Examinando por Autor "Briones, C."

Mostrando 1 - 11 de 11

Restringido
Amino acid substitutions associated with treatment failure for Hepatitis C virus infection
(American Society for Microbiology, 2020-12) Soria, María Eugenia; García Crespo, Carlos; Martínez González, Brenda; Vázquez Sirvent, L.; Lobo Vega, Rebeca; Ávila, Ana Isabel de; Gallego, Isabel; Chen, Qian; García Cehic, Damir; Llorens Revull, Meritxell; Briones, C.; Gómez, Jordi; Ferrer Orta, Cristina; Verdaguer, Nuria; Gregori, Josep; Rodríguez Frías, Francisco; Buti, María; Ignacio Esteban, Juan; Domingo, Esteban; Quer, Josep; Perales, Celia; Ministerio de Economía y Competitividad (MINECO); Agencia Estatal de Investigación (AEI); Instituto de Salud Carlos III (ISCIII); Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas, España; Centro para el Desarrollo Tecnológico Industrial (CDTI); Fundación Ramón Areces; Banco de Santander; CSIC-INTA - Centro de Astrobiología, CAB; Unidad de Excelencia Científica María de Maeztu Centro de Astrobiología del Instituto Nacional de Técnica Aeroespacial y CSIC, MDM-2017-0737
Despite the high virological response rates achieved with current directly acting antiviral agents (DAAs) against hepatitis C virus (HCV), around 2% to 5% of treated patients do not achieve a sustained viral response. The identification of amino acid substitutions associated with treatment failure requires analytical designs, such as subtype-specific ultradeep sequencing (UDS) methods, for HCV characterization and patient management. Using this procedure, we have identified six highly represented amino acid substitutions (HRSs) in NS5A and NS5B of HCV, which are not bona fide resistance-associated substitutions (RAS), from 220 patients who failed therapy. They were present frequently in basal and posttreatment virus of patients who failed different DAA-based therapies. Contrary to several RAS, HRSs belong to the acceptable subset of substitutions according to the PAM250 replacement matrix. Their mutant frequency, measured by the number of deep sequencing reads within the HCV quasispecies that encode the relevant substitutions, ranged between 90% and 100% in most cases. They also have limited predicted disruptive effects on the three-dimensional structures of the proteins harboring them. Possible mechanisms of HRS origin and dominance, as well as their potential predictive value for treatment response, are discussed.
Restringido
Bioelectrocatalytic platforms based on chemically modified nanodiamonds by diazonium salt chemistry
(Elsevier BV, 2020-08-05) Revenga Parra, M.; Villa Manso, A. M.; Briones, C.; Mateo Martí, Eva; Martínez Periñán, E.; Lorenzo, E.; Pariente, F.; Agencia Estatal de Investigación (AEI); Comunidad de Madrid; 0000-0002-0699-7185; 0000-0003-4709-4676; 0000-0003-4709-4676; Unidad de Excelencia Científica María de Maeztu Centro de Astrobiología del Instituto Nacional de Técnica Aeroespacial y CSIC, MDM-2017-0737
Detonation nanodiamonds immobilized onto screen-printed gold electrodes have been modified with a phenothiazine (Azure A) by electrografting of the corresponding in situ generated diazonium salt in acidic medium in the presence of nitrite. The resulting disposable electrochemical platform has been extensively characterized, confirming that is very stable and highly reactive. It shows an excellent electrocatalytic activity towards the oxidation of substances of interest and can be employed to prepare bioelectrocatalytic platforms. Hence, as proof of concept, nicotinamide adenine dinucleotide (NAD+)-dependent alcohol dehydrogenase has been directly immobilized on the Azure A electroactive film to develop an ethanol biosensor based on the measurement of the enzymatically generated β-nicotinamide adenine dinucleotide (NADH). Considering the excellent results obtained, it can be concluded that the modification of electrodes with detonation nanodiamonds can be a good strategy to generate sensing and biosensing electrochemical devices.
Restringido
Broad and dynamic diversification of infectious hepatitis c virus in a cell culture environment
(American Society for Microbiology, 2020-02-28) Gallego, Isabel; Eugenia Soria, M.; García Crespo, Carlos; Chen, Q.; Martínez Barragán, P.; Khalfaoui, S.; Martínez González, B.; Sánchez Martín, I.; Palacios Blanco, I.; Isabel de Ávila, A.; García Cehic, Damir; Ignacio Esteban, J.; Gómez, Jordi; Briones, C.; Gregori, Josep; Quer, J.; Perales, C.; Domingo, Esteban; Instituto de Salud Carlos III (ISCIII); Comunidad de Madrid; Ministerio de Economia y Competitividad (MINECO); Fundación Ramón Areces; Banco Santander; Agencia Estatal de Investigación (AEI); Eugenia Soria, M. [0000-0003-1755-6382]; García Crespo, C. [0000-0001-6561-5389]; García Cehic, D. [0000-0002-0009-038X]; Briones, C. [0000-0003-2213-8353]; Domingo, E. [0000-0002-0573-1676]; Martínez González, B. [0000-0002-4482-5181]; Perales Viejo, C. B. [0000-0003-1618-1937]; García Crespo, C. [0000-0001-6561-5389]; Gregori Font, J. [0000-0002-4253-8015]; Gómez, J. [0000-0002-7806-1503]; Quer, J. [0000-0003-0014-084X]
Previous studies documented that long-term hepatitis C virus (HCV) replication in human hepatoma Huh-7.5 cells resulted in viral fitness gain, expansion of the mutant spectrum, and several phenotypic alterations. In the present work, we show that mutational waves (changes in frequency of individual mutations) occurred continuously and became more prominent as the virus gained fitness. They were accompanied by an increasing proportion of heterogeneous genomic sites that affected 1 position in the initial HCV population and 19 and 69 positions at passages 100 and 200, respectively. Analysis of biological clones of HCV showed that these dynamic events affected infectious genomes, since part of the fluctuating mutations became incorporated into viable genomes. While 17 mutations were scored in 3 biological clones isolated from the initial population, the number reached 72 in 3 biological clones from the population at passage 200. Biological clones differed in their responses to antiviral inhibitors, indicating a phenotypic impact of viral dynamics. Thus, HCV adaptation to a specific constant environment (cell culture without external influences) broadens the mutant repertoire and does not focus the population toward a limited number of dominant genomes. A retrospective examination of mutant spectra of foot-and-mouth disease virus passaged in cell cultures suggests a parallel behavior here described for HCV. We propose that virus diversification in a constant environment has its basis in the availability of multiple alternative mutational pathways for fitness gain. This mechanism of broad diversification should also apply to other replicative systems characterized by high mutation rates and large population sizes. IMPORTANCE The study shows that extensive replication of an RNA virus in a constant biological environment does not limit exploration of sequence space and adaptive options. There was no convergence toward a restricted set of adapted genomes. Mutational waves and mutant spectrum broadening affected infectious genomes. Therefore, profound modifications of mutant spectrum composition and consensus sequence diversification are not exclusively dependent on environmental alterations or the intervention of population bottlenecks.
Acceso Abierto
Discovery in space of ethanolamine, the simplest phospholipid head group
(National Academy of Sciences, 2021-06-01) Rivilla, V. M.; Jiménez Serra, I.; Martín Pintado, J.; Briones, C.; Rodríguez Almeida, L. F.; Rico Villas, F.; Tercero, B.; Zeng, S.; Colzi, L.; De Vicente, P.; Martín, S.; Requena Torres, M. A.; European Commission (EC); Agencia Estatal de Investigación (AEI); Comunidad de Madrid; Rivilla, V. M. [0000-0002-2887-5859]; Tercero, B. [0000-0002-4782-5259]; Martín, S. [0000-0001-9281-2919]; Unidad de Excelencia Científica María de Maeztu Centro de Astrobiología del Instituto Nacional de Técnica Aeroespacial y CSIC, MDM-2017-0737
Cell membranes are a key element of life because they keep the genetic material and metabolic machinery together. All present cell membranes are made of phospholipids, yet the nature of the first membranes and the origin of phospholipids are still under debate. We report here the presence of ethanolamine in space, NH2CH2CH2OH, which forms the hydrophilic head of the simplest and second-most-abundant phospholipid in membranes. The molecular column density of ethanolamine in interstellar space is N = (1.51 +/- 0.07) x 1013 cm-2, implying a molecular abundance with respect to H2 of (0.9 - 1.4) x 10-10. Previous studies reported its presence in meteoritic material, but they suggested that it is synthesized in the meteorite itself by decomposition of amino acids. However, we find that the proportion of the molecule with respect to water in the interstellar medium is similar to the one found in the meteorite (10-6). These results indicate that ethanolamine forms efficiently in space and, if delivered onto early Earth, could have contributed to the assembling and early evolution of primitive membranes.
Acceso Abierto
Dissimilar Conservation Pattern in Hepatitis C Virus Mutant Spectra, Consensus Sequences, and Data Banks
(Multidisciplinary Digital Publishing Institute (MDPI), 2020-10-27) García Crespo, Carlos; Eugenia Soria, M.; Gallego, Isabel; Isabel de Ávila, A.; Martínez González, B.; Vázquez Sirvent, L.; Gómez, Jordi; Briones, C.; Gregori, Josep; Quer, J.; Perales, C.; Domingo, Esteban; Ministerio de Economía y Competitividad (MINECO); Comunidad de Madrid; Agencia Estatal de Investigación (AEI); Instituto de Salud Carlos III (ISCIII); Fundación Ramón Areces; García Crespo, C. [0000-0001-6561-5389]; Soria Benito, M. E. [0000-0002-4719-3351]; Martínez González, B. [0000-0002-4482-5181]; Briones, C. [0000-0003-2213-8353]; Gregori, J. [0000-0002-4253-8015]; Quer, J. [0000-0003-0014-084X]; Perales, C. [0000-0003-1618-1937]; Unidad de Excelencia Científica María de Maeztu Centro de Astrobiología del Instituto Nacional de Técnica Aeroespacial y CSIC, MDM-2017-0737
The influence of quasispecies dynamics on long-term virus diversification in nature is a largely unexplored question. Specifically, whether intra-host nucleotide and amino acid variation in quasispecies fit the variation observed in consensus sequences or data bank alignments is unknown. Genome conservation and dynamics simulations are used for the computational design of universal vaccines, therapeutic antibodies and pan-genomic antiviral agents. The expectation is that selection of escape mutants will be limited when mutations at conserved residues are required. This strategy assumes long-term (epidemiologically relevant) conservation but, critically, does not consider short-term (quasispecies-dictated) residue conservation. We calculated mutant frequencies of individual loci from mutant spectra of hepatitis C virus (HCV) populations passaged in cell culture and from infected patients. Nucleotide or amino acid conservation in consensus sequences of the same populations, or in the Los Alamos HCV data bank did not match residue conservation in mutant spectra. The results relativize the concept of sequence conservation in viral genetics and suggest that residue invariance in data banks is an insufficient basis for the design of universal viral ligands for clinical purposes. Our calculations suggest relaxed mutational restrictions during quasispecies dynamics, which may contribute to higher calculated short-term than long-term viral evolutionary rates.
Acceso Abierto
Esto es lo que los virólogos sabemos hasta hoy sobre el coronavirus SARS-CoV-2
(Asociación The Conversation España, 2020-04-28) Bosch, A.; Nieto, A.; Doménech, A.; Briones, C.; Alonso, C.; Casas, I.; Buesa, J.; Navas Castillo, J.; López Guerrero, J. A.; Quer, J.; Echevarría, J. E.; Pallás Benet, V.
Para Peter Medawar, premio Nobel de Medicina en 1960, los virus eran un conjunto de “malas noticias envueltas en proteína”. Aunque no responde a ningún criterio científico, esta definición refleja perfectamente la percepción que tenemos de la pandemia del coronavirus SARS-CoV-2 en estos días de confinamiento. Las “malas noticias” en un virus pueden venir escritas en dos “alfabetos” ligeramente distintos, según su genoma sea de ADN o ARN. Los coronavirus (familia Coronaviridae) constituyen uno de los grupos de virus con el genoma de ARN más largo que se conoce. La información que contiene puede servir para sintetizar al menos 16 proteínas. Las más esenciales son las que le permiten hacer copias de su propio genoma, las que protegen su ARN y las que le permiten entrar en la célula que va a infectar. Esta última es una proteína que contiene azúcares en su esqueleto y que se proyecta a modo de espículas (proteína S, de spike en inglés) desde la envuelta hacia el exterior. Al microscopio electrónico crean una imagen que recuerda a una corona, de ahí el nombre del virus. La fidelidad de copia de las moléculas de ARN viral es siempre mucho menor que las de ADN, por lo que los virus de ARN tienden a acumular más mutaciones y adaptarse a nuevos huéspedes con más facilidad que los que poseen un genoma de ADN. Dentro de los virus con genoma de ARN, los coronavirus son una excepción: poseen un sistema de corrección de copia que hace que muestren una menor variabilidad.
Acceso Abierto
Morphology Clustering Software for AFM Images, Based on Particle Isolation and Artificial Neural Networks
(Institute of Electrical and Electronics Engineers, 2019-11-04) Delgado, A.; Moreno, M.; Vázquez, L. F.; Martín Gago, J. A.; Briones, C.; Ministerio de Economía y Competitividad (MINECO); Comunidad de Madrid; Agencia Estatal de Investigación (AEI); Delgado, A. [0000-0003-4868-3712]; Moreno, M. [0000-0002-6065-4095]; MartínGago, J. A. [0000-0003-2663-491X]; Briones, C. [0000-0003-2213-8353]; Unidad de Excelencia Científica María de Maeztu Centro de Astrobiología del Instituto Nacional de Técnica Aeroespacial y CSIC, MDM-2017-0737
Advanced microscopy techniques currently allow scientists to visualize biomolecules at high resolution. Among them, atomic force microscopy (AFM) shows the advantage of imaging molecules in their native state, without requiring any staining or coating of the sample. Biopolymers, including proteins and structured nucleic acids, are flexible molecules that can fold into alternative conformations for any given monomer sequence, as exemplified by the different three-dimensional structures adopted by RNA in solution. Therefore, the manual analysis of images visualized by AFM and other microscopy techniques becomes very laborious and time-consuming (and may also be inadvertently biased) when large populations of biomolecules are studied. Here we present a novel morphology clustering software, based on particle isolation and artificial neural networks, which allows the automatic image analysis and classification of biomolecules that can show alternative conformations. It has been tested with a set of AFM images of RNA molecules (a 574 nucleotides-long functional region of the hepatitis C virus genome that contains its internal ribosome entry site element) structured in folding buffers containing 0, 2, 4, 6 or 10 mM Mg 2+ . The developed software shows a broad applicability in the microscopy-based analysis of biopolymers and other complex biomolecules.
Acceso Abierto
Population Disequilibrium as Promoter of Adaptive Explorations in Hepatitis C Virus
(Multidisciplinary Digital Publishing Institute (MDPI), 2021-04-03) García Crespo, Carlos; Gallego, Isabel; Eugenia Soria, M.; Isabel de Ávila, A.; Martínez González, B.; Vázquez Sirvent, L.; Lobo Vega, Rebeca; Moreno, E.; Gómez, Jordi; Briones, C.; Gregori, Josep; Quer, J.; Domingo, Esteban; Perales, C.; Banco Santander; Fundación Ramón Areces; Instituto de Salud Carlos III (ISCIII); Agencia Estatal de Investigación (AEI); Ministerio de Economía y Competitividad (MINECO); García Crespo, C. [0000-0001-6561-5389]; Martínez González, B. [0000-0002-4482-5181]; Moreno, E. [0000-0002-2301-4558]; Briones, C. [0000-0003-2213-8353]; Quer, J. [0000-0003-0014-084X]; Unidad de Excelencia Científica María de Maeztu Centro de Astrobiología del Instituto Nacional de Técnica Aeroespacial y CSIC, MDM-2017-0737
Replication of RNA viruses is characterized by exploration of sequence space which facilitates their adaptation to changing environments. It is generally accepted that such exploration takes place mainly in response to positive selection, and that further diversification is boosted by modifications of virus population size, particularly bottleneck events. Our recent results with hepatitis C virus (HCV) have shown that the expansion in sequence space of a viral clone continues despite prolonged replication in a stable cell culture environment. Diagnosis of the expansion was based on the quantification of diversity indices, the occurrence of intra-population mutational waves (variations in mutant frequencies), and greater individual residue variations in mutant spectra than those anticipated from sequence alignments in data banks. In the present report, we review our previous results, and show additionally that mutational waves in amplicons from the NS5A-NS5B-coding region are equally prominent during HCV passage in the absence or presence of the mutagenic nucleotide analogues favipiravir or ribavirin. In addition, by extending our previous analysis to amplicons of the NS3- and NS5A-coding region, we provide further evidence of the incongruence between amino acid conservation scores in mutant spectra from infected patients and in the Los Alamos National Laboratory HCV data banks. We hypothesize that these observations have as a common origin a permanent state of HCV population disequilibrium even upon extensive viral replication in the absence of external selective constraints or changes in population size. Such a persistent disequilibrium—revealed by the changing composition of the mutant spectrum—may facilitate finding alternative mutational pathways for HCV antiviral resistance. The possible significance of our model for other genetically variable viruses is discussed
Acceso Abierto
Prebiotic Precursors of the Primordial RNA World in Space: Detection of NH2OH
(The Institute of Physics (IOP), 2020-08-19) Rivilla, V. M.; Martín Pintado, J.; Jiménez Serra, I.; Martín, S.; Rodríguez Almeida, L. F.; Requeña Torres, M. A.; Rico Villas, F.; Zeng, S.; Briones, C.; European Research Council (ERC); Agencia Estatal de Investigación (AEI); Comunidad de Madrid; Briones, C. [0000-0003-2213-8353]; Martín Ruiz, S. [0000-0001-9281-2919]; Rico Villas, F. [0000-0002-5351-3497]; Rivilla, V. M. [0000-0002-2887-5859]; Unidad de Excelencia Científica María de Maeztu Centro de Astrobiología del Instituto Nacional de Técnica Aeroespacial y CSIC, MDM-2017-0737
One of the proposed scenarios for the origin of life is the primordial RNA world, which considers that RNA molecules were likely responsible for the storage of genetic information and the catalysis of biochemical reactions in primitive cells, before the advent of proteins and DNA. In the last decade, experiments in the field of prebiotic chemistry have shown that RNA nucleotides can be synthesized from relatively simple molecular precursors, most of which have been found in space. An important exception is hydroxylamine, NH2OH, which, despite several observational attempts, it has not been detected in space yet. Here we present the first detection of NH2OH in the interstellar medium toward the quiescent molecular cloud G+0.693-0.027 located in the Galactic Center. We have targeted the three groups of transitions from the J = 2−1, 3−2, and 4−3 rotational lines, detecting five transitions that are unblended or only slightly blended. The derived molecular abundance of NH2OH is (2.1 ± 0.9) × 10−10. From the comparison of the derived abundance of NH2OH and chemically related species, with those predicted by chemical models and measured in laboratory experiments, we favor the formation of NH2OH in the interstellar medium via hydrogenation of NO on dust grain surfaces, with possibly a contribution of ice-mantle NH3 oxidation processes. Further laboratory studies and quantum chemical calculations are needed to completely rule out the formation of NH2OH in the gas phase.
Restringido
Silicon Surface Nanostructuring for Covalent Immobilization of Biomolecules
(ACS Publications, 2008-06-03) Rogero, Celia; Chaffey, Benjamin T.; Mateo Martí, Eva; Sobrado, J. M.; Horrocks, Benjamin R.; Houlton, Andrew; Lakey, Jeremy H.; Briones, C.; Martín Gago, J. A.; Instituto Nacional de Técnica Aeroespacial (INTA); Ministerio de Ciencia e Innovación (MICINN)
We present a straightforward strategy to control the average distance of immobilized biomolecules on silicon surfaces. We exploit the reaction taking place between the amino residues within the biomolecules (lysine groups of proteins or the N-terminus of oligomers of peptide nucleic acid, PNA) and the aldehyde-terminated groups presented in a mixed aldehyde/alkyl organic monolayer on a silicon surface. The mixed monolayers were prepared by a thermal reaction of hydrogen-terminated Si(111) with a mixture of undecene and undecenyl-aldehyde. We quantitatively evaluate the surface concentration of aldehyde in the monolayer by atomic force microscopy and an intensity analysis of core level X-ray photoemission spectroscopy peaks. These complementary techniques show that the surface density of the reactive terminal groups reflects the mole fraction of aldehyde in the reactive solution used to modify the silicon surface. The further immobilization of proteins or peptide nucleic acids on the monolayer shows that the density of biomolecules reproduces the aldehyde surface density, which indicates a specific covalent attachment and a negligible nonspecific adsorption. The proposed procedure makes possible to control the average distance of the immobilized active biomolecules on the silicon surface, which could be of great relevance for applications in the interdisciplinary field of biosensors.
Acceso Abierto
The Complex Molecules Detector (CMOLD): A Fluidic-Based Instrument Suite to Search for (Bio)chemical Complexity on Mars and Icy Moons
(Mary Ann Liebert Publishers, 2020-09-15) Fairén, Alberto G.; Gómez Elvira, J.; Briones, C.; Prieto Ballesteros, O.; Rodríguez Manfredi, J. A.; López Heredero, R.; Belenguer, T.; Moral, A.; Moreno Paz, M.; Parro García, V.; European Research Council (ERC); Agencia Estatal de Investigación (AEI); Briones, C. [0000-0003-2213-8353]; Prieto Ballesteros, O. [0000-0002-2278-1210]; López Heredero, R. [0000-0002-2197-8388]; Unidad de Excelencia Científica María de Maeztu Centro de Astrobiología del Instituto Nacional de Técnica Aeroespacial y CSIC, MDM-2017-0737
Organic chemistry is ubiquitous in the Solar System, and both Mars and a number of icy satellites of the outer Solar System show substantial promise for having hosted or hosting life. Here, we propose a novel astrobiologically focused instrument suite that could be included as scientific payload in future missions to Mars or the icy moons: the Complex Molecules Detector, or CMOLD. CMOLD is devoted to determining different levels of prebiotic/biotic chemical and structural targets following a chemically general approach (i.e., valid for both terrestrial and nonterrestrial life), as well as their compatibility with terrestrial life. CMOLD is based on a microfluidic block that distributes a liquid suspension sample to three instruments by using complementary technologies: (1) novel microscopic techniques for identifying ultrastructures and cell-like morphologies, (2) Raman spectroscopy for detecting universal intramolecular complexity that leads to biochemical functionality, and (3) bioaffinity-based systems (including antibodies and aptamers as capture probes) for finding life-related and nonlife-related molecular structures. We highlight our current developments to make this type of instruments flight-ready for upcoming Mars missions: the Raman spectrometer included in the science payload of the ESAs Rosalind Franklin rover (Raman Laser Spectrometer instrument) to be launched in 2022, and the biomarker detector that was included as payload in the NASA Icebreaker lander mission proposal (SOLID instrument). CMOLD is a robust solution that builds on the combination of three complementary, existing techniques to cover a wide spectrum of targets in the search for (bio)chemical complexity in the Solar System.