9,795 research outputs found

    Towards personalized medicine for metastatic urothelial cancer

    Get PDF

    Genomic investigation of antimicrobial resistant enterococci

    Get PDF
    Enterococcus faecium and Enterococcus faecalis are important causes of healthcare-associated infections in immunocompromised patients. Enterococci thrive in modern healthcare settings, being able to resist killing by a range of antimicrobial agents, persist in the environment, and adapt to changing circumstances. In Scotland, rates of vancomycin resistant E. faecium (VREfm) have risen almost 150% in recent years leaving few treatment options and challenging healthcare delivery. Resistance to the last line agent linezolid has also been detected in E. faecalis. Whole genome sequencing (WGS) allows investigation of the population structure and transmission of microorganisms, and identification of antimicrobial resistance mechanisms. The aim of this thesis was to use WGS to understand the molecular epidemiology of antimicrobial resistant enterococci from human healthcare settings in Scotland. Analysis of some of the earliest identified Scottish linezolid-resistant E. faecalis showed the resistance mechanism, optrA, was present in unrelated lineages and in different genetic elements, suggesting multiple introductions from a larger reservoir. To inform transmission investigations, within-patient diversity of VREfm was explored showing ~30% of patients carried multiple lineages and identifying a within-patient diversity threshold for transmission studies. WGS was then applied to a large nosocomial outbreak of VREfm, highlighting a complex network of related variants across multiple wards. Having examined within-hospital transmission, the role of regional relationships was investigated which showed that VREfm in Scotland is driven by multiple clones transmitted within individual Health Boards with occasional spread between regions. The most common lineage in the national collection (ST203) was estimated to have been present in Scotland since around 2005, highlighting its persistence in the face of increasing infection prevention and control measures. This thesis provides a starting point for genomic surveillance of enterococci in Scotland, and a basis for interventional studies aiming to reduce the burden of enterococcal infections."This work was supported by the Chief Scientist Office (Scotland) [grant number SIRN/10]; the Wellcome Trust [grant numbers 105621/Z/14/Z, 206194]; and the BBSRC [grant number BB/S019669/1]."—Fundin

    Towards personalized medicine for metastatic urothelial cancer

    Get PDF

    Breeding Melons for Resistance to Viral and Fungal Diseases. Exploiting the Multi-Resistant Accession TGR-1551

    Full text link
    [ES] Las cucurbitáceas son la segunda familia de hortícolas más importante a nivel mundial, solo por detrás de las solanáceas. Tradicionalmente su cultivo se ha llevado a cabo en las zonas templadas del planeta. Sin embargo, las condiciones de cambio climático, el comercio internacional y los modelos de agricultura intensiva favorecen la aparición de nuevas virosis y enfermedades fúngicas en zonas donde antes no estaban presentes. En este sentido, resulta esencial el monitoreo periódico de las principales zonas productoras, para así poder detectar los virus y hongos emergentes en cada territorio y adaptar los programas de mejora a los objetivos específicos de cada zona. En el caso concreto del melón (Cucumis melo) existe una gran variabilidad intraespecífica que puede servir como fuente de alelos de resistencia frente a estos patógenos. Sin embargo, las fuentes de resistencia suelen encontrarse dentro del germoplasma silvestre, normalmente originario de África o Asia, y en el que el nivel de domesticación es reducido. Para un mejor aprovechamiento de las accesiones resistentes, resulta necesario un estudio del control genético de los caracteres de interés, que permita localizar las regiones asociadas a la resistencia y diseñar marcadores moleculares asociadas a las mismas. Esto facilita los programas de mejora orientados a la introgresión de las resistencias manteniendo el fondo genético de las variedades de interés En la presente tesis doctoral, durante las campañas de verano de 2019 y 2020, se ha llevado a cabo un estudio de la incidencia y diversidad genética de 9 especies virales potencialmente limitantes para el cultivo de cucurbitáceas en el sur este español. Se ha podido observar que los virus transmitidos por pulgones son prevalentes frente a los transmitidos por mosca blanca. Dentro del primer grupo destacó la presencia de watermelon mosaic virus (WMV), cucurbits aphid borne yellows virus (CABYV) y cucumber mosaic virus (CMV), ya que fueron detectados en todas las zonas y cultivos estudiados, apareciendo frecuentemente en infecciones mixtas. Moroccan watermelon mosaic virus (MWMV) y tomato leaf curl New Delhi virus (ToLCNDV) también fueron detectados en algunas zonas, pero con porcentajes de infección más bajos y normalmente en infecciones mixtas con WMV. Los análisis filogenéticos de los distintos aislados encontrados ha permitido la identificación de 7 nuevos perfiles moleculares de WMV y de aislados recombinantes de CMV, lo que es consistente con los resultados obtenidos en otros países y pone de manifiesto la gran variabilidad de estos patógenos. Las accesiones silvestres de melón recogidas en distintos bancos de germoplasma son un valioso recurso para los programas de mejora genética frente a estreses bióticos. La accesión africana TGR-1551 ha sido descrita previamente como resistente a WMV, CYSDV (cucurbit yellow stunting disorder virus), CABYV y el hongo Podosphaera xanthii (Px, razas 1, 2 y 5) agente causal del oídio en melón. Además, es tolerante a la mosca blanca (Bemisia tabaci) y portadora del gen Vat (virus aphid transmission), el cual limita la transmisión de virus por pulgón. Por lo tanto, esta accesión constituye una buena fuente de alelos de resistencia y, al poder utilizar un único parental donante, su uso acortaría los programas de mejora. En el marco de la presente tesis doctoral, mediante el desarrollo de poblaciones segregantes de mapeo y el aprovechamiento de las tecnologías de genotipado masivo se han podido cartografiar los QTLs asociados a la resistencia a CYSDV derivados de esta entrada. En el caso de la resistencia a CYSDV, se han detectado dos QTL en el cromosoma 5. El primero de ellos es de efecto mayor y herencia dominante, estando asociado al desarrollo de síntomas. El segundo QTL, de efecto menor y también de herencia dominante, no confiere resistencia por sí mismo y está asociado a la carga viral durante la infección. Siguiendo una estrategia similar se han podido cartografiar y estrecha[CA] Les cucurbitàcies són la segona família d'hortícoles més important a nivell mundial, només per darrere de les solanàcies. Tradicionalment el seu cultiu s'ha dut a terme a les zones temperades del planeta. No obstant això, les condicions de canvi climàtic, el comerç internacional i els models d'agricultura intensiva afavoreixen l'aparició de noves virosis i malalties fúngiques en zones on abans no estaven presents. En aquest sentit, resulta essencial el monitoratge periòdic de les principals zones productores, per a d'aquesta manera, poder detectar els virus i fongs emergents en cada territori i adaptar els programes de millora als objectius específics de cada zona. En el cas concret del meló (Cucumis melo) existeix una gran variabilitat intraespecífica que pot servir com a font d'al·lels de resistència enfront d'aquests patògens. No obstant això, les fonts de resistència solen trobar-se dins del germoplasma silvestre, normalment originari d'Àfrica o Àsia, i en el qual el nivell de domesticació és reduït. Per a un millor aprofitament de les accessions resistents, resulta necessari un estudi del control genètic dels caràcters d'interés, que permeta localitzar les regions associades a la resistència i dissenyar marcadors moleculars associats a aquestes. Això facilita els programes de millora orientats a la introgressió de les resistències mantenint el fons genètic de les varietats d'interés. En la present tesi doctoral, durant les campanyes d'estiu de 2019 i 2020, s'ha dut a terme un estudi de la incidència i diversitat genètica de nou espècies virals potencialment limitants per al cultiu de cucurbitàcies en el sud-est espanyol. S'ha pogut observar que els virus transmesos per pugons són prevalents enfront dels transmesos per mosca blanca. Dins del primer grup va destacar la presència de watermelon mosaic virus (WMV), cucurbits aphid born yellows virus (CABYV) i cucumber mosaic virus (CMV), ja que van ser detectats en totes les zones i cultius estudiats, apareixent sovint en infeccions mixtes. Moroccan watermelon mosaic virus (MWMV) i tomatoleaf curl New Delhi virus (ToLCNDV) també van ser detectats en algunes zones, però amb percentatges d'infecció més baixos i normalment en infeccions mixtes amb WMV. Les anàlisis filogenètiques dels diferents aïllats trobats ha permés la identificació de set nous perfils moleculars de WMV i d'aïllats recombinants de CMV, la qual cosa és consistent amb els resultats obtinguts en altres països i posa de manifest la gran variabilitat d'aquests patògens. Les accessions silvestres de meló recollides en diferents bancs de germoplasma són un valuós recurs per als programes de millora genètica enfront d'estressos biòtics. L'accessió africana *TGR-1551 ha sigut descrita prèviament com a resistent a WMV, CYSDV (cucurbit yellow stunting disorder virus), CABYV i el fong Podosphaera xanthii (Px, races 1, 2 i 5) agent causal de l'oïdi en meló. A més, és tolerant a la mosca blanca (Bemisia tabaci) i portadora del gen Vat (virus aphid transmission), el qual limita la transmissió de virus per pugó. Per tant, aquesta accessió constitueix una bona font d'al·lels de resistència i, en poder utilitzar un únic parental donant, el seu ús acurtaria els programes de millora. En el marc de la present tesi doctoral, mitjançant el desenvolupament de poblacions segregants de mapatge i l'aprofitament de les tecnologies de genotipat massiu s'ha pogut cartografiar els QTLs associats a la resistència a CYSDV derivats d'aquesta entrada. En el cas de la resistència a CYSDV, s'han detectat dues QTL en el cromosoma cinc. El primer d'ells és d'efecte major i herència dominant, estant associat al desenvolupament de símptomes. El segon QTL, d'efecte menor i també d'herència dominant, no confereix resistència per si mateix i està associat a la càrrega viral durant la infecció. Seguint una estratègia similar s'han pogut cartografiar i estrényer els *QTLs de resistència enfront de Px. En aquest cas es tracta d'una epistàsia dominant-re[EN] Cucurbits represent the second most important horticultural family worldwide, second only the Solanaceae family. Traditionally, their cultivation has been concentrated in temperate regions across the globe. However, climate change conditions, international trade, and intensive agricultural practices are contributing to the emergence of new viral and fungal diseases in regions where they were previously absent. In this regard, it is crucial to regularly monitor major production areas to detect emerging viruses and fungi specific to each region. This monitoring allows for the adaptation of breeding programs to the unique goals of each area. In the case of melon (Cucumis melo), it exists significant intraspecific variability that can serve as a source of resistance alleles against these pathogens. However, sources of resistance are often found within wild germplasm, typically originating from Africa or Asia, and characterized by limited domestication. To better utilize these resistant accessions, a study of the genetic control of desirable traits is necessary. This study aims to locate regions associated with resistance and design molecular markers linked to these regions. Such an approach streamlines breeding programs focused on introgressing resistance traits while preserving the genetic background of the desired varieties. During the summer campaigns of 2019 and 2020, this doctoral thesis conducted a study on the incidence and genetic diversity of nine viral species potentially affecting cucurbit cultivation in southeastern Spain. It was observed that viruses transmitted by aphids were more prevalent than those transmitted by whiteflies. Within the first group, the presence of watermelon mosaic virus (WMV), cucurbits aphid borne yellows virus (CABYV), and cucumber mosaic virus (CMV) stood out, as they were detected in all the studied areas and crops, often in mixed infections. Moroccan watermelon mosaic virus (MWMV) and tomato leaf curl New Delhi virus (ToLCNDV) were also detected in some areas but with lower infection percentages, typically in mixed infections with WMV. Phylogenetic analyses of the found isolates have identified seven new molecular profiles of WMV and recombinant CMV isolates, which is consistent with results from other countries, highlighting the extensive variability of these pathogens. Wild melon accessions preserved in various germplasm banks represent a valuable resource for breeding programs against biotic stresses. The African accession TGR-1551 has been previously described as resistant to WMV, CYSDV (cucurbit yellow stunting disorder virus), CABYV, and the fungus Podosphaera xanthii (Px, races 1, 2, and 5), which causes powdery mildew in melons. Additionally, it is tolerant to whiteflies (Bemisia tabaci) and carries the Vat gene (Virus Aphid Transmission), limiting virus transmission by aphids. Therefore, this accession constitutes as an excellent source of resistance alleles, and its use, as a single donor parent, can expedite breeding programs. Within the scope of this doctoral thesis, through the development of segregating mapping populations and the utilization of high-throughput genotyping technologies, the QTLs associated with CYSDV resistance from this accession have been mapped. In the case of CYSDV resistance, two QTLs have been detected on chromosome 5. The first of these, with major effects and dominant inheritance, is associated with symptom development. The second QTL, with minor effects and also dominant inheritance, does not confer resistance by itself and is linked to viral load during infection. A similar strategy was employed to map and narrow down the QTLs for resistance against Px. In this case, it involves a dominant-recessive epistasis, with the recessive gene located on chromosome 12 and the dominant gene on chromosome 5, specifically in the same region where the major CYSDV resistance QTL is located. Regarding resistance against WMV, previous studies conducted by the researchThis research was funded by the Spanish Ministerio de Ciencia e Innovación (MCIN/AEI/10.13039/501100011033), grant number PID2020-116055RB (C21 and C22), and by the Conselleria d’Educació, Investigació, Cultura i Esports de la Generalitat Valenciana, grant number PROMETEO/2021/072 (to promote excellence groups, cofinanced with FEDER funds). M.L. is a recipient of a predoctoral fellowship (PRE2018-083466) of the Spanish Ministerio de Ciencia, Innovación y Universidades co-financed with FSE funds.López Martín, M. (2023). Breeding Melons for Resistance to Viral and Fungal Diseases. Exploiting the Multi-Resistant Accession TGR-1551 [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/20206

    Limitations of Protein Structure Prediction Algorithms in Therapeutic Protein Development

    Get PDF
    The three-dimensional protein structure is pivotal in comprehending biological phenomena. It directly governs protein function and hence aids in drug discovery. The development of protein prediction algorithms, such as AlphaFold2, ESMFold, and trRosetta, has given much hope in expediting protein-based therapeutic discovery. Though no study has reported a conclusive application of these algorithms, the efforts continue with much optimism. We intended to test the application of these algorithms in rank-ordering therapeutic proteins for their instability during the pre-translational modification stages, as may be predicted according to the confidence of the structure predicted by these algorithms. The selected molecules were based on a harmonized category of licensed therapeutic proteins; out of the 204 licensed products, 188 that were not conjugated were chosen for analysis, resulting in a lack of correlation between the confidence scores and structural or protein properties. It is crucial to note here that the predictive accuracy of these algorithms is contingent upon the presence of the known structure of the protein in the accessible database. Consequently, our conclusion emphasizes that these algorithms primarily replicate information derived from existing structures. While our findings caution against relying on these algorithms for drug discovery purposes, we acknowledge the need for a nuanced interpretation. Considering their limitations and recognizing that their utility may be constrained to scenarios where known structures are available is important. Hence, caution is advised when applying these algorithms to characterize various attributes of therapeutic proteins without the support of adequate structural information. It is worth noting that the two main algorithms, AlfphaFold2 and ESMFold, also showed a 72% correlation in their scores, pointing to similar limitations. While much progress has been made in computational sciences, the Levinthal paradox remains unsolved

    Long-Molecule Assessment of Ribosomal DNA and RNA

    Get PDF
    The genes encoding ribosomal RNA and their transcriptional products are essential for life, however, remain poorly understood. Even with the advent of long-range sequencing methodologies, rDNA loci are difficult to study and remain obscure, prompting the consideration of alternative methods to probing this critical region of the genome. The research outlined in this thesis utilises molecular combing, a fibre stretching technique, to isolate DNA molecules measuring more than 5 Mbp in length. The capture of DNA molecules of this size should assist in exploring the architecture of entire rDNA clusters at the single-molecule level. Combining molecular combing with SNP targeting probes, this study aims to distinguish and assess the arrangement of rDNA promoter variants which have been shown to exhibit dramatically different environmental sensitivity. Additionally, through the application of Oxford Nanopore Technologies direct RNA sequencing, the work here has demonstrated the capture of near full-length rRNA primary transcripts, which will allow for assessing post-transcriptional modification across the length of multiple coding subunits within a single molecule, for the first time. Furthermore, an exploration of RNA modification profiles across sample types representative of different developmental stages has been conducted. This study predicts many sites to be differentially modified across these different developmental conditions, several of which are known to be important for, if not crucial in ribosome biogenesis and function. The work outlined in this thesis provides a framework for future studies to conduct long-molecule, genetic, and epitranscriptome profiling of this vital region of the genome, and its dynamic response to a changing environment

    On the robustness of Bayesian phylogenetic gene tree estimation

    Get PDF

    Differences in well-being:the biological and environmental causes, related phenotypes, and real-time assessment

    Get PDF
    Well-being is a complex, and multifaceted construct that includes feeling good and functioning well. There is a growing global recognition of well-being as an important research topic and public policy goal. Well-being is related to less behavioral and emotional problems, and is associated with many positive aspects of daily life, including longevity, higher educational achievement, happier marriage, and more productivity at work. People differ in their levels of well-being, i.e., some people are in general happier or more satisfied with their lives than others. These individual differences in well-being can arise from many different factors, including biological (genetic) influences and environmental influences. To enhance the development of future mental health prevention and intervention strategies to increase well-being, more knowledge about these determinants and factors underlying well-being is needed. In this dissertation, I aimed to increase the understanding of the etiology in a series of studies using different methods, including systematic reviews, meta-analyses, twin designs, and molecular genetic designs. In part I, we brought together all published studies on the neural and physiological factors underlying well-being. This overview allowed us to critically investigate the claims made about the biology involved in well-being. The number of studies on the neural and physiological factors underlying well-being is increasing and the results point towards potential correlates of well-being. However, samples are often still small, and studies focus mostly on a single biomarker. Therefore, more well-powered, data-driven, and integrative studies across biological categories are needed to better understand the neural and physiological pathways that play a role in well-being. In part II, we investigated the overlap between well-being and a range of other phenotypes to learn more about the etiology of well-being. We report a large overlap with phenotypes including optimism, resilience, and depressive symptoms. Furthermore, when removing the genetic overlap between well-being and depressive symptoms, we showed that well-being has unique genetic associations with a range of phenotypes, independently from depressive symptoms. These results can be helpful in designing more effective interventions to increase well-being, taking into account the overlap and possible causality with other phenotypes. In part III, we used the extreme environmental change during the COVID-19 pandemic to investigate individual differences in the effects of such environmental changes on well-being. On average, we found a negative effect of the pandemic on different aspects of well-being, especially further into the pandemic. Whereas most previous studies only looked at this average negative effect of the pandemic on well-being, we focused on the individual differences as well. We reported large individual differences in the effects of the pandemic on well-being in both chapters. This indicates that one-size-fits-all preventions or interventions to maintain or increase well-being during the pandemic or lockdowns will not be successful for the whole population. Further research is needed for the identification of protective factors and resilience mechanisms to prevent further inequality during extreme environmental situations. In part IV, we looked at the real-time assessment of well-being, investigating the feasibility and results of previous studies. The real-time assessment of well-being, related variables, and the environment can lead to new insights about well-being, i.e., results that we cannot capture with traditional survey research. The real-time assessment of well-being is therefore a promising area for future research to unravel the dynamic nature of well-being fluctuations and the interaction with the environment in daily life. Integrating all results in this dissertation confirmed that well-being is a complex human trait that is influenced by many interrelated and interacting factors. Future directions to understand individual differences in well-being will be a data-driven approach to investigate the complex interplay of neural, physiological, genetic, and environmental factors in well-being
    corecore