Detection of miRNA cancer biomarkers using light activated Molecular Beacons

Early detection of cancer biomarkers can reduce cancer mortality rate. miRNAs are small non-coding RNAs whose expression changes upon the onset of various types of cancer. Biosensors that specifically detect such biomarkers can be engineered and integrated into point-of-care devices (POC) using label-free detection, high sensibility and compactness. In this paper, a new engineered Molecular Beacon (MB) construct used to detect miRNAs is presented. Such a construct is immobilized onto biosensor surfaces in a covalent and spatially oriented way using the photonic technology Light Assisted Molecular Immobilization (LAMI). The construct consists of a Cy3 labelled MB covalently attached to a light-switchable peptide. One MB construct contains a poly-A sequence in its loop region while the other contains a sequence complementary to the cancer biomarker miRNA-21. The constructs have been characterized by UV-Vis spectroscopy, mass spectrometry and HPLC. LAMI led to the successful immobilization of the engineered constructs onto thiol functionalized optically flat quartz slides and Silicon on Insulator (SOI) sensor surfaces. The immobilized Cy3 labelled MB construct has been imaged using confocal fluorescence microscopy (CFM). The bioavailability of the immobilized engineered MB biosensors was confirmed through specific hybridization with the Cy5 labelled complementary sequence and imaged by CFM and FRET. Hybridization kinetics have been monitored using steady state fluorescence spectroscopy. The label-free detection of miRNA-21 was also achieved by using integrated photonic sensing structures. The engineered light sensitive constructs can be immobilized onto thiol reactive surfaces and are currently being integrated in a POC device for the detection of cancer biomarkers

Impact of the COVID-19 pandemic on tuberculosis management in Spain

Coronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Impacte; TuberculosiCoronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Impacto; TuberculosisCoronavirus SARS-CoV-2; COVID-19; 2019-nCoV; Impact; TuberculosisBackground The impact of COVID-19 on the diagnosis and management of tuberculosis (TB) patients is unknown. Methods Participating centres completed a structured web-based survey regarding changes to TB patient management during the COVID-19 pandemic. The study also included data from participating centres on patients aged ≥18 diagnosed with TB in 2 periods: March 15 to June 30, 2020 and March 15 to June 30, 2019. Clinical variables and information about patient household contacts were retrospectively collected. Results A total of 7 (70%) TB units reported changes in their usual TB team operations. Across both periods of study, 169 patients were diagnosed with active TB (90 in 2019, 79 in 2020). Patients diagnosed in 2020 showed more frequent bilateral lesions in chest X-ray than patients diagnosed in 2019 ( P = 0.004). There was a higher percentage of latent TB infection and active TB among children in households of patients diagnosed in 2020, compared with 2019 ( P = 0.001). Conclusions The COVID-19 pandemic has caused substantial changes in TB care. TB patients diagnosed during the COVID-19 pandemic showed more extended pulmonary forms. The increase in latent TB infection and active TB in children of patient households could reflect increased household transmission due to anti-COVID-19 measures.This research did not receive any specific grant from funding agencies in the public, commercial or not-for-profit sectors.MLA was supported by a postdoctoral grant “Rio Hortega” and ASM was supported by a postdoctoral grant “Juan Rodés” (JE18/00022) from the Instituto de Salud Carlos III through the Spanish Ministry of economy and competitiveness

Molecular characterization of rpoB gene mutations in isolates from tuberculosis patients in Cubal, Republic of Angola

Angola; Rifampicina; Mutaciones rpoBAngola; Rifampicina; Mutacions rpoBAngola; Rifampicin; rpoB mutationsBackground The importance of Mycobacterium tuberculosis strains with disputed rpoB mutations remains to be defined. This study aimed to assess the frequency and types of rpoB mutations in M. tuberculosis isolates from Cubal, Angola, a country with a high incidence of tuberculosis. Methods All isolates included (n = 308) were analyzed using phenotypic drug susceptibility testing and GenoType MTBDRplus assay. DNA sequencing of the rpoB gene and determination of rifampicin MIC by macrodilution method were additionally performed on isolates yielding discordant results (n = 12) and those in which the mutation detected was not characterized (n = 8). Results In total, 85.1% (74/87) of rifampicin-resistant strains had undisputed rpoB mutations -S450L (49), D435V (15), H445D (3), H445Y (2), Q432ins (1), L449M plus S450F (1), S450F (1), S450W (1) and S450Y (1)-; 10.3% (9/87) had disputed rpoB mutations—L430P plus S493L (1), N437del (1), H445L (3), D435Y (2), L452P (2)-, 2.3% (2.3%) showed no rpoB mutations and 2.3% (2/87) showed heteroresistance—D435Y plus L452P and L430P plus S493L-. Conclusion Disputed rpoB mutations were common, occurring in 10.3% of rifampicin resistant isolates. Current phenotyping techniques may be unable to detect this resistance pattern. To increase their sensitivity, a lower concentration of RIF could be used in these tests or alternatively, rpoB mutations could be screened and characterized in all M. tuberculosis strains.This work was supported by Probitas Foundation. Thanks to the financial support received from Probitas Foundation it was possible not only purchase the equipment and reagents to launch the study but to strengthen the capacity of the laboratory and local staff

Experimental study of the evanescent-wave photonic sensors response in presence of molecular beacon conformational changes

An experimental study of the influence of the conformational change suffered by molecular beacon (MB) probes ‐upon the biorecognition of nucleic acid target oligonucleotides over evanescent wave photonic sensors‐ is reported. To this end, high sensitivity photonic sensors based on silicon photonic bandgap (PBG) structures were used, where the MB probes were immobilized via their 5’ termination. Those MBs incorporate a biotin moiety close to their 3’ termination in order to selectively bind a streptavidin molecule to them. The different photonic sensing responses obtained towards the target oligonucleotide detection, when the streptavidin molecule was bound to the MB probes or not, demonstrate the conformational change suffered by the MB upon hybridization, which promotes the displacement of the streptavidin molecule away from the surface of the photonic sensing structure. Schematic diagram of the PBG sensing structure on which the streptavidin‐labeled MB probes were immobilized

Un estudio de estereotipos de género en alumnado de secundaria en el marco de Proyecto Meitner

[ES] Este artículo presenta Proyecto Meitner como una acción de divulgación científica diseñada para abordar, entre otras cuestiones, la problemática de las mujeres en Física a través de las artes escénicas. Se presenta, también, un estudio de sesgos y estereotipos de género en ciencia realizado al alumnado de los centros de secundaria de la Comunitat Valenciana que participaron en dos sesiones matinales de la obra de teatro Proyecto Meitner. Se utilizó un cuestionario que rellenaron 134 estudiantes estudiantes antes de las funciones. Las respuestas revelan una perpetuación de los estereotipos asociados al personal científico, definido principalmente como muy inteligente, culto, occidental, hombre, mayor, solitario y con bata. Además, el alumnado encuestado cree que los chicos tienen mejores aptitudes que las chicas para las carreras universitarias aun cuando las capacidades en ambos casos son las mismas

Quantum gravity phenomenology at the dawn of the multi-messenger era—A review

The exploration of the universe has recently entered a new era thanks to the multi-messenger paradigm, characterized by a continuous increase in the quantity and quality of experimental data that is obtained by the detection of the various cosmic messengers (photons, neutrinos, cosmic rays and gravitational waves) from numerous origins. They give us information about their sources in the universe and the properties of the intergalactic medium. Moreover, multi-messenger astronomy opens up the possibility to search for phenomenological signatures of quantum gravity. On the one hand, the most energetic events allow us to test our physical theories at energy regimes which are not directly accessible in accelerators; on the other hand, tiny effects in the propagation of very high energy particles could be amplified by cosmological distances. After decades of merely theoretical investigations, the possibility of obtaining phenomenological indications of Planck-scale effects is a revolutionary step in the quest for a quantum theory of gravity, but it requires cooperation between different communities of physicists (both theoretical and experimental). This review, prepared within the COST Action CA18108 “Quantum gravity phenomenology in the multi-messenger approach”, is aimed at promoting this cooperation by giving a state-of-the art account of the interdisciplinary expertise that is needed in the effective search of quantum gravity footprints in the production, propagation and detection of cosmic messengers.publishedVersio

Accuracy of Xpert Ultra for the diagnosis of paediatric tuberculosis in a low TB burden country: a prospective multicentre study

[Introduction] Childhood pulmonary tuberculosis (TB) remains a diagnostic challenge. This study aimed to evaluate the performance of Xpert Ultra for the diagnosis of pulmonary TB in children in a low TB prevalence setting.[Methods] Prospective, multicentre, diagnostic accuracy study. Children with clinical or radiological suspicion of pulmonary TB were recruited at 11 paediatric units in Spain. Up to three gastric or sputum specimens were taken on 3 consecutive days, and analysed by Xpert MTB/RIF, Xpert Ultra and culture in parallel.[Results] 86 children were included (median age 4.9 years, IQR 2.0–10.0; 51.2% male). The final diagnosis was pulmonary TB in 75 patients (87.2%); 33 (44.0%) were microbiologically confirmed. A total of 219 specimens, comprising gastric aspirates (n=194; 88.6%) and sputum specimens (n=25; 11.4%), were analysed. Using culture as reference standard and comparing individual specimens, the sensitivity was 37.8% (14/37) for Xpert MTB/RIF and 81.1% (30/37) for Xpert Ultra (p<0.001); specificity was 98.4% (179/182) and 93.4% (170/182), respectively (p=0.02). In the per-patient analysis, considering positive results on any specimen, the sensitivity was 42.9% (9/21) for Xpert MTB/RIF and 81.0% for Xpert Ultra (17/21, p=0.01); specificity was 96.9% (63/65) and 87.7% (57/65, p=0.07), respectively.[Conclusions] In children with pulmonary TB in a low burden setting, Xpert Ultra has significantly higher sensitivity than the previous generation of Xpert assay and only marginally lower specificity. Therefore, in children undergoing evaluation for suspected pulmonary TB, Xpert Ultra should be used in preference to Xpert MTB/RIF whenever possible.This study did not receive any project-specific funding. DA-A was supported by the Spanish Ministry of Health – Instituto de Salud Carlos III (ISCIII) and cofunded by the European Union (FEDER) (Contrato Río Hortega CM18/00100). AN-J was supported by 'Subvencions per a la Intensificació de Facultatius Especialistes' (Departament de Salut de la Generalitat de Catalunya, Programa PERIS 2016-2020) (SLT008/18/00193). DBG was supported by the Spanish Ministry of Science and Innovation – Instituto de Salud Carlos III and Fondos FEDER by 'Contratos para la intensificación de la actividad investigadora en el Sistema Nacional de Salud, 2020 (INT20/00086)'. BS-G was supported by the Spanish Ministry of Health – Instituto de Salud Carlos III (ISCIII) and cofunded by the European Union (FEDER) (Contrato Juan Rodés JR16/00036).Peer reviewe

Quantum gravity phenomenology at the dawn of the multi-messenger era -- A review

The exploration of the universe has recently entered a new era thanks to the multi-messenger paradigm, characterized by a continuous increase in the quantity and quality of experimental data that is obtained by the detection of the various cosmic messengers (photons, neutrinos, cosmic rays and gravitational waves) from numerous origins. They give us information about their sources in the universe and the properties of the intergalactic medium. Moreover, multi-messenger astronomy opens up the possibility to search for phenomenological signatures of quantum gravity. On the one hand, the most energetic events allow us to test our physical theories at energy regimes which are not directly accessible in accelerators; on the other hand, tiny effects in the propagation of very high energy particles could be amplified by cosmological distances. After decades of merely theoretical investigations, the possibility of obtaining phenomenological indications of Planck-scale effects is a revolutionary step in the quest for a quantum theory of gravity, but it requires cooperation between different communities of physicists (both theoretical and experimental). This review is aimed at promoting this cooperation by giving a state-of-the art account of the interdisciplinary expertise that is needed in the effective search of quantum gravity footprints in the production, propagation and detection of cosmic messengers

Desarrollo de biosensores nanofotónicos de alta sensibilidad para la detección de biomarcadores microRNA en aplicaciones de diagnóstico médico

[ES] El interés en desarrollar biosensores de alta sensibilidad para identificar y cuantificar una amplia gama de moléculas ha aumentado notablemente durante las últimas décadas en numerosos campos de aplicación. Entre ellos probablemente el más demandado sea el diagnóstico médico, el cual ha sido impulsado por el descubrimiento de nuevos biomarcadores de enfermedades, tales como los miRNAs. No obstante, la mayoría de las técnicas existentes para realizar la detección requieren el uso de marcadores debido a la falta de sensibilidad para detectar analitos en bajas concentraciones. Las estructuras ópticas basadas en campo evanescente, donde la luz es usada para transformar interacciones bioquímicas en variaciones de las señales ópticas, constituyen una interesante alternativa para el desarrollo de este tipo de biosensores sin la necesidad de utilizar marcadores (label-free). Concretamente las estructuras fotónicas integradas en tecnología Silicon On Insulator exhiben alta sensibilidad, bajo límite de detección y alto nivel de multiplexación en aplicaciones de detección, especialmente cuando se utilizan materiales y procesos basados en silicio y compatibles con CMOS. En esta Tesis Doctoral se muestra el desarrollo de un biosensor fotónico integrado label-free para la detección de oligonucleótidos, y más concretamente biomarcadores de cáncer miRNAs. Este biosensor está basado en la combinación de estructuras de band gap fotónico y la inmovilización de sondas de tipo molecular beacon sobre su superficie. La combinación de sendos elementos de transducción y bioreconomiento ha proporcionado una elevada sensibilidad en la detección de oligonucleótidos manteniendo un footprint por debajo de 100 µm2. El uso de este biosensor fotónico ha permitido también estudiar experimentalmente una novedosa técnica de amplificación de detección. Esta técnica explota el cambio conformacional sufrido por la sonda molecular beacon tras la hibridación con su oligonucleótido complementario, permitiendo alejar una partícula/molécula de la superficie del sensor, lo cual podría ser utilizado para amplificar la respuesta de detección del sensor. Finalmente se propone una estrategia de regeneración en línea de los biosensores nanofotónicos desarrollados mediante una estrategia química basada en el uso de formamida. Esta estrategia no solo permite ahorrar tiempo sino que también reduce la variación entre las medidas obtenidas en experimentos diferentes, siendo especialmente útil cuando se testean niveles similares de analito.[CA] L'interés en desenvolupar biosensors d'alta sensibilitat per a identificar i quantificar una àmplia gamma de molècules ha augmentat notablement durant les últimes dècades en nombrosos camps d'aplicació. Entre ells probablement el més demandat siga el diagnòstic mèdic, el qual ha sigut impulsat pel descobriment de nous biomarcadors de malalties, com ara els miRNAs. No obstant això, la majoria de les tècniques existents per a realitzar la detecció requereixen l'ús de marcadors a causa de la falta de sensibilitat per a detectar anàlits en baixes concentracions. Les estructures òptiques basades en camp evanescent, on la llum és usada per a transformar interaccions bioquímiques en variacions dels senyals òptics, constitueixen una interessant alternativa per al desenvolupament d'aquesta tipus de biosensors sense la necessitat d'utilitzar marcadors (label-free). Concretament les estructures fotòniques integrades en tecnologia Silicon On Insulator exhibeixen alta sensibilitat, baix límit de detecció i alt nivell de multiplexació en aplicacions de detecció, especialment quan s'utilitzen materials i processos basats en silici i compatibles amb CMOS. En aquesta Tesi Doctoral es mostra el desenvolupament d'un biosensor fotònic integrat label-free per a la detecció d'oligonucleòtids, i més concretament biomarcadors de càncer miRNAs. Aquest biosensor està basat en la combinació d'estructures de band gap fotònic i la immobilització de sondes de tipus molecular beacon sobre la seua superfície. La combinació d'ambdós elements de transducció i bioreconeixement ha proporcionat una elevada sensibilitat en la detecció d'oligonucleòtids mantenint un footprint per davall de 100 µm². L'ús d'aquest biosensor fotònic ha permés també estudiar experimentalment una nova tècnica d'amplificació de detecció. Aquesta tècnica explota el canvi conformacional patit per la sonda molecular beacon després de la hibridació amb el seu oligonucleòtid complementari, permetent allunyar una partícula/molècula de la superfície del sensor, la qual cosa podria ser utilitzada per amplificar la resposta de detecció del sensor. Finalment es proposa una estratègia de regeneració en línia dels biosensors nanofotònics desenvolupats mitjançant una estratègia química basada en l'ús de formamida. Aquesta estratègia no sols permet estalviar temps sinó que també redueix la variació entre les mesures obtingudes en experiments diferents, sent especialment útil quan es testen nivells similars d'anàlit.[EN] The interest in developing highly sensitive biosensors to identify and quantify a wide range of molecules has remarkably been increasing during the last decades in numerous application fields. Among them, medical diagnosis is probably the most demanded, which has been driven by the discovery of new biomarkers of diseases, such as miRNAs. However, most of the existing techniques to perform the detection require the use of labels due to the lack of sensitivity to detect analytes at low concentrations. Evanescent-wave optical structures, where light is used to transduce biochemical interactions into variations of the optical signals, are an interesting alternative for the development of this type of biosensors allowing a label-free detection. Specifically, the planar integrated photonic structures based on Silicon On Insulator technology exhibit an extremely high sensitivity, a low detection limit and a high level of multiplexing in detection applications, especially when using materials and processes based on silicon and being CMOS compatible. This PhD Thesis is focused on the development of label-free integrated photonic biosensors for the detection of oligonucleotides, and more specifically miRNA cancer biomarkers. This biosensor is based on the combination of photonic band gap structures and the immobilization of molecular beacon probes on its surface. The combination of both transduction and biorecognition elements has provided a very high sensitivity towards the detection of target oligonucleotides while keeping a sensor footprint below 100 µm2. The use of this photonic biosensor also allowed the experimental study of a novel detection amplification technique. This technique exploits the conformational change suffered by the molecular beacon probe after hybridization with its complementary oligonucleotide, allowing the displacement of a particle/molecule away from the sensor surface, what might be used for amplifying the sensor's detection response. Finally, an online regeneration strategy for nanophotonic biosensors developed through a chemical strategy based on the use of formamide is proposed. This strategy not only saves time but also reduces the variation between measurements obtained in different experiments, being especially useful when testing similar levels of analyte.Ruiz Tórtola, Á. (2021). Desarrollo de biosensores nanofotónicos de alta sensibilidad para la detección de biomarcadores microRNA en aplicaciones de diagnóstico médico [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/172631TESI

Diseño y caracterización de nanoestructuras plasmónicas para sensado

El presente proyecto final de carrera está estructurado en 7 capítulos, a lo largo de los cuales se realiza un estudio exhaustivo sobre la caracterización y diseño de nanoestructuras plasmónicas en el dominio óptico, así como un análisis de sus aplicaciones presentes y futuras en la detección de nanopartículas, que justificarán la relevancia que han cobrado estos dispositivos en los últimos años dentro del campo de la nanofotónica.Ruiz Tórtola, Á. (2014). Diseño y caracterización de nanoestructuras plasmónicas para sensado. http://hdl.handle.net/10251/46589.Archivo delegad