8,362 research outputs found
Genetic and functional analysis of the adaptive immune response
The cells of the adaptive immune system rely on somatic recombination of V, D and J genes to obtain a vast range of specificities. T cells use four chains encoded by three genomic loci, to produce alpha/beta or gamma/delta T cell receptors (TCRs). B cell receptors (BCRs) are encoded by three loci, a single heavy chain and two light chain loci, kappa and lambda. Because these genomic regions are highly polymorphic, the germline TCR and BCR repertoires are individual, shaping the elicited response against infections and vaccines in each person. In this thesis, I used a set of specialized tools and analysis pipelines to explore the adaptive immune receptors at the genomic and functional levels in both humans and non-human primates (NHP), highlighting the benefits of integrating individualized TCR/BCR repertoire analysis with functional studies to understand adaptive immune responses.
In paper I, we sequence expressed TCR repertoires of 45 individuals from four human populations: African, East Asian, South Asian, and European. Analysis of these repertoires with the germline gene inference tool, IgDiscover, identified 175 novel V and J alleles, most of which were characterized by codon changes or non-functional variants. The germline TCR repertoires were highly diverse between individuals, with some of the novel alleles identified only in specific populations. Furthermore, we report three introgressed regions inherited from Homo neanderthalensis. One of these regions includes a novel variant of TRGV4, frequent in Eurasians populations, which display altered reactivity to the ligand butyrophilin-like molecule 3 (BTNL3).
In papers II and III, we analyzed the humoral immune response in NHPs elicited by a series of immunizations with SARS-CoV-2 Spike-derived subunit proteins. In paper II, we observed detectable neutralization titers after priming with ancestral spike (S) protein with very high antibody titers obtained after boosting. The immunization regimen resulted in durable neutralization titers as well as S-specific memory B cells. In paper III, we used a heterotypic boosting strategy with beta-derived receptor binding domain (RBD) to broaden the response to circulating SARS-CoV-2 variants. The boost elicits potent and protective cross-neutralizing humoral immune responses.
In paper IV, we analyzed multi-compartmental longitudinal samples from two macaques used in paper II. We combined single cell and next generation sequencing (NGS) of BCR repertoires to characterize S-specific antibodies and S-specific B cell lineages elicited by immunizations with ancestral SARS-CoV-2 S proteins. Lineage tracing analysis identified persistent antibody lineages that were present after priming and were widely disseminated in blood, bone marrow (BM), spleen and different lymph nodes (LN), including a broadly neutralizing RBD-binding lineage. Through structural cryo-EM studies, we showed that this antibody achieved cross-neutralization by targeting conserved RBD residues with crucial interactions through its heavy chain CDR3 (HCDR3)
Polyphenolic Compounds in Wine and Beer
This reprint describes the polyphenolic composition of wine and beer, with a special emphasis on extractive and analytical aspects. Furthermore, the effects of wine and beer polyphenols on human health are studied in the depth
Stabilization and Resuscitation of Newborns
The majority of newborns do not need medical interventions to manage the neonatal transition after birth. However, every year millions of newborns worldwide require respiratory support immediately after birth, and another considerable number of newborns additionally require extensive resuscitation including chest compressions and drug administration. Despite a significant increase in knowledge and development of enhanced therapy strategies over the past few years, morbidity and mortality caused by failures in neonatal transition remain an important health issue. The purpose of this reprint is to support or introduce novel concepts and add information in the area of the “Stabilization and Resuscitation of Newborns”, aiming to improve neonatal care and, as the major objective, to enhance neuro-developmental outcomes
Deriving a mathematical framework for data-driven analyses of immune cell dynamics
Zelluläre Entscheidungen, wie z. B. die Differenzierung von T-Helferzellen (Th-Zellen) in spezialisierte Effektorlinien, haben großen Einfluss auf die Spezifität von Immunreaktionen. Solche Reaktionen sind das Ergebnis eines komplexen Zusammenspiels einzelner Zellen, die über kleine Signalmoleküle, so genannte Zytokine, kommunizieren. Die hohe Anzahl der Komponenten, sowie deren komplizierte und oft nichtlineare Interaktionen erschweren dabei die Vorhersage, wie bestimmte zelluläre Reaktionen erzeugt werden. Aus diesem Grund sind die globalen Auswirkungen der gezielten Beeinflussung einzelner Zellen oder spezifischer Signalwege nur unzureichend verstanden. So wirken beispielsweise etablierte Behandlungen von Autoimmunkrankheiten oft nur bei einem Teil der Patienten. Durch Einzelzellmethoden wie Live-Cell-Imaging, Massenzytometrie und Einzelzellsequenzierung, können Immunzellen heutzutage quantitativ auf mehreren Ebenen charakterisiert werden. Diese Ansammlung quantitativer Daten erlaubt die Formulierung datengetriebener Modelle zur Vorhersage von zellulären Entscheidungen, allerdings fehlen in vielen Fällen Methoden, um die verschiedenen Daten auf geeignete Weise zu integrieren und zu annotieren. Die vorliegende Arbeit befasst sich mit quantitativen Modellformulierungen für die Entscheidungsfindung von Zellen im Immunsystem mit dem Schwerpunkt auf Lymphozytenproliferation, -differenzierung und -tod.Cellular decisions, such as the differentiation of T helper (Th) cells into specialized effector lineages, largely impact the direction of immune responses. Such population-level responses are the result of a complex interplay of individual cells which communicate via small signaling molecules called cytokines. The system's complexity, stemming not only from the number of components but also from their intricate and oftentimes non-linear interactions, makes it difficult to develop intuition for how cellular responses are actually generated. Not surprisingly, the global effects of targeting individual cells or specific signaling pathways through perturbations are poorly understood. For instance, common treatments of autoimmune diseases often work for some patients, but not for others. Recently developed methods such as live-cell imaging, mass cytometry and single-cell sequencing now enable quantitative characterization of individual immune cells. This accumulating wealth of quantitative data has laid the basis to derive predictive, data-driven models of immune cell behavior, but in many cases, methods to integrate and annotate the data in a way suitable for model formulation are missing. In this thesis, quantitative workflows and methods are introduced that allow to formulate data-driven models of immune cell decision-making with a particular focus on lymphocyte proliferation, differentiation and death
Designing Advanced Nanocatalysts: Synthesis of complex CeO2-based Nanostructures
[eng] The main objective of this dissertation has been to stablish a bridge between materials science and its fields of application. The scope of this thesis work, under this premise, is aimed towards understanding the catalytical properties of CeO2 nanocrystals and the applications arising from them. In order to tackle it, the chemist labour consists in providing a cutting-edge nanosynthesis technology able to improve efficiencies of the chemical processes, reducing energy consumption and minimizing the environmental impact of both activity and waste products. At the same time, research on nanomaterial synthesis involves the design and formulation of nanomaterials under total control of their physicochemical, morphological, and colloidal properties. Coupled with the appropriate description of the structure-activity relations, the current aim of nanomaterial synthesis is an application-oriented design strategy towards programmable properties of the products.
Within this framework, this thesis work is divided into two parts. The first part revolves around nanomaterial synthesis. It pursues the optimised formulation of nanostructured CeO2, a semiconductor material that holds a broad set of intrinsic catalytic properties, describing the synthesis of the minimal stable size for colloidal monocrystalline particles of the material and its complete physicochemical characterization (size, composition, morphology, crystal structure, optical and colloidal properties). It is followed by the extension of the material’s functionality through different derivation strategies, such as doping with different trivalent lanthanide ions and coupling to plasmonic metal domains (Au and Ag) via different synthetic approaches to produce several types of hybrid architectures (core-shell, heterodimers, hollow structures, and other anisotropic shapes) of controlled size.
The second part of this work involves the characterization of structure-activity relations of the CeO2-based nanomaterials synthesised in the first part. These are evaluated first through the catalytic performance of each nanomaterial. It has been carried out for two different processes. As a heterogeneous catalyst for methanol production and as ROS scavenger for biomedical applications, coupled with the correspondent assessment of the nanomaterials’ toxicity through in vitro assays. To complete the description of the structure-activity relations, the characterization of the singular electronic structure of CeO2, that confers its characteristic catalytical properties, has been also carried out. Employing core-level spectroscopic techniques, the differences between bulk and nanosized CeO2 have been evaluated through the Ce 3d and O 1s spectra in XPS and Ce L3 edge in XANES.[cat] L'objectiu principal d'aquesta tesi doctoral és fomentar ponts entre la ciència de materials i els seus diferents camps d'aplicació. Partint d'aquesta premissa, la finalitat concreta del treball és assolir uns millor coneixement de les propietats catalítiques del CeO2 nanoestructurat i les aplicacions que en poden emergir. Per abordar aquesta qüestió, des de l'àmbit de la química s'ha de proveir d’una tecnologia capdavantera de síntesi de nanomaterials, capaç de millorar les eficiències dels processos químics reduint el consum d'energia i la producció de residus per minimitzar-ne l'impacte ambiental. Alhora, la investigació actual en síntesi de nanomaterials es fonamenta en el disseny i formulació dels mateixos sota el control total de les seves propietats fisicoquímiques, morfològiques i col·loidals. En conjunt amb la descripció adequada de les relacions activitat-estructura dels materials formulats, l'objectiu actual de la síntesi de nanomaterials és el disseny orientat a la aplicació final mitjançant la programació de les propietats del producte.
Dins d'aquest marc, aquesta tesi compta amb dues parts. La primera gira al voltant de la síntesi de nanomaterials. Es busca la formulació optimitzada de nanocristalls de CeO2, un material semiconductor que posseeix un ampli ventall de propietats catalítiques, a través de la descripció de la síntesi de partícules col·loidals monocristal·lines de menor mida possible dins de la seva estabilitat termodinàmica. Aquesta part es completa amb l'extensió de la funcionalitat del material mitjançant diferents estratègies d'hibridació d'aquest, com ara bé el dopatge amb cations trivalents lantànids o l'acoblament de dominis de metalls plasmònics (Au i Ag) seguint diferents estratègies de síntesi.
La segona part d'aquest treball tracta la caracterització de les relacions estructura-activitat dels materials ja sintetitzats en la primera. Aquestes són avaluades, en primer lloc, a través de la activitat catalítica de cada nanomaterial per a un procés de catàlisi heterogènia (producció de metanol) i com a neutralitzador de radicals lliures per aplicacions biomèdiques. En segon lloc, l'origen de les propietats catalítiques del material es descriu a través de la caracterització de la singular estructura electrònica del CeO2 nanostructurat, emprant tècniques d'espectroscòpia com XPS i XANES
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