1
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Oróstica KY, Saez-Hidalgo J, de Santiago PR, Rivas S, Contreras S, Navarro G, Asenjo JA, Olivera-Nappa Á, Armisén R. Total mutational load and clinical features as predictors of the metastatic status in lung adenocarcinoma and squamous cell carcinoma patients. Lab Invest 2022; 20:373. [PMID: 35982500 PMCID: PMC9389677 DOI: 10.1186/s12967-022-03572-8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 08/04/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Recently, extensive cancer genomic studies have revealed mutational and clinical data of large cohorts of cancer patients. For example, the Pan-Lung Cancer 2016 dataset (part of The Cancer Genome Atlas project), summarises the mutational and clinical profiles of different subtypes of Lung Cancer (LC). Mutational and clinical signatures have been used independently for tumour typification and prediction of metastasis in LC patients. Is it then possible to achieve better typifications and predictions when combining both data streams? METHODS In a cohort of 1144 Lung Adenocarcinoma (LUAD) and Lung Squamous Cell Carcinoma (LSCC) patients, we studied the number of missense mutations (hereafter, the Total Mutational Load TML) and distribution of clinical variables, for different classes of patients. Using the TML and different sets of clinical variables (tumour stage, age, sex, smoking status, and packs of cigarettes smoked per year), we built Random Forest classification models that calculate the likelihood of developing metastasis. RESULTS We found that LC patients different in age, smoking status, and tumour type had significantly different mean TMLs. Although TML was an informative feature, its effect was secondary to the "tumour stage" feature. However, its contribution to the classification is not redundant with the latter; models trained using both TML and tumour stage performed better than models trained using only one of these variables. We found that models trained in the entire dataset (i.e., without using dimensionality reduction techniques) and without resampling achieved the highest performance, with an F1 score of 0.64 (95%CrI [0.62, 0.66]). CONCLUSIONS Clinical variables and TML should be considered together when assessing the likelihood of LC patients progressing to metastatic states, as the information these encode is not redundant. Altogether, we provide new evidence of the need for comprehensive diagnostic tools for metastasis.
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Affiliation(s)
- Karen Y Oróstica
- Instituto de Investigación Interdisciplinaria, Vicerrectoría Académica, Universidad de Talca, 3460000, Talca, Chile
| | - Juan Saez-Hidalgo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, 8370456, Santiago, Chile.,Department of Computer Science, University of Chile, 8370459, Santiago, Chile
| | - Pamela R de Santiago
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Solange Rivas
- Department of Basic Clinical Oncology, Faculty of Medicine, University of Chile, Santiago, Chile.,Centro de Genética Y Genómica, Instituto de Ciencias E Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, 7590943, Santiago, Chile
| | - Sebastian Contreras
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, 8370456, Santiago, Chile.,Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - Gonzalo Navarro
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, 8370456, Santiago, Chile.,Department of Computer Science, University of Chile, 8370459, Santiago, Chile
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, 8370456, Santiago, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, 8370456, Santiago, Chile.
| | - Ricardo Armisén
- Centro de Genética Y Genómica, Instituto de Ciencias E Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, 7590943, Santiago, Chile.
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2
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Medina-Ortiz D, Contreras S, Amado-Hinojosa J, Torres-Almonacid J, Asenjo JA, Navarrete M, Olivera-Nappa Á. Generalized Property-Based Encoders and Digital Signal Processing Facilitate Predictive Tasks in Protein Engineering. Front Mol Biosci 2022; 9:898627. [PMID: 35911960 PMCID: PMC9329607 DOI: 10.3389/fmolb.2022.898627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Computational methods in protein engineering often require encoding amino acid sequences, i.e., converting them into numeric arrays. Physicochemical properties are a typical choice to define encoders, where we replace each amino acid by its value for a given property. However, what property (or group thereof) is best for a given predictive task remains an open problem. In this work, we generalize property-based encoding strategies to maximize the performance of predictive models in protein engineering. First, combining text mining and unsupervised learning, we partitioned the AAIndex database into eight semantically-consistent groups of properties. We then applied a non-linear PCA within each group to define a single encoder to represent it. Then, in several case studies, we assess the performance of predictive models for protein and peptide function, folding, and biological activity, trained using the proposed encoders and classical methods (One Hot Encoder and TAPE embeddings). Models trained on datasets encoded with our encoders and converted to signals through the Fast Fourier Transform (FFT) increased their precision and reduced their overfitting substantially, outperforming classical approaches in most cases. Finally, we propose a preliminary methodology to create de novo sequences with desired properties. All these results offer simple ways to increase the performance of general and complex predictive tasks in protein engineering without increasing their complexity.
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Affiliation(s)
- David Medina-Ortiz
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas, Chile
| | - Sebastian Contreras
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- *Correspondence: Sebastian Contreras, ; Álvaro Olivera-Nappa,
| | - Juan Amado-Hinojosa
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Jorge Torres-Almonacid
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas, Chile
| | - Juan A. Asenjo
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | | | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
- *Correspondence: Sebastian Contreras, ; Álvaro Olivera-Nappa,
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3
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Oróstica KY, Contreras S, Sanchez-Daza A, Fernandez J, Priesemann V, Olivera-Nappa Á. New year, new SARS-CoV-2 variant: Resolutions on genomic surveillance protocols to face Omicron. The Lancet Regional Health - Americas 2022; 7:100203. [PMID: 35187522 PMCID: PMC8837806 DOI: 10.1016/j.lana.2022.100203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Karen Y. Oróstica
- Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile
| | - Sebastian Contreras
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, Göttingen DE-37077, Germany
- Corresponding author.
| | | | - Jorge Fernandez
- Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile
| | - Viola Priesemann
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, Göttingen DE-37077, Germany
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4
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Olivera-Nappa Á, Contreras S, Tevy MF, Medina-Ortiz D, Leschot A, Vigil P, Conca C. Patient-Wise Methodology to Assess Glycemic Health Status: Applications to Quantify the Efficacy and Physiological Targets of Polyphenols on Glycemic Control. Front Nutr 2022; 9:831696. [PMID: 35252308 PMCID: PMC8892255 DOI: 10.3389/fnut.2022.831696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
A growing body of evidence indicates that dietary polyphenols could be used as an early intervention to treat glucose-insulin (G-I) dysregulation. However, studies report heterogeneous information, and the targets of the intervention remain largely elusive. In this work, we provide a general methodology to quantify the effects of any given polyphenol-rich food or formulae over glycemic regulation in a patient-wise manner using an Oral Glucose Tolerance Test (OGTT). We use a mathematical model to represent individual OGTT curves as the coordinated action of subsystems, each one described by a parameter with physiological interpretation. Using the parameter values calculated for a cohort of 1198 individuals, we propose a statistical model to calculate the risk of dysglycemia and the coordination among subsystems for each subject, thus providing a continuous and individual health assessment. This method allows identifying individuals at high risk of dysglycemia—which would have been missed with traditional binary diagnostic methods—enabling early nutritional intervention with a polyphenol-supplemented diet where it is most effective and desirable. Besides, the proposed methodology assesses the effectiveness of interventions over time when applied to the OGTT curves of a treated individual. We illustrate the use of this method in a case study to assess the dose-dependent effects of Delphinol® on reducing dysglycemia risk and improving the coordination between subsystems. Finally, this strategy enables, on the one hand, the use of low-cost, non-invasive methods in population-scale nutritional studies. On the other hand, it will help practitioners assess the effectiveness of an intervention based on individual vulnerabilities and adapt the treatment to manage dysglycemia and avoid its progression into disease.
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Affiliation(s)
- Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Santiago, Chile
- Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Santiago, Chile
- *Correspondence: Álvaro Olivera-Nappa
| | - Sebastian Contreras
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Sebastian Contreras
| | - María Florencia Tevy
- Laboratory of Cell Biology, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - David Medina-Ortiz
- Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Santiago, Chile
- Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Santiago, Chile
| | | | - Pilar Vigil
- Reproductive Health Research Institute, Santiago, Chile
| | - Carlos Conca
- Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Santiago, Chile
- Center for Mathematical Modelling (CMM), University of Chile, Santiago, Chile
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5
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Contreras S, Olivera-Nappa Á, Priesemann V. Rethinking COVID-19 vaccine allocation: it is time to care about our neighbours. Lancet Reg Health Eur 2022; 12:100277. [PMID: 34870258 PMCID: PMC8633795 DOI: 10.1016/j.lanepe.2021.100277] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sebastian Contreras
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering (CeBiB), Dpt. of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Viola Priesemann
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
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6
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Quiroz C, Saavedra YB, Armijo-Galdames B, Amado-Hinojosa J, Olivera-Nappa Á, Sanchez-Daza A, Medina-Ortiz D. Peptipedia: a user-friendly web application and a comprehensive database for peptide research supported by Machine Learning approach. Database (Oxford) 2021; 2021:6363751. [PMID: 34478499 PMCID: PMC8415426 DOI: 10.1093/database/baab055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/30/2021] [Accepted: 08/11/2021] [Indexed: 12/12/2022]
Abstract
Peptides have attracted attention during the last decades due to their extraordinary therapeutic properties. Different computational tools have been developed to take advantage of existing information, compiling knowledge and making available the information for common users. Nevertheless, most related tools available are not user-friendly, present redundant information, do not clearly display the data, and usually are specific for particular biological activities, not existing so far, an integrated database with consolidated information to help research peptide sequences. To solve these necessities, we developed Peptipedia, a user-friendly web application and comprehensive database to search, characterize and analyse peptide sequences. Our tool integrates the information from 30 previously reported databases with a total of 92 055 amino acid sequences, making it the biggest repository of peptides with recorded activities to date. Furthermore, we make available a variety of bioinformatics services and statistical modules to increase our tool’s usability. Moreover, we incorporated a robust assembled binary classification system to predict putative biological activities for peptide sequences. Our tools’ significant differences with other existing alternatives become a substantial contribution for developing biotechnological and bioengineering applications for peptides. Peptipedia is available for non-commercial use as an open-access software, licensed under the GNU General Public License, version GPL 3.0. The web platform is publicly available at peptipedia.cl. Database URL: Both the source code and sample data sets are available in the GitHub repository https://github.com/ProteinEngineering-PESB2/peptipedia
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Affiliation(s)
- Cristofer Quiroz
- Facultad de Ingeniería, Universidad Autonóma de Chile, Cinco Pte. 1670, Talca 3467987, Chile
| | - Yasna Barrera Saavedra
- Escuela de Ingeniería en Bioinformática, Universidad de Talca, Avenida Lircay SN, Talca 3460000, Chile
| | - Benjamín Armijo-Galdames
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile.,Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
| | - Juan Amado-Hinojosa
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile.,Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile.,Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
| | - Anamaria Sanchez-Daza
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile.,Institute for Cell Dynamics and Biotechnology, Beauchef 851, Santiago 8370456, Chile
| | - David Medina-Ortiz
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile.,Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
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7
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Freire-Flores D, Llanovarced-Kawles N, Sanchez-Daza A, Olivera-Nappa Á. On the heterogeneous spread of COVID-19 in Chile. Chaos Solitons Fractals 2021; 150:111156. [PMID: 34149204 PMCID: PMC8196305 DOI: 10.1016/j.chaos.2021.111156] [Citation(s) in RCA: 3] [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: 12/03/2020] [Revised: 05/19/2021] [Accepted: 06/07/2021] [Indexed: 05/22/2023]
Abstract
Non-pharmaceutical interventions (NPIs) have played a crucial role in controlling the spread of COVID-19. Nevertheless, NPI efficacy varies enormously between and within countries, mainly because of population and behavioral heterogeneity. In this work, we adapted a multi-group SEIRA model to study the spreading dynamics of COVID-19 in Chile, representing geographically separated regions of the country by different groups. We use national mobilization statistics to estimate the connectivity between regions and data from governmental repositories to obtain COVID-19 spreading and death rates in each region. We then assessed the effectiveness of different NPIs by studying the temporal evolution of the reproduction number R t . Analysing data-driven and model-based estimates of R t , we found a strong coupling of different regions, highlighting the necessity of organized and coordinated actions to control the spread of SARS-CoV-2. Finally, we evaluated different scenarios to forecast the evolution of COVID-19 in the most densely populated regions, finding that the early lifting of restriction probably will lead to novel outbreaks.
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Affiliation(s)
- Danton Freire-Flores
- Department of Chemical Engineering, Biotechnology, and Materials, Universidad de Chile, Beauchef 851, 8370448 Santiago, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, 8370448 Santiago, Chile
| | - Nyna Llanovarced-Kawles
- Department of Chemical Engineering, Biotechnology, and Materials, Universidad de Chile, Beauchef 851, 8370448 Santiago, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, 8370448 Santiago, Chile
| | - Anamaria Sanchez-Daza
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, 8370448 Santiago, Chile
- Institute for Cell Dynamics and Biotechnology, Beauchef 851, 8370456, Santiago, Chile
| | - Álvaro Olivera-Nappa
- Department of Chemical Engineering, Biotechnology, and Materials, Universidad de Chile, Beauchef 851, 8370448 Santiago, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, 8370448 Santiago, Chile
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8
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Saez Hidalgo J, Oróstica KY, Sanchez-Daza A, Olivera-Nappa Á. BEST: a Shiny/R web-based application to easily retrieve cross-related enzyme functional parameters and information from BRENDA. Bioinformatics 2021; 37:1480-1481. [PMID: 32997753 DOI: 10.1093/bioinformatics/btaa848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/03/2020] [Accepted: 09/17/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION BRENDA is the largest enzyme functional database, containing information of 84 000 experimentally characterized enzyme entries. This database is an invaluable resource for researchers in the biological field, which classifies enzyme-related information in categories that are very useful to obtain specific functional and protein engineering information for enzyme families. However, the BRENDA web interface, the most used by researchers with a non-informatic background, does not allow the user to cross-reference data from different categories or sub-categories in the database. Obtaining information in an easy and fast way, in a friendly web interface, without the necessity to have a deep informatics knowledge, will facilitate and improve research in the enzymology and protein engineering field. RESULTS We developed the Brenda Easy Search Tool (BEST), an interactive Shiny/R application that enables querying the BRENDA database for complex cross-tabulated characteristics, and retrieving enzyme-related parameters and information readily and efficiently, which can be used for the study of enzyme function or as an input for other bioinformatics tools. AVAILABILITY AND IMPLEMENTATION BEST and its tutorial are freely available from https://pesb2.cl/best/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Juan Saez Hidalgo
- Centre for Biotechnology and Bioengineering - CeBiB, Department of Chemical Engineering, Biotechnology and Materials, University of Chile, 8370456 Santiago, Chile.,Department of Computer Science, University of Chile, 8370459 Santiago, Chile
| | - Karen Y Oróstica
- Centre for Biotechnology and Bioengineering - CeBiB, Department of Chemical Engineering, Biotechnology and Materials, University of Chile, 8370456 Santiago, Chile
| | - Anamaria Sanchez-Daza
- Centre for Biotechnology and Bioengineering - CeBiB, Department of Chemical Engineering, Biotechnology and Materials, University of Chile, 8370456 Santiago, Chile.,Faculty of Physical and Mathematical Sciences, University of Chile, Institute for Cell Dynamics and Biotechnology (ICDB), 8370450 Santiago, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering - CeBiB, Department of Chemical Engineering, Biotechnology and Materials, University of Chile, 8370456 Santiago, Chile
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9
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González-Puelma J, Aldridge J, Montes de Oca M, Pinto M, Uribe-Paredes R, Fernández-Goycoolea J, Alvarez-Saravia D, Álvarez H, Encina G, Weitzel T, Muñoz R, Olivera-Nappa Á, Pantano S, Navarrete MA. Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Viruses 2021; 13:883. [PMID: 34064904 PMCID: PMC8151058 DOI: 10.3390/v13050883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 03/26/2021] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
The emergence of SARS-CoV-2 variants, as observed with the D614G spike protein mutant and, more recently, with B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1) lineages, represent a continuous threat and might lead to strains of higher infectivity and/or virulence. We report on the occurrence of a SARS-CoV-2 haplotype with nine mutations including D614G/T307I double-mutation of the spike. This variant expanded and completely replaced previous lineages within a short period in the subantarctic Magallanes Region, southern Chile. The rapid lineage shift was accompanied by a significant increase of cases, resulting in one of the highest incidence rates worldwide. Comparative coarse-grained molecular dynamic simulations indicated that T307I and D614G belong to a previously unrecognized dynamic domain, interfering with the mobility of the receptor binding domain of the spike. The T307I mutation showed a synergistic effect with the D614G. Continuous surveillance of new mutations and molecular analyses of such variations are important tools to understand the molecular mechanisms defining infectivity and virulence of current and future SARS-CoV-2 strains.
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Affiliation(s)
- Jorge González-Puelma
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
| | - Jacqueline Aldridge
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.A.); (M.M.d.O.); (R.U.-P.)
| | - Marco Montes de Oca
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.A.); (M.M.d.O.); (R.U.-P.)
| | - Mónica Pinto
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Enfermedades Infecciosas, Hospital Clínico de Magallanes, Punta Arenas 6210005, Chile
| | - Roberto Uribe-Paredes
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.A.); (M.M.d.O.); (R.U.-P.)
| | | | - Diego Alvarez-Saravia
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
| | - Hermy Álvarez
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
| | - Gonzalo Encina
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610658, Chile;
| | - Thomas Weitzel
- Laboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610658, Chile;
- Instituto de Ciencias e Innovación en Medicina (ICIM), Universidad del Desarrollo, Santiago 7610658, Chile
| | - Rodrigo Muñoz
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Enfermedades Infecciosas, Hospital Clínico de Magallanes, Punta Arenas 6210005, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago 8370456, Chile;
- Facultad de Ciencias, Físicas y Matemáticas, Universidad de Chile, Santiago 8370456, Chile
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Marcelo A. Navarrete
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
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10
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Contreras S, Villavicencio HA, Medina-Ortiz D, Saavedra CP, Olivera-Nappa Á. Real-Time Estimation of R t for Supporting Public-Health Policies Against COVID-19. Front Public Health 2020; 8:556689. [PMID: 33415091 PMCID: PMC7783316 DOI: 10.3389/fpubh.2020.556689] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 11/30/2020] [Indexed: 11/17/2022] Open
Abstract
In the absence of a consensus protocol to slow down the spread of SARS-CoV-2, policymakers need real-time indicators to support decisions in public health matters. The Effective Reproduction Number (R t ) represents the number of secondary infections generated per each case and can be dramatically modified by applying effective interventions. However, current methodologies to calculate R t from data remain somewhat cumbersome, thus raising a barrier between its timely calculation and application by policymakers. In this work, we provide a simple mathematical formulation for obtaining the effective reproduction number in real-time using only and directly daily official case reports, obtained by modifying the equations describing the viral spread. We numerically explore the accuracy and limitations of the proposed methodology, which was demonstrated to provide accurate, timely, and intuitive results. We illustrate the use of our methodology to study the evolution of the pandemic in different iconic countries, and to assess the efficacy and promptness of different public health interventions.
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Affiliation(s)
- Sebastián Contreras
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
| | | | - David Medina-Ortiz
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Claudia P. Saavedra
- Laboratorio de Microbiologia Molecular, Departamento de Ciencias de la Vida, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
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11
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Contreras S, Biron-Lattes JP, Villavicencio HA, Medina-Ortiz D, Llanovarced-Kawles N, Olivera-Nappa Á. Statistically-based methodology for revealing real contagion trends and correcting delay-induced errors in the assessment of COVID-19 pandemic. Chaos Solitons Fractals 2020; 139:110087. [PMID: 32834623 PMCID: PMC7341964 DOI: 10.1016/j.chaos.2020.110087] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/19/2020] [Accepted: 07/02/2020] [Indexed: 05/14/2023]
Abstract
COVID-19 pandemic has reshaped our world in a timescale much shorter than what we can understand. Particularities of SARS-CoV-2, such as its persistence in surfaces and the lack of a curative treatment or vaccine against COVID-19, have pushed authorities to apply restrictive policies to control its spreading. As data drove most of the decisions made in this global contingency, their quality is a critical variable for decision-making actors, and therefore should be carefully curated. In this work, we analyze the sources of error in typically reported epidemiological variables and usual tests used for diagnosis, and their impact on our understanding of COVID-19 spreading dynamics. We address the existence of different delays in the report of new cases, induced by the incubation time of the virus and testing-diagnosis time gaps, and other error sources related to the sensitivity/specificity of the tests used to diagnose COVID-19. Using a statistically-based algorithm, we perform a temporal reclassification of cases to avoid delay-induced errors, building up new epidemiologic curves centered in the day where the contagion effectively occurred. We also statistically enhance the robustness behind the discharge/recovery clinical criteria in the absence of a direct test, which is typically the case of non-first world countries, where the limited testing capabilities are fully dedicated to the evaluation of new cases. Finally, we applied our methodology to assess the evolution of the pandemic in Chile through the Effective Reproduction Number Rt , identifying different moments in which data was misleading governmental actions. In doing so, we aim to raise public awareness of the need for proper data reporting and processing protocols for epidemiological modelling and predictions.
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Affiliation(s)
- Sebastián Contreras
- Laboratory for Rheology and Fluid Dynamics, Universidad de Chile, Beauchef 850, Santiago 8370448, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
| | - Juan Pablo Biron-Lattes
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
- Department of Chemical Engineering, Biotechnology, and Materials, Universidad de Chile, Beauchef 851, Santiago,8370448 Chile
| | - H Andrés Villavicencio
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
| | - David Medina-Ortiz
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nyna Llanovarced-Kawles
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
- Department of Chemical Engineering, Biotechnology, and Materials, Universidad de Chile, Beauchef 851, Santiago,8370448 Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
- Department of Chemical Engineering, Biotechnology, and Materials, Universidad de Chile, Beauchef 851, Santiago,8370448 Chile
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12
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Contreras S, Villavicencio HA, Medina-Ortiz D, Biron-Lattes JP, Olivera-Nappa Á. A multi-group SEIRA model for the spread of COVID-19 among heterogeneous populations. Chaos Solitons Fractals 2020; 136:109925. [PMID: 32501373 PMCID: PMC7247502 DOI: 10.1016/j.chaos.2020.109925] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/20/2020] [Indexed: 05/03/2023]
Abstract
The outbreak and propagation of COVID-19 have posed a considerable challenge to modern society. In particular, the different restrictive actions taken by governments to prevent the spread of the virus have changed the way humans interact and conceive interaction. Due to geographical, behavioral, or economic factors, different sub-groups among a population are more (or less) likely to interact, and thus to spread/acquire the virus. In this work, we present a general multi-group SEIRA model for representing the spread of COVID-19 among a heterogeneous population and test it in a numerical case of study. By highlighting its applicability and the ease with which its general formulation can be adapted to particular studies, we expect our model to lead us to a better understanding of the evolution of this pandemic and to better public-health policies to control it.
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Affiliation(s)
- Sebastián Contreras
- Laboratory for Rheology and Fluid Dynamics, Universidad de Chile, Beauchef 850, Santiago 8370448, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
| | - H Andrés Villavicencio
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
| | - David Medina-Ortiz
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Juan Pablo Biron-Lattes
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
- Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
- Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago 8370448, Chile
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13
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Contreras S, Medina-Ortiz D, Conca C, Olivera-Nappa Á. A Novel Synthetic Model of the Glucose-Insulin System for Patient-Wise Inference of Physiological Parameters From Small-Size OGTT Data. Front Bioeng Biotechnol 2020; 8:195. [PMID: 32232039 PMCID: PMC7083079 DOI: 10.3389/fbioe.2020.00195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/27/2020] [Indexed: 01/31/2023] Open
Abstract
Existing mathematical models for the glucose-insulin (G-I) dynamics often involve variables that are not susceptible to direct measurement. Standard clinical tests for measuring G-I levels for diagnosing potential diseases are simple and relatively cheap, but seldom give enough information to allow the identification of model parameters within the range in which they have a biological meaning, thus generating a gap between mathematical modeling and any possible physiological explanation or clinical interpretation. In the present work, we present a synthetic mathematical model to represent the G-I dynamics in an Oral Glucose Tolerance Test (OGTT), which involves for the first time for OGTT-related models, Delay Differential Equations. Our model can represent the radically different behaviors observed in a studied cohort of 407 normoglycemic patients (the largest analyzed so far in parameter fitting experiments), all masked under the current threshold-based normality criteria. We also propose a novel approach to solve the parameter fitting inverse problem, involving the clustering of different G-I profiles, a simulation-based exploration of the feasible set, and the construction of an information function which reshapes it, based on the clinical records, experimental uncertainties, and physiological criteria. This method allowed an individual-wise recognition of the parameters of our model using small size OGTT data (5 measurements) directly, without modifying the routine procedures or requiring particular clinical setups. Therefore, our methodology can be easily applied to gain parametric insights to complement the existing tools for the diagnosis of G-I dysregulations. We tested the parameter stability and sensitivity for individual subjects, and an empirical relationship between such indexes and curve shapes was spotted. Since different G-I profiles, under the light of our model, are related to different physiological mechanisms, the present method offers a tool for personally-oriented diagnosis and treatment and to better define new health criteria.
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Affiliation(s)
- Sebastián Contreras
- Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Santiago, Chile
| | - David Medina-Ortiz
- Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Santiago, Chile.,Department of Chemical Engineering, Biotechnology and Materials, Faculty of Physical and Mathematical Sciences, University of Chile, Santiago, Chile
| | - Carlos Conca
- Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Santiago, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Santiago, Chile.,Department of Chemical Engineering, Biotechnology and Materials, Faculty of Physical and Mathematical Sciences, University of Chile, Santiago, Chile
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14
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Medina-Ortiz D, Contreras S, Quiroz C, Olivera-Nappa Á. Development of Supervised Learning Predictive Models for Highly Non-linear Biological, Biomedical, and General Datasets. Front Mol Biosci 2020; 7:13. [PMID: 32118039 PMCID: PMC7031350 DOI: 10.3389/fmolb.2020.00013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/22/2020] [Indexed: 11/13/2022] Open
Abstract
In highly non-linear datasets, attributes or features do not allow readily finding visual patterns for identifying common underlying behaviors. Therefore, it is not possible to achieve classification or regression using linear or mildly non-linear hyperspace partition functions. Hence, supervised learning models based on the application of most existing algorithms are limited, and their performance metrics are low. Linear transformations of variables, such as principal components analysis, cannot avoid the problem, and even models based on artificial neural networks and deep learning are unable to improve the metrics. Sometimes, even when features allow classification or regression in reported cases, performance metrics of supervised learning algorithms remain unsatisfyingly low. This problem is recurrent in many areas of study as, per example, the clinical, biotechnological, and protein engineering areas, where many of the attributes are correlated in an unknown and very non-linear fashion or are categorical and difficult to relate to a target response variable. In such areas, being able to create predictive models would dramatically impact the quality of their outcomes, generating an immediate added value for both the scientific and general public. In this manuscript, we present RV-Clustering, a library of unsupervised learning algorithms, and a new methodology designed to find optimum partitions within highly non-linear datasets that allow deconvoluting variables and notoriously improving performance metrics in supervised learning classification or regression models. The partitions obtained are statistically cross-validated, ensuring correct representativity and no over-fitting. We have successfully tested RV-Clustering in several highly non-linear datasets with different origins. The approach herein proposed has generated classification and regression models with high-performance metrics, which further supports its ability to generate predictive models for highly non-linear datasets. Advantageously, the method does not require significant human input, which guarantees a higher usability in the biological, biomedical, and protein engineering community with no specific knowledge in the machine learning area.
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Affiliation(s)
- David Medina-Ortiz
- Departamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile.,Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
| | - Sebastián Contreras
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
| | - Cristofer Quiroz
- Facultad de Ingeniería, Universidad Autónoma de Chile, Talca, Chile
| | - Álvaro Olivera-Nappa
- Departamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile.,Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
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15
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Jiménez NE, Gerdtzen ZP, Olivera-Nappa Á, Salgado JC, Conca C. A systems biology approach for studying Wolbachia metabolism reveals points of interaction with its host in the context of arboviral infection. PLoS Negl Trop Dis 2019; 13:e0007678. [PMID: 31469838 PMCID: PMC6742412 DOI: 10.1371/journal.pntd.0007678] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 09/12/2019] [Accepted: 07/31/2019] [Indexed: 01/08/2023] Open
Abstract
Wolbachia are alpha-proteobacteria known to infect arthropods, which are of interest for disease control since they have been associated with improved resistance to viral infection. Although several genomes for different strains have been sequenced, there is little knowledge regarding the relationship between this bacterium and their hosts, particularly on their dependency for survival. Motivated by the potential applications on disease control, we developed genome-scale models of four Wolbachia strains known to infect arthropods: wAlbB (Aedes albopictus), wVitA (Nasonia vitripennis), wMel and wMelPop (Drosophila melanogaster). The obtained metabolic reconstructions exhibit a metabolism relying mainly on amino acids for energy production and biomass synthesis. A gap analysis was performed to detect metabolic candidates which could explain the endosymbiotic nature of this bacterium, finding that amino acids, requirements for ubiquinone precursors and provisioning of metabolites such as riboflavin could play a crucial role in this relationship. This work provides a systems biology perspective for studying the relationship of Wolbachia with its host and the development of new approaches for control of the spread of arboviral diseases. This approach, where metabolic gaps are key objects of study instead of just additions to complete a model, could be applied to other endosymbiotic bacteria of interest. The expansion of the geographic distribution of arthropods has led to an increase in the number of infections of Zika and Dengue. This motivates the search for new alternative approaches for disease control. Wolbachia pipientis, an obligate intracellular bacteria known to provide pathogen-blocking capabilities to its host, has been used to this end. Wolbachia-infected mosquitoes have been released into the environment as a strategy for controlling the mosquito population and hence the spread of arboviral-derived diseases. However, there is little knowledge regarding the specific interactions that occur between Wolbachia and its host, particularly those associated with its obligate intracellular nature. In this work we studied Wolbachia endosymbiosis from a systems biology perspective. By analyzing the gaps in the metabolic networks of four Wolbachia strains we were able to identify key interaction points between this intracellular bacteria and its host, which play a crucial role in their metabolic relationship. This approach focuses on what is missing to allow unveiling new information regarding the interplay between interacting metabolic networks, and it is especially useful in the case of intracellular bacteria where experimental information is scarce. This additional insight on the metabolic interactions between host and parasite hold great potential for the development of arboviral disease control strategies.
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Affiliation(s)
- Natalia E. Jiménez
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Santiago, Chile
- Center for Mathematical Modeling (CMM) (UMI CNRS 2807), Department of Mathematical Engineering, University of Chile, Santiago, Chile
- * E-mail:
| | - Ziomara P. Gerdtzen
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Santiago, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Santiago, Chile
| | - J. Cristian Salgado
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Santiago, Chile
| | - Carlos Conca
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Santiago, Chile
- Center for Mathematical Modeling (CMM) (UMI CNRS 2807), Department of Mathematical Engineering, University of Chile, Santiago, Chile
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16
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Moglia I, Santiago M, Olivera-Nappa Á, Soler M. An optimized low-cost protocol for standardized production of iron-free apoferritin nanocages with high protein recovery and suitable conformation for nanotechnological applications. J Inorg Biochem 2017; 183:184-190. [PMID: 29279245 DOI: 10.1016/j.jinorgbio.2017.11.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/24/2017] [Accepted: 11/17/2017] [Indexed: 11/28/2022]
Abstract
Ferritin is a globular protein that consists of 24 subunits forming a hollow nanocage structure that naturally stores iron oxyhydroxides. Elimination of iron atoms to obtain the empty protein called apoferritin is the first step to use this organic shell as a nanoreactor for different nanotechnological applications. Different protocols have been reported for apoferritin formation, but some are time consuming, others are difficult to reproduce and protein recovery yields are seldom reported. Here we tested several protocols and performed a complete material characterization of the apoferritin products using size exclusion chromatography, UV-vis spectroscopy, inductively coupled plasma optical emission spectrometry and dynamic light scattering. Our best method removes more than 99% of the iron from loaded holoferritin, recovering 70-80% of the original protein as monomeric apoferritin nanocages. Our work shows that pH conditions of the reduction step and the presence and nature of chelating agents affect the efficiency of iron removal. Furthermore, process conditions also seem to have an influence on the monomer:aggregate proportion present in the product. We also demonstrate that iron contents markedly increase ferritin absorbance at 280nm. The influence of iron contents on absorbance at 280nm precludes using this simple spectrophotometric measure for protein determination in ferritin‑iron complexes. Apoferritin produced following our protocol only requires readily-available, cheap and biocompatible reagents, which makes this process standardizable, scalable and applicable to be used for in vivo applications of ferritin derivatives as well as nanotechnological and biotechnological uses.
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Affiliation(s)
- Italo Moglia
- Department of Chemical Engineering, Biotechnology and Materials, FCFM, University of Chile, Beauchef 851, Santiago, Chile
| | - Margarita Santiago
- Center for Biotechnology and Bioengineering - CeBiB, FCFM, University of Chile, Beauchef 851, Santiago, Chile
| | - Álvaro Olivera-Nappa
- Department of Chemical Engineering, Biotechnology and Materials, FCFM, University of Chile, Beauchef 851, Santiago, Chile; Center for Biotechnology and Bioengineering - CeBiB, FCFM, University of Chile, Beauchef 851, Santiago, Chile.
| | - Mónica Soler
- Department of Chemical Engineering, Biotechnology and Materials, FCFM, University of Chile, Beauchef 851, Santiago, Chile.
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17
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Gossage L, Pires DEV, Olivera-Nappa Á, Asenjo J, Bycroft M, Blundell TL, Eisen T. An integrated computational approach can classify VHL missense mutations according to risk of clear cell renal carcinoma. Hum Mol Genet 2014; 23:5976-88. [PMID: 24969085 PMCID: PMC4204774 DOI: 10.1093/hmg/ddu321] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 05/25/2014] [Accepted: 06/17/2014] [Indexed: 12/26/2022] Open
Abstract
Mutations in the von Hippel-Lindau (VHL) gene are pathogenic in VHL disease, congenital polycythaemia and clear cell renal carcinoma (ccRCC). pVHL forms a ternary complex with elongin C and elongin B, critical for pVHL stability and function, which interacts with Cullin-2 and RING-box protein 1 to target hypoxia-inducible factor for polyubiquitination and proteasomal degradation. We describe a comprehensive database of missense VHL mutations linked to experimental and clinical data. We use predictions from in silico tools to link the functional effects of missense VHL mutations to phenotype. The risk of ccRCC in VHL disease is linked to the degree of destabilization resulting from missense mutations. An optimized binary classification system (symphony), which integrates predictions from five in silico methods, can predict the risk of ccRCC associated with VHL missense mutations with high sensitivity and specificity. We use symphony to generate predictions for risk of ccRCC for all possible VHL missense mutations and present these predictions, in association with clinical and experimental data, in a publically available, searchable web server.
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Affiliation(s)
- Lucy Gossage
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Douglas E V Pires
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Álvaro Olivera-Nappa
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK, Centre for Biochemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile
| | - Juan Asenjo
- Centre for Biochemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile
| | - Mark Bycroft
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Research Centre, Cambridge CB2 0QH, UK and
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Tim Eisen
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Box 193 (R4) Addenbrooke's Hospital, Cambridge Biomedical Campus, Hill's Road, Cambridge CB2 0QQ, UK
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