo‐Romero, Patricia, additional, Signorelli, Santiago, additional, Gibbs, Daniel J., additional, Considine, John A., additional, Foyer, Christine H., additional, and Considine, Michael J., additional
- Published
- 2018
- Full Text
- View/download PDF
39. Roles for Light, Energy, and Oxygen in the Fate of Quiescent Axillary Buds
- Author
-
Signorelli, Santiago, primary, Agudelo-Romero, Patricia, additional, Meitha, Karlia, additional, Foyer, Christine H., additional, and Considine, Michael J., additional
- Published
- 2017
- Full Text
- View/download PDF
40. The LATERAL ORGAN BOUNDARIES Domain gene family in grapevine: genome-wide characterization and expression analyses during developmental processes and stress responses
- Author
-
Grimplet, Jérôme, primary, Pimentel, Diana, additional, Agudelo-Romero, Patricia, additional, Martinez-Zapater, Jose Miguel, additional, and Fortes, Ana Margarida, additional
- Published
- 2017
- Full Text
- View/download PDF
41. The lateral organ boundaries Domain gene family in grapevine: Genome-wide characterization and expression analyses during developmental processes and stress responses
- Author
-
Fundação para a Ciência e a Tecnologia (Portugal), Ministerio de Economía y Competitividad (España), Australian Research Council, Grimplet, Jérôme [0000-0002-3265-4012], Martínez-Zapater, José M. [0000-0001-7217-4454], Grimplet, Jérôme, Pimentel, Diana, Agudelo-Romero, Patricia, Martínez-Zapater, José M., Fortes, Ana M., Fundação para a Ciência e a Tecnologia (Portugal), Ministerio de Economía y Competitividad (España), Australian Research Council, Grimplet, Jérôme [0000-0002-3265-4012], Martínez-Zapater, José M. [0000-0001-7217-4454], Grimplet, Jérôme, Pimentel, Diana, Agudelo-Romero, Patricia, Martínez-Zapater, José M., and Fortes, Ana M.
- Abstract
Lateral organ boundaires (LOB) Domain (LBD) constitute a family of plant-specific transcription factors with key roles in the regulation of plant organ development, pollen development, plant regeneration, pathogen response, and anthocyanin and nitrogen metabolisms. However, the role of LBDs in fruit ripening and in grapevine (Vitis vinifera L.) development and stress responses is poorly documented. By performing a model curation of LBDs in the latest genome annotation 50 genes were identified. Phylogenetic analysis showed that LBD genes can be grouped into two classes mapping on 16 out of the 19 V. vinifera chromosomes. New gene subclasses were identified that have not been characterized in other species. Segmental and tandem duplications contributed significantly to the expansion and evolution of the LBD gene family in grapevine as noticed for other species. The analysis of cis-regulatory elements and transcription factor binding sites in the VviLBD promoter regions suggests the involvement of several hormones in the regulation of LBDs expression. Expression profiling suggest the involvement of LBD transcription factors in grapevine development, berry ripening and stress responses. Altogether this study provides valuable information and robust candidate genes for future functional analysis aiming to clarify mechanisms responsible for the onset of fruit ripening and fruit defense strategies.
- Published
- 2017
42. Structural and functional analyses of the GRAS and LOB gene family in grapevine indicate a role of GRAS and LOB proteins in the control of grape ripening and stress responses
- Author
-
Grimplet, Jérôme, Pimentel, Diana, Agudelo-Romero, Patricia, Martínez-Zapater, José M., and Fortes, Ana M.
- Abstract
Trabajo presentado en el Annual Conference COST FA1106 “Quality Fruit”, celebrado en Oporto del 6 al 8 de octubre de 2016., GRAS and LOB are transcription factors involved in many processes of plant growth and development as well as abiotic and biotic stress responses. However, little information is available concerning these genes families in grapevine (Vitis viniferaL.). We performed a model curation of genes identified in the latest genome annotation leading to the identification of 52 GRAS genes and 50 LOB genes. Gene models were improved and new genes were identified that could be grapevine-or woody-plant specific. Phylogenetic analysis showed that GRAS genes could be classified into 13 groups and LOB genes into two classes. Multiple sequence alignment showed typical GRAS domain in the proteins and new motifs were also described. In LOB domain proteins the zinc finger-like domain was conserved; the leucine zipper-like motif was absent in class II. Expression patterns across a variety of tissues and upon abiotic and biotic conditions revealed possible divergent functions of GRAS and LOB genes in grapevine development and stress responses. Promoter analysis of LOB genes revealed several transcription factor binding sites associated with development and abiotic and biotic stress responses. Candidate genes that might constitute transcriptional regulators of grape ripening were identified. Altogether this study provides robust candidate genes for future functional analysis aiming at improving the quality of fleshy fruits.
- Published
- 2016
43. Learning To Breathe: Developmental Phase Transitions in Oxygen Status
- Author
-
Considine, Michael J., primary, Diaz-Vivancos, Pedro, additional, Kerchev, Pavel, additional, Signorelli, Santiago, additional, Agudelo-Romero, Patricia, additional, Gibbs, Daniel J., additional, and Foyer, Christine H., additional
- Published
- 2017
- Full Text
- View/download PDF
44. Structural and functional analysis of the gras gene family in grapevine indicates a role of GRAS proteins in the control of development and stress responses
- Author
-
Fundação para a Ciência e a Tecnologia (Portugal), European Cooperation in Science and Technology, Ministerio de Economía y Competitividad (España), Grimplet, Jérôme, Agudelo-Romero, Patricia, Teixeira, Rita T., Martínez-Zapater, José M., Fortes, Ana M., Fundação para a Ciência e a Tecnologia (Portugal), European Cooperation in Science and Technology, Ministerio de Economía y Competitividad (España), Grimplet, Jérôme, Agudelo-Romero, Patricia, Teixeira, Rita T., Martínez-Zapater, José M., and Fortes, Ana M.
- Abstract
GRAS transcription factors are involved in many processes of plant growth and development (e.g., axillary shoot meristem formation, root radial patterning, nodule morphogenesis, arbuscular development) as well as in plant disease resistance and abiotic stress responses. However, little information is available concerning this gene family in grapevine (Vitis vinifera L.), an economically important woody crop. We performed a model curation of GRAS genes identified in the latest genome annotation leading to the identification of 52 genes. Gene models were improved and three new genes were identified that could be grapevine- or woody-plant specific. Phylogenetic analysis showed that GRAS genes could be classified into 13 groups that mapped on the 19. V. vinifera chromosomes. Five new subfamilies, previously not characterized in other species, were identified. Multiple sequence alignment showed typical GRAS domain in the proteins and new motifs were also described. As observed in other species, both segmental and tandem duplications contributed significantly to the expansion and evolution of the GRAS gene family in grapevine. Expression patterns across a variety of tissues and upon abiotic and biotic conditions revealed possible divergent functions of GRAS genes in grapevine development and stress responses. By comparing the information available for tomato and grapevine GRAS genes, we identified candidate genes that might constitute conserved transcriptional regulators of both climacteric and non-climacteric fruit ripening. Altogether this study provides valuable information and robust candidate genes for future functional analysis aiming at improving the quality of fleshy fruits.
- Published
- 2016
45. Structural and Functional Analysis of the GRAS Gene Family in Grapevine Indicates a Role of GRAS Proteins in the Control of Development and Stress Responses
- Author
-
Grimplet, Jérôme, primary, Agudelo-Romero, Patricia, additional, Teixeira, Rita T., additional, Martinez-Zapater, Jose M., additional, and Fortes, Ana M., additional
- Published
- 2016
- Full Text
- View/download PDF
46. Transcriptome and metabolome reprogramming in Vitis vinifera cv. Trincadeira berries upon infection with Botrytis cinerea
- Author
-
Fundação para a Ciência e a Tecnologia (Portugal), European Cooperation in Science and Technology, Agudelo-Romero, Patricia, Erban, Alexander, Rego, Cecilia, Carbonell-Bejerano, Pablo, Nascimento, Teresa, Sousa, Lisete, Martínez-Zapater, José M., Kopka, Joachim, Fortes, Ana M., Fundação para a Ciência e a Tecnologia (Portugal), European Cooperation in Science and Technology, Agudelo-Romero, Patricia, Erban, Alexander, Rego, Cecilia, Carbonell-Bejerano, Pablo, Nascimento, Teresa, Sousa, Lisete, Martínez-Zapater, José M., Kopka, Joachim, and Fortes, Ana M.
- Abstract
© The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. Vitis vinifera berries are sensitive towards infection by the necrotrophic pathogen Botrytis cinerea, leading to important economic losses worldwide. The combined analysis of the transcriptome and metabolome associated with fungal infection has not been performed previously in grapes or in another fleshy fruit. In an attempt to identify the molecular and metabolic mechanisms associated with the infection, peppercorn-sized fruits were infected in the field. Green and veraison berries were collected following infection for microarray analysis complemented with metabolic profiling of primary and other soluble metabolites and of volatile emissions. The results provided evidence of a reprogramming of carbohydrate and lipid metabolisms towards increased synthesis of secondary metabolites involved in plant defence, such as trans-resveratrol and gallic acid. This response was already activated in infected green berries with the putative involvement of jasmonic acid, ethylene, polyamines, and auxins, whereas salicylic acid did not seem to be involved. Genes encoding WRKY transcription factors, pathogenesis-related proteins, glutathione S-transferase, stilbene synthase, and phenylalanine ammonia-lyase were upregulated in infected berries. However, salicylic acid signalling was activated in healthy ripening berries along with the expression of proteins of the NBS-LRR superfamily and protein kinases, suggesting that the pathogen is able to shut down defences existing in healthy ripening berries. Furthermore, this study provided metabolic biomarkers of infection such as azelaic acid, a substance known to prime plant defence responses, arabitol, ribitol, 4-amino butanoic acid, 1-O-methyl- glucopyranoside, and several fatty acids that alone or in combination can be used to monitor Botrytis infection early in the vineyard.
- Published
- 2015
47. Complex Interplay of Hormonal Signals during Grape Berry Ripening
- Author
-
Fortes, Ana, primary, Teixeira, Rita, additional, and Agudelo-Romero, Patricia, additional
- Published
- 2015
- Full Text
- View/download PDF
48. Evolución experimental de la gama de huéspedes del Virus del grabado del tabaco (TEV)
- Author
-
Agudelo-Romero, Patricia and Elena, Santiago F.
- Subjects
Tabaco ,Virus - Abstract
xxi+97 pp., En la actualidad, la aparición o emergencia de nuevos virus de plantas representa una amenaza directa para la agricultura. La incidencia de nuevos virus de plantas aumenta debido a cambios en el medio ambiente y a malas prácticas agrícolas. Por esto, es importante determinar los factores genéticos y evolutivos implicados en la aparición de estos nuevos virus. Los virus de RNA son excelentes modelos experimentales para el estudio de procesos evolutivos en escalas temporales imposibles con otros organismos modelos pluricelulares. Esta rápida evolución es consecuencia de sus genomas compactos, elevadas tasas de mutación, rápidas tasas de replicación y enormes tamaños poblacionales que, en conjunto, generan poblaciones tremendamente polimórficas. Esta enorme variabilidad es clave para entender la patogenicidad en sus huéspedes. Trabajar con virus de plantas permite el uso de huéspedes reales sin las incomodidades de manejo ni las implicaciones éticas propias de los virus de animales. Aprovechando las ventajas que nos ofrece el estudio de la evolución experimental con virus de RNA de plantas, en este trabajo perseguimos adquirir conocimientos básicos sobre la evolución de la interacción virus-huésped, y qué factores condicionan la gama de nuevos huéspedes de un virus, lo cual puede determinar potencialmente el fenómeno de emergencia viral. El objetivo fundamental de esta Tesis es simular un proceso de emergencia viral. En general, los virus de plantas muestran una alta variabilidad en sus gamas de huéspedes: mientras algunos infectan sólo una o pocas especies afines (especialistas), otros pueden infectar un amplio rango e incluso especies pertenecientes a grupos taxonómicos diferentes (generalistas). En un primer conjunto de experimentos exploraremos el coste que en términos de eficacia viral supone la ampliación de la gama de huéspedes del Potyvirus del grabado del tabaco (TEV). Estos estudios los realizaremos a dos niveles. En primer lugar empleando huéspedes pertenecientes a la misma familia taxonómica (tabaco y pimiento). En segundo lugar, en huéspedes pertenecientes a familias taxonómicas muy alejadas (tabaco y arabidopsis). Estos experimentos muestran que la adaptación a un nuevo huésped tiene un efecto pleiotrópico antagonista en el huésped original. Estos resultados nos permiten concluir que ampliar la gama de huéspedes implica un coste en términos de eficacia promedio, de manera que la eficacia viral no se maximiza para cada huésped sino que existe un compromiso. En un segundo conjunto de experimentos, hemos pretendido explorar si la adaptación del virus a arabidopsis conlleva cambios en el tipo de interacciones que éste establece con la, planta a nivel del transcriptoma. Más concretamente, las preguntas que perseguimos responder son dos: (1) ¿Qué cambios se observan en el patrón de expresión génica en el huésped tras la infección con un virus emergente, en este caso TEV? (2) Una vez identificados los genes o rutas metabólicas afectadas por un genotipo de TEV no adaptado a arabidopsis, es el momento de preguntarse si esta red de interacciones cambia a medida que el virus se adapta a su nuevo huésped. Para desarrollar este trabajo utilizamos micromatrices de cDNA de alta densidad (26173 genes y 87 microRNAs), que nos permiten monitorizar cientos de genes al mismo tiempo de manera adecuada y eficiente. Hemos identificado un conjunto de genes de la planta cuya expresión se ve alterada por la infección con TEV, muchos de ellos implicados en respuesta a estreses bióticos y abióticos. Este conjunto de genes cambió a medida que el virus se adaptó a su nuevo huésped aumentando su eficacia y virulencia, observándose que muchos genes de respuesta a estrés biótico dejaron de ser activados tras la infección. Estos cambios tan acusados fueron consecuencia de un número limitado de mutaciones en el genoma de TEV. De hecho, un solo cambio en una proteína clave del virus era el responsable de los nuevos síntomas en la planta. Por último, hemos querido comprobar si la adaptación de TEV al ecotipo de arabidopsis elegido para los experimentos arriba descritos (Ler-0) implica también un aumento de su eficacia y virulencia en otros ecotipos. Dicho de otra manera, si la adaptación viral es específica de un genotipo del huésped o si, por el contrario, facilita el acceso del virus a otros genotipos. Existe un buen número de grados de susceptibilidad a TEV en arabidopsis. Trabajos previos del grupo del Prof. J. C. Carrington mostraron que esta variabilidad es consecuencia del alelo dominante presente en un locus llamado RTM1 (restricción del movimiento de TEV 1). Hemos evaluado 9 ecotipos diferentes de arabidopsis con diferentes niveles de susceptibilidad a TEV. Hemos observado que el virus adaptado a Ler-0 era capaz de infectar y generar síntomas en ecotipos que eran resistentes a la infección con el TEV ancestral. Estos resultados sugieren que poseer el alelo de resistencia en el locus RTM1 no es condición suficiente para que la planta sea resistente a TEV., Esta tesis doctoral ha sido realizada con la financiación de los proyectos: (1) BMC2003-00066 “Evolución experimental de plantas: Caracterización de efectos mutacionales e implicaciones evolutivas de la segmentación genómica” (2003 – 2006). (2) BFU2006-14819-C02-01/BMC “Evolución experimental de virus vegetales: mutaciones deletéreas, mecanismos de robustez genómica y evolución de la interacción con los mecanismos de defensa de la planta” (2006 – 2009). Concedidos por el Ministerio de Ciencia y Tecnología (MEC). La realización de esta tesis también ha sido financiada gracias a la concesión de una beca predoctoral de Formación de Personal Investigador (FPI) BMC2003-00066 del Ministerio de Educación y Ciencia (2004-2008).
- Published
- 2009
49. Perturbation of polyamine catabolism affects grape ripening of Vitis vinifera cv. Trincadeira
- Author
-
Agudelo-Romero, Patricia, primary, Ali, Kashif, additional, Choi, Young H., additional, Sousa, Lisete, additional, Verpoorte, Rob, additional, Tiburcio, Antonio F., additional, and Fortes, Ana M., additional
- Published
- 2014
- Full Text
- View/download PDF
50. Transcript and metabolite analysis in Trincadeira cultivar reveals novel information regarding the dynamics of grape ripening
- Author
-
Institut National de la Recherche Agronomique (France), Fortes, Ana M., Agudelo-Romero, Patricia, Silva, Marta S., Ali, Kashif, Sousa, Lisete, Maltese, Federica, Choi, Young H., Grimplet, Jérôme, Martínez-Zapater, José M., Verpoorte, Robert, Pais, María Salomé, Institut National de la Recherche Agronomique (France), Fortes, Ana M., Agudelo-Romero, Patricia, Silva, Marta S., Ali, Kashif, Sousa, Lisete, Maltese, Federica, Choi, Young H., Grimplet, Jérôme, Martínez-Zapater, José M., Verpoorte, Robert, and Pais, María Salomé
- Abstract
Background Grapes (Vitis vinifera L.) are economically the most important fruit crop worldwide. However, the complexity of molecular and biochemical events that lead to the onset of ripening of nonclimacteric fruits is not fully understood which is further complicated in grapes due to seasonal and cultivar specific variation. The Portuguese wine variety Trincadeira gives rise to high quality wines but presents extremely irregular berry ripening among seasons probably due to high susceptibility to abiotic and biotic stresses. Results Ripening of Trincadeira grapes was studied taking into account the transcriptional and metabolic profilings complemented with biochemical data. The mRNA expression profiles of four time points spanning developmental stages from pea size green berries, through véraison and mature berries (EL 32, EL 34, EL 35 and EL 36) and in two seasons (2007 and 2008) were compared using the Affymetrix GrapeGen® genome array containing 23096 probesets corresponding to 18726 unique sequences. Over 50% of these probesets were significantly differentially expressed (1.5 fold) between at least two developmental stages. A common set of modulated transcripts corresponding to 5877 unigenes indicates the activation of common pathways between years despite the irregular development of Trincadeira grapes. These unigenes were assigned to the functional categories of "metabolism", "development", "cellular process", "diverse/miscellanenous functions", "regulation overview", "response to stimulus, stress", "signaling", "transport overview", "xenoprotein, transposable element" and "unknown". Quantitative RT-PCR validated microarrays results being carried out for eight selected genes and five developmental stages (EL 32, EL 34, EL 35, EL 36 and EL 38). Metabolic profiling using 1H NMR spectroscopy associated to two-dimensional techniques showed the importance of metabolites related to oxidative stress response, amino acid and sugar metabolism as well as second
- Published
- 2011
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.