Boletín que incluye información científica sobre el COVID-19, incluye artículos científicos y artículos preprint actualizados al 19 de Junio de 2020.

Indiana University-Purdue University Indianapolis (IUPUI) / Designing and developing a diagnostic technology that is capable of highly sensitive and specific, multiplexed, high-throughput, and quantitative biomarker assays for disease diagnosis and progression is of the upmost importance in modern medicine and patient care. Current diagnostic assays capable of multiplexed and high-throughput analysis include mass spectrometry, electrochemistry, polymerase chain reaction (PCR), and fluorescence-based techniques, however, these techniques suffer from a lack in sensitivity, false responses, or extensive sample processing that are detrimental to clinical diagnostics. To overcome these sensitivity challenges, the field of nanoplasmonics has become utilized when developing diagnostic assays. Plasmonic-based diagnostic tests utilize the unique optical, chemical, and physical property of nanoparticles to increase the sensitivity of the assay. In this dissertation, novel diagnostic platforms that utilize nanoparticles and their localized surface plasmon resonance (LSPR) property will be introduced. LSPR is an optical property in noble metallic nanoparticles that is referred to as the collective oscillation of free electrons upon light irradiation. It is highly dependent on the shape, size, and dielectric constant (refractive index) of the surrounding medium of the nanoparticle and LSPR sensing is based on a change in these properties. In this dissertation, the LSPR property is utilized to fabricate nanoplasmonic-based diagnostic platforms that are capable of multiplexed and high-throughput biomarker assays, with high sensitivity and specificity. The work presented in this dissertation is presented as six chapters, (1) Introduction. (2) Methods, (3) Fabrication of a LSPR-based multiplexed and high-throughput biosensor platform and its application in performing microRNA assays for the diagnosis of bladder cancer. In this chapter, the advancement of single-plex solid state LSPR-based biosensors into a multiplexed and high-throughput diagnostic biosensor platform is reported for the first time. The diagnostic biosensor platform is first fabricated utilizing different gold nanoparticles (spherical nanoparticles, nanorods, and triangular nanoprisms), and then with the gold triangular nanoprisms as the nanoparticle of choice, microRNA assays were performed. The developed biosensor platform is capable of assaying five different types of microRNAs simultaneously at an attomolar limit of detection. Additionally, five microRNA were assayed in 20-bladder cancer patient plasma samples. (4) Development/optimization of the biosensor platform presented in Chapter 3 for the detection of COVID-19 biomarkers. In this chapter, the biosensor platform utilized in Chapter 3 was designed to assay 10 different COVID-19 specific biomarkers from three classes (six viral nucleic acid gene sequences, two spike protein subunits, and two antibodies) with limit of detections in the attomolar range and with high specificity. The high-throughput capability of the biosensor platform was advanced, with the platform performing analysis of a single biomarker in 92 patient samples simultaneously. Additionally, the biomarker platform was utilized to assay all 10 biomarkers in a total of 80 COVID-19 patient samples. (5) Further optimization of the biosensor platform for the development of a highly specific antibody detection test for COVID-19. During the COVID-19 pandemic, knowledge was gained on the specificity of antibodies produced against COVID-19. In this chapter, that knowledge was applied towards the optimization of the biosensor platform presented in Chapter 4 in order to assay SARS-CoV-2 neutralizing antibody IgG. The optimization of the biosensor platform included the size of the gold triangular nanoprisms and the receptor molecule of choice. The biosensor platform assayed this highly specific COVID-19 IgG antibody with a limit of detection as low as 30.0 attomolar with high specificity and no cross reactivity. Additionally, as a proof of concept, the biosensor platform was utilized in a high-throughput format to assay SARS-CoV-2 IgG in a large cohort of 121 COVID-19 patient samples simultaneously. (6) Advancement of the biosensor platform from a 96-well plate to a 384-well plate and its application in assaying microRNA for early diagnosis of pancreatic cancer. In this chapter, the high-throughput capabilities of the biosensor platform presented in Chapters 3-5 was expanded by increasing the sensor amount in one platform from 92 to 359. The 384-well plate biosensor platform was designed, optimized, and utilized to perform microRNA assays for early-stage pancreatic cancer diagnosis. The optimization of the biosensor platform included the manipulation of LSPR-based parameters and the -ssDNA receptor molecule in order to obtain low limit of detections (high sensitivity). Additionally, the biosensor platform assayed two microRNA in a large cohort (n=110) of pancreatic cancer and chronic pancreatitis patient samples.

Background: At the end of 2019, a novel coronavirus denominated SARS-CoV-2 rapidly spread through the world causing the pandemic coronavirus disease known as COVID-19. The difference in the inflammatory response against SARS-CoV-2 infection among people living at different altitudes is a variable not yet studied. Methods: A descriptive cross-sectional study was performed in two Peruvian cities at different altitudes for comparison: Lima and Huaraz. Five important proinflammatory cytokines were measured including: IL-6, IL-2, IL-10, IFN-γ and TNF-α using ELISA assays. Results: A total of 35 COVID-19 patients and 10 healthy subjects were recruited from each study site. The mean levels of IL-6 (p < 0.03) and TNF-α (p < 0.01) were significantly different among the study groups. In the case of IL-6, patients from Lima had a mean level of 16.2 pg/ml (healthy) and 48.3 pg/ml (COVID-19), meanwhile, patients from Huaraz had levels of 67.3 pg/ml (healthy) and 97.9 pg/ml (COVID-19). Regarding TNF-α, patients from Lima had a mean level of 25.9 pg/ml (healthy) and 61.6 pg/ml (COVID-19), meanwhile, patients from Huaraz had levels of 89.0 pg/ml (healthy) and 120.6 pg/ml (COVID-19). The levels of IL-2, IL-10 and IFN-γ were not significantly different in the study groups. Conclusion: Patients with COVID-19 residing at high-altitude tend to have higher levels of inflammatory cytokines compared to patients living at sea level, particularly IL-6 and TNF-α. A better understanding of the inflammatory response in different populations can contribute to the implementation of therapeutic and preventive approaches. Further studies evaluating more patients, a greater variety of cytokines and their clinical impact are required. / National Research Foundation of Korea / Revisión por pares

La rápida propagación mundial de un nuevo coronavirus denominado SARS-CoV-2, detectado en la cuidad de Wuhan, China, hace necesario del conocimiento e implementación de métodos de diagnóstico confiables para detectar y tratar adecuadamente a los pacientes. Para ello, los métodos más utilizados para el diagnóstico son: la técnica de inmunocromatografía (IC), la cual enmarca tanto a las pruebas detectoras de anticuerpos como a la prueba de detección de antígenos; y las pruebas de diagnóstico molecular basadas en tecnología de PCR, detectando cuantitativa y cualitativamente al virus, como por ejemplo qRT-PCR y al LAMP. Mediante la revisión de las bases de Scielo, Pubmed y Scopus se compara la utilidad diagnóstica de las pruebas LAMP, qRT-PCR e IC aplicadas al diagnóstico de SARS-CoV-2, y cómo las distintas variantes del virus han impactado sobre la confiabilidad de estas pruebas.

Global lifespans are longer than ever before and there is an increasing shift towards a more aged global population. Also, the majority of severe disease and deaths in the recent and ongoing COVID-19 pandemic is found in individuals over 60 years of age. Therefore, there is an urgent need to gain insight into how the immune system changes with age; specifically: (1) what are the drivers of chronic, systemic inflammation (‘inflammaging’) that occur in some but not all older individuals and (2) how, in turn, numerical aging and chronic inflammation collide to impact anti-viral immunity and lead to poor infection outcomes. In this body of work, two focused research questions were addressed as part of an overarching goal to determine the links between numerical age, chronic inflammatory status, and immune cell function. First, the role of iNKT cells in the inflammation found with ART-suppressed HIV infection and aging was studied, and second, connections between age and pre-existing immunity to SARS-CoV-2 were investigated. Invariant natural killer T (iNKT) cells are a unique, innate-like T cell subset known to bridge innate and adaptive immune responses and can exert inflammatory and immunosuppressive effector functions. The role of iNKT cells in the chronic inflammation found with ART-suppressed HIV infection and/or normal aging is unclear. Therefore, iNKT cell frequencies and surface phenotypes were measured from a HIV and Aging cohort comprised of ART-suppressed HIV+ subjects and matched uninfected controls stratified by age into younger and older groups and iNKT cell signature were correlated with plasma markers of chronic inflammation. Specific characteristics of iNKT cells were associated with aviremic HIV infection and/or advanced age, and distinct links between iNKT cell signatures and markers of chronic inflammation were found. Further, multivariate analysis (PLS-DA) of the collected dataset revealed that iNKT cell and plasma markers stratified younger from older subjects within both the uninfected and aviremic HIV+ groups. Older age is arguably the strongest predictor of severe clinical outcomes and mortality after SARS-CoV-2 infection. The role of pre-existing, cross-reactive immunity in COVID-19 outcomes is unclear to date. A newly developed, highly sensitive serological assay (the BU ELISA) was used to elucidate links between pre-existing immunity to SARS-CoV-2 and age. We found SARS-CoV-2 receptor binding domain (RBD) and/or nucleocapsid protein (N) reactive antibodies (IgG, IgM, and/or IgA isotypes) in all pre-pandemic subjects tested, with a wide range in antibody levels. SARS-CoV-2 reactive immunoglobulin levels tracked with antibodies specific for analogous viral proteins from endemic coronavirus strains and were lowest in subjects over 70 years of age compared with younger counterparts. In sum, these findings provide evidence of lower pre-existing immunity to SARS-CoV-2 in elderly individuals, and this may account for their poor infection outcomes. In conclusion, the findings in this work provide new insight into the impact of age and chronic inflammation on productive and protective immune responses. These results underscore the need for further investigations into the immune cell mechanisms and inflammaging pathways that subvert healthy aging.

Carta al editor / Revisión por pares

Le méthane a la deuxième plus grande contribution à au forçage radiatif global des gaz à effet de serre anthropiques. Après une période de stabilité, son taux de croissance atmosphérique a augmenté rapidement depuis 2007. Les émissions anthropiques de méthane ont un potentiel important d'atténuation ce qui encourage les efforts visant à réduire ses émissions conformément à l'accord de Paris. Toutefois, beaucoup d’incertitudes demeurent concernant la contribution de différentes sources de méthane, les processus et les estimations des émissions, même à une échelle locale ; ce qui entrave la mise en œuvre efficace des stratégies d'atténuation du méthane. Jusqu’à maintenant, de nombreuses études ont été réalisées pour mesurer les flux globaux de méthane, la répartition et la caractérisation des sources de méthane par région mais les processus doivent encore être mieux déterminés.Cette thèse présente et applique des méthodes pour caractériser les différentes sources de CH4 présentes dans les mesures de l'air ambiant des sites industriels et développe des outils ciblés pour répondre à cette question. Le premier chapitre traite des améliorations apportées à un instrument CRDS fréquemment déployé pour les mesures de CH4 et de δ13CH4. Nous proposons un schéma d'étalonnage pour corriger les interférences C2H6 sur δ13CH4 et permettre des mesures fiables de C2H6. Les résultats de ces travaux sont ensuite utilisés pour explorer la valeur ajoutée sur les données de la mise en œuvre de cette méthode sur une station de compresseur de gaz naturel, où une forte corrélation de C2H6 et de CH4 est normalement attendue. Le deuxième chapitre poursuit la caractérisation des sources de CH4 sur le même site mais porte plus sur l'application et la comparaison des différentes méthodes de répartition des sources. Les contributions des sources de CH4 et composés organiques volatils (COV) sont explorées selon la méthode de l'analyse isotopique, de l'analyse des séries temporelles multi-espèces à l’aide de modèles source-récepteur (PCA et PMF), des données météorologiques et des échantillons directs de gaz naturel. Le troisième chapitre présente une utilisation des méthodes de répartition des sources de CH4 sur les mesures ambiantes des sources de CH4 biogénique dans la région Ile de France et aide ainsi à compléter l'étude des sources anthropiques de CH4 les plus pertinentes.Cette thèse identifie et documente les signatures en δ13CH4 de différentes sources de CH4 sur des environnements contrastés à proximité de fermes d’élevage intensif, de stations d’épuration des eaux usées, de décharges d’enfouissement des déchets ou encore de sites de compression du gaz naturel, et étudie leur variabilité spatiale et temporelle pour faciliter la contrainte des émissions. Les résultats obtenus suggèrent que l’identification de différentes sources biogéniques et thermogéniques avec le δ13CH4 est robuste et adaptable à une grande diversité d’environnements. L'utilisation d'une combinaison d'outils est idéale pour étudier la variabilité à court terme et long terme. Cette thèse présente différentes utilisations de ces nouveaux outils pour diriger les investigations des émissions anthropiques de méthane et sont la base pour de futurs travaux dans ce domaine. / Methane has the second largest contribution to global radiative forcing impact of anthropogenic greenhouse gasses. Since 2007 its atmospheric growth rate, after a period of stability, has again been rising rapidly. Anthropogenic methane emissions hold a large mitigation potential, promoting efforts to curb emissions in accordance with the Paris Agreement. However, the considerable uncertainties regarding methane contributors, drivers and emission estimates even at local scales, hinder the effective implementation of methane mitigation strategies. While many approaches have been established to measure total methane fluxes, the partitioning and characterisation of methane sources by region and processes still need to be better constrained.This thesis presents practical methods for characterising different CH4 sources in ambient air measurements at industrial sites, as well as developing more targeted tools. The first chapter focuses on improvements to a CRDS instrument that is commonly deployed for CH4 and δ13CH4 field measurements. We propose a calibration scheme to correct for C2H6 interference on δ13CH4, and enable robust C2H6 measurements. The results of this work are then used to explore the added value gained when implemented on data from a natural gas compressor station, a site where high correlation of C2H6 and CH4 is expected. The second chapter continues the investigation of CH4 sources at the same site; with focus shifted towards the application and comparison of different source apportionment methods from time series analysis based on measurements of multiple species, some co-emitted with CH4. Here the CH4 and Volatile Organic Compounds (VOC) source contributions are explored through the use of isotopic analysis, receptor model analysis (PCA and PMF), metrological data and direct samples of natural gas. The third chapter applies a selection of the developed CH4 source apportionment methods to ambient measurements at biogenic CH4 sites in the Ile de France region and helps complete the survey of the most relevant anthropogenic CH4 sources.This thesis identifies and reports local δ13CH4 source signatures for livestock, wastewater, landfill and natural gas and studies their spatial and temporal variability to aid the constraint of emission inventories. Our findings suggest that source apportionment from δ13CH4 is robust, and adaptable to the majority of sites. Using a combination of tools is ideal for more specific source determination and for an understanding of long and short term variability. The work presented in this thesis offers example applications of these new tools to directed investigations of anthropogenic methane emissions and lays the foundation for future work in this field.

京都大学 / 新制・課程博士 / 博士(人間・環境学) / 甲第23392号 / 人博第1005号 / 新制||人||237(附属図書館) / 2021||人博||1005(吉田南総合図書館) / 京都大学大学院人間・環境学研究科相関環境学専攻 / (主査)准教授 三浦 智行, 教授 川本 卓男, 准教授 西川 完途 / 学位規則第4条第1項該当 / Doctor of Human and Environmental Studies / Kyoto University / DFAM

As central components of life, DNA and RNA encode the genetic information. However, RNA performs several functions that exceed the competences stated in the ‘central dogma of life‘. RNAs undergo extensive post-transcriptional processing like chemical modifications. Among all classes of RNA, tRNAs are the most extensively modified. Their modifications are chemically diverse and vary from simple methylations (e.g. m3C, m6A) to more complex residues, like isopentenyl group (e.g. i6A, hypermodifications: e.g. ms2i6A) or even amino acids (e.g. t6A). Depending on their location within the overall structure, modifications can have an impact on tRNA stability and structure, as well as affinity for the ribosome and translation efficiency and fidelity. Given the importance of tRNA modifications new tools are needed for their detection and to study their recognition by proteins and enzymatic transformations. The chemical synthesis of these naturally occurring tRNA modifications as phosphoramidite building blocks is a prerequisite to incorporate the desired modification via solid-phase synthesis into oligonucleotides. With the help of the m3C, (ms2)i6A, and t6A oligonucleotides, the importance and impact of tRNA modifications was investigated in this thesis. To this end, the role of METTL8 as the methyltransferase responsible for the installation of the methyl group at C32 for mt-tRNAThr and mt-tRNASer(UCN) was resolved. Thereby, the respective adenosine modification on position 37 is essential for the effectiveness of the enzyme. Besides, by means of NMR analysis, CD spectroscopy, thermal denaturation experiments, and native page separation, the impact of m3C32 on the structure of the tRNA ASLs was shown. The modification appeared to fine-tune the tRNA structure to optimize mitochondrial translation. To investigate the regulation of the dynamic modification pathway of m3C, demethylation assays were performed with the modified tRNA-ASLs and the (α-KG)- and Fe(II)-dependent dioxygenase ALKBH1 and ALKHB3. A demethylation activity of ALKBH3 on the mt-tRNAs was observed, even though it has so far only been described as a cytoplasmic enzyme. Whether this is physiologically relevant and ALKBH3 present a mitochondrial localization needs further validation. In addition, ALKBH1 was confirmed to not be able to demethylate m3C on mt-tRNAs, but indications for a deprenylation and exonuclease activity were found. Furthermore, the aforementioned naturally occurring modifications were utilized to find analytical tools that can determine the modification levels by DNAzymes, which cleave RNA in the presence of a specific modification. Selective DNA enzymes for i6A, as well as the three cytidine isomers m3C, m4C, and m5C have been identified and characterized. Besides the naturally occurring tRNA modifications, the investigation on artificially modified nucleosides is also part of this thesis. Nucleosides with specific properties for desired applications can be created by modifying the scaffold of native nucleosides. During the pandemic, the potential of antiviral nucleoside analogues was highlighted for the treatment of the SARS-CoV-2 infection. For examinations of the potential drug-candidate Molnupiravir, the N4-hydroxycytidine phosphoramidite building block was synthesized and incorporated into several RNA oligonucleotides. A two-step model for the NHC-induced mutagenesis of SARS-CoV-2 was proposed based on RNA elongation, thermal denaturation, and cryo-EM experiments using the modified RNA strands with the recombinant SARS-CoV-2 RNA-dependent RNA polymerase. Two tautomeric forms of NHC enable base pairing with guanosine in the amino and with adenosine in the imino form, leading to error catastrophe after the incorporation into viral RNA. These findings were further corroborated by thermal melting curve analysis and NMR spectroscopy of the NHC-containing Dickerson Drew sequence. In conclusion, the anti-amino form in the NHC-G base pair was assigned by NMR analysis using a 15N-labeld NHC building block incorporated into the Dickerson Drew sequence. This thesis also addressed the synthesis of a 7-deazaguanosine crosslinker with a masked aldehyde as a diol linker for investigations of DNA-protein interactions. The diol functional group can be unmasked to release the reactive aldehyde, which can specifically form a covalent bond with amino acids Lys or Arg within the protein complex condensin. The incorporation of the synthesized phosphoramidite and triphosphate building blocks were shown and the functionality of the PCR product containing the crosslinker was demonstrated by oxidation and the formation of a covalent bond with a fluorescein label. The development of assays that detect changes in this methylation pattern of m6A could provide new insights into important biological processes. In the last project of this thesis, the influence of RNA methylation states on the structural properties of RNA was analyzed and a fluorescent nucleoside analog (8-vinyladenosine) as molecular tools for such assays was developed. Initial experiments with the fluorescent nucleoside analog N6-methyl-8-vinyladenosine (m6v8A) were performed and revealed a strong fluorescence enhancement of the free m6v8A nucleoside by the installation of the vinyl moiety at position 8. Overall, this thesis contributes to various research topics regarding the application of naturally occurring and artificial nucleoside analogues. Starting with the chemical synthesis of RNA and DNA modifications, this thesis has unveiled several open questions regarding the dynamic (de-)methylation pathway of m3C and the mechanism of action of molnupiravir through in-depth analysis and provided the basis for further investigations of the protein complex condensin, and a new fluorescent nucleoside analog m6v8A. / Als zentrale Bestandteile des Lebens kodieren DNA und RNA die genetische Information. Die RNA erfüllt jedoch noch mehr Funktionen, die über die im 'zentralen Dogma des Lebens' ge-nannten Kompetenzen hinausreichen. RNA Stränge werden posttranskriptionell verändert, wie zum Beispiel durch chemische Modifikationen. tRNAs sind unter allen RNA-Klassen am umfangreichsten und chemisch vielfältigsten modifiziert. Ihre Modifikationen reichen von ein-fachen Methylierungen (z. B. m3C oder m6A) bis hin zu komplexeren Resten, wie einer Iso-pentenyl-Gruppe (i6A, Hypermodifikation: z. B. ms2i6A) oder sogar Aminosäuren (t6A). Ab-hängig von ihrer Position innerhalb der tRNA können Modifikationen Einfluss auf die tRNA Stabilität und Struktur, sowie die Affinität zu den Ribosomen und die Translationseffizienz und Genauigkeit, haben. Angesichts dieser Bedeutung von tRNA-Modifikationen werden zum einen Nachweisemethoden zur Detektion von Modifikationen, als auch Werkzeuge zur Unter-suchung der Erkennungsmechanismen spezifischer Proteine und deren enzymatischer Funk-tionalisierung benötigt. Dabei ist die chemische Synthese dieser natürlichen Modifikationen als Phosphoramidit-Bausteine die Voraussetzung, um die gewünschte Modifikation überhaupt erst über Festpha-sensynthese in Oligonukleotide einbauen zu können. Mit Hilfe der m3C-, (ms2)i6A- und t6A-modifizierten Oligonukleotide wurde die Bedeutung dieser tRNA-Modifikationen für die Struk-tur und Funktionalität des jeweiligen tRNA Anticodon-Loops (ACL) untersucht. Ein Kapitel dieser Arbeit klärte die tatsächliche Rolle von METTL8 auf. Als Methyltransferase ist das Protein für den Einbau der Methylgruppe an C32 in den mitochondrialen tRNAThr und tRNASer(UCN) verantwortlich, kann dies aber nur bewerkstelligen, wenn zuvor bereits eine ent-sprechende Adenosin-Modifikation an A37 installiert wurde. Außerdem wurde mittels NMR-Analyse, CD-Spektroskopie, Schmelzkurvenanalysen und Gelelektrophorese der Einfluss von m3C32 auf die Struktur der tRNA Anticodon-Stem-Loops (ASLs) gezeigt. Die Modifikation scheint die tRNA-Struktur anzupassen, um die mitochondriale Translation zu optimieren. Um herauszufinden, wie die dynamischen Modifikationswege von m3C reguliert werden, wurden mit den modifizierten tRNA-ASLs und den (α-KG)- und Fe(II)-abhängigen Dio-xygenasen ALKBH1 und ALKHB3 Demethylierungsassays durchgeführt. Obwohl ALKBH3 bisher nur als cytoplasmatisches Enzym bekannt war, konnte es mt-tRNAs demethylieren. Inwiefern diese Aktivität physiologisch relevant ist und ob ALKBH3 vielleicht zusätzlich auch eine mitochond-riale Lokalisierung aufweist, muss noch weiter untersucht werden. Zudem wurde gezeigt, dass ALKBH1 m3C32-modifizierte mt-tRNAs nicht demethylieren kann, es jedoch Hinweise darauf gibt, dass ALKBH1 zusätzlich zu der bereits beschriebenen Aktivität der Oxidation von m5C zu f5C in mitochondrialer tRNAMet eine noch näher zu untersuchende Deprenylierungs- und Exonuklease-Aktivität besitzt. Außerdem wurden die zuvor erwähnten natürlichen Modifikationen verwendet, um DNA-Enzyme als analytische Werkzeuge zur Bestimmung des Modifikationsgrades zu finden. Die Enzyme katalysieren die Spaltung von RNA, falls eine spezielle Modifikation vorhanden ist. Es wurden selektive DNA-Enzyme für i6A sowie die drei Cytidin-Isomere m3C, m4C und m5C identifiziert und charakterisiert. Neben den posttranskriptionalen Modifikationen war auch die Untersuchung künstlich modifi-zierter Nukleoside ein Teil dieser Arbeit. Das Gerüst nativer Nukleoside kann so modifiziert werden, dass die Nukleoside spezifischen Eigenschaften für die gewünschte Anwendung erhalten. Während der Pandemie wurde antiviralen Nukleosidanaloga zur Behandlung der SARS-CoV-2-Infektion eine große Bedeutung zugeschrieben. Um den potenziellen Arzneimittelkandidaten Molnupiravir zu untersuchen, wurde N4-Hydroxycytidin als Phosphoramidit-Baustein syntheti-siert und in mehrere RNA-Oligonukleotide mittels Festphasensynthese eingebaut. Basierend auf den Ergebnissen von RNA-Elongations-, thermischen Denaturierungs- und Cryo-EM-Experimenten, bei denen die modifizierten RNA-Stränge und die rekombinante SARS-CoV-2-RNA-abhängige RNA-Polymerase verwendet wurde, wurde ein zweistufiges Modell für die NHC-induzierte Mutagenese von SARS-CoV-2 postuliert. Dieser Mechanismus wird durch die zwei tautomeren Formen von NHC ermöglicht, wobei die Amino-Form ein Basenpaar mit Guanosin bildet und die Imino-Form mit Adenosin basenpaaren kann. Nach dem Einbau in die virale RNA kommt es zu Mutationen und zur sogenannten Fehlerkatastrophe. Diese Er-kenntnisse wurden durch thermische Schmelzkurvenanalyse und NMR-Spektroskopie der NHC-haltigen Dickerson Drew Sequenz ergänzt. Mit Hilfe eines 15N-markierten NHC-Bausteins, der in die Dickerson Drew Sequenz eingebaut wurde, konnte schließlich die Anti-Amino Form in dem NHC-G Basenpaar durch NMR-Analyse eindeutig nachgewiesen wer-den. Ein weiteres Forschungsprojekt dieser Arbeit befasste sich mit der Synthese eines 7-Deazaguanosin-Crosslinkers, welcher einen geschützten Aldehyd als Diol-Linker enthielt. Die-ser Crosslinker sollte zur Untersuchung von DNA-Protein-Interaktionen dienen. Der Einbau der synthetisierten Phosphoramidit- und Triphosphat-Bausteine konnte erfolgreich durchge-führt werden und die Funktionalität des PCR-Produktes, welches den Crosslinker enthielt, wurde durch Oxidation und die Bildung einer kovalenten Bindung mit einem Fluorescein-Label demonstriert. Der letzte Teil dieser Arbeit beschäftigte sich mit der der Entwicklung eines Assays, um Ver-änderungen im Methylierungslevel von m6A nachweisen zu können. Dies könnte neue Einbli-cke in wichtige biologische Prozesse liefern. Daher wurde im letzten Projekt der Einfluss von RNA-Methylierungszuständen auf die strukturellen Eigenschaften von RNA untersucht und dafür ein fluoreszierendes Nukleosidanalog (8-Vinyladenosin) als molekulares Werkzeug ent-wickelt. Die ersten Experimente mit dem Nukleosidanalog N6-Methyl-8-Vinyladenosin (m6v8A) zeigten einen deutlichen Fluoreszenzanstieg durch den Einbau der Vinyleinheit an Position 8 im Vergleich zu dem nicht fluoreszierenden m6A. Insgesamt trägt diese Arbeit zu verschiedenen Forschungsthemen bezüglich der Anwendung von natürlich vorkommenden und künstlichen Nukleosidanaloga bei. Ausgehend von der chemischen Synthese von RNA- und DNA-Modifikationen hat diese Arbeit durch eingehende Analysen mehrere offene Fragestellungen zum dynamischen (De-)Methylierungsweg von m3C und zum Wirkmechanismus von Molnupiravir aufgedeckt und die Grundlage für weitere Untersuchungen des Proteinkomplexes Condensin und eines neuen fluoreszierenden Nukle-osidanalogons m6v8A geschaffen.

Viral infection severity often varies with host factors such as age and sex. The pathogenesis of infections caused by a broad range of viruses, from neurotropic viruses like Rabies and Zika to respiratory viruses such as Influenza and SARS-CoV-2, differ between the sexes and across the lifespan. Typically, older males are more susceptible to severe acute outcomes, while females are more vulnerable to the post-acute sequelae of infections. All of these complications can include neuroinflammation, stroke, cognitive dysfunction, and delirium. While these symptoms can be secondary to infection, recent studies suggest that even peripheral infections can lead to neuropathological changes in the brain. However, few studies have characterized the expression of viral receptors in the human brain or examined age- or sex-related differences in such expression. In this study, we used a publicly accessible transcriptomic database to assess the impact of age and sex on the expression of 67 viral host factor genes, associated with ten virus families. Analyzing data from 15 brain areas (n=33, F=14, M=19, age:4 mo-80 yrs), we determined the lifespan trajectory for each gene in each area via LOESS regressions. We used unsupervised hierarchical clustering to determine if a brain-wide pattern or virus family pattern can be detected. Using Dense-tSNE, a dimension-reduction and visualization technique, we discovered four distinct developmental trajectories, clustering the areas into two mixed-sex subcortical clusters and one each of male and female cortical clusters. Applying Differential Expression Sliding Window Analysis (DeSWAN), we identified the genes driving these age- and sex-related differences. Many sex differences were noted in childhood, potentially impacting the brain's susceptibility to viral infections and underscoring a broader dimorphic organization of male and female brains. These insights contribute to our understanding of sex-specific responses to viral infections, offering the potential for more personalized treatment strategies. / Thesis / Master of Science (MSc) / Viral infections, like Influenza and SARS-CoV-2, vary in severity based on a person's age and sex. Generally, older men suffer severe immediate symptoms such as stroke and seizures, while women endure long-term effects, including brain inflammation and cognitive issues. Recent research suggests even non-brain-related infections can lead to changes within the brain. Yet, our understanding of how our brains' viral receptors - key to infection - change with age and between sexes is limited. We used a public database to explore these changes, studying receptor-related genes in different brain areas across various ages and sexes. Our analysis revealed unique patterns of gene expression, grouping the brain into different regions based on development and sex. We noticed many differences between men and women during childhood, potentially influencing how their brains respond to viruses. This research aids our understanding of why viral infections impact individuals differently based on age and sex, offering insights that could help develop personalized treatments.