@phdthesis{Nadernezhad2024,
  author    = {Nadernezhad, Ali},
  title     = {Engineering approaches in biofabrication of vascularized structures},
  doi       = {10.25972/OPUS-34589},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-345892},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {Biofabrication technologies must address numerous parameters and conditions to reconstruct tissue complexity in vitro. A critical challenge is vascularization, especially for large constructs exceeding diffusion limits. This requires the creation of artificial vascular structures, a task demanding the convergence and integration of multiple engineering approaches. This doctoral dissertation aims to achieve two primary objectives: firstly, to implement and refine engineering methods for creating artificial microvascular structures using Melt Electrowriting (MEW)-assisted sacrificial templating, and secondly, to deepen the understanding of the critical factors influencing the printability of bioink formulations in 3D extrusion bioprinting. In the first part of this dissertation, two innovative sacrificial templating techniques using MEW are explored. Utilizing a carbohydrate glass as a fugitive material, a pioneering advancement in the processing of sugars with MEW with a resolution under 100 microns was made. Furthermore, by introducing the "print-and-fuse" strategy as a groundbreaking method, biomimetic branching microchannels embedded in hydrogel matrices were fabricated, which can then be endothelialized to mirror in vivo vascular conditions. The second part of the dissertation explores extrusion bioprinting. By introducing a simple binary bioink formulation, the correlation between physical properties and printability was showcased. In the next step, employing state-of-the-art machine-learning approaches revealed a deeper understanding of the correlations between bioink properties and printability in an extended library of hydrogel formulations. This dissertation offers in-depth insights into two key biofabrication technologies. Future work could merge these into hybrid methods for the fabrication of vascularized constructs, combining MEW's precision with fine-tuned bioink properties in automated extrusion bioprinting.},
  subject      = {3D-Druck},
  language  = {en}
}
@phdthesis{Albrecht2024,
  author    = {Albrecht, Christina},
  title     = {Kardiorestriktiver Knockout desmosomaler Proteine f{\"u}hrt zu einer Beeintr{\"a}chtigung der elektromechanischen Kopplung ohne mitochondriale Dysfunktion bei arrhythmogener Kardiomyopathie},
  doi       = {10.25972/OPUS-34847},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-348472},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {Arrhythmogene Kardiomyopathie (ACM) ist eine genetische Herzerkrankung, die durch Herzinsuffizienz, ventrikul{\"a}re Arrhythmien und pl{\"o}tzlichen Herztod gekennzeichnet ist. Mutationen in desmosomalen Proteinen der Zelladh{\"a}sion, wie Plakophilin 2 (PKP2) und Plakoglobin (PG), sind die h{\"a}ufigste Ursache der famili{\"a}ren ACM. Wie gest{\"o}rte Zelladh{\"a}sion zum ACM-Ph{\"a}notyp f{\"u}hrt, ist jedoch nur teilweise gekl{\"a}rt. Potentielle Mechanismen sind eine gest{\"o}rte Kalzium-(Ca2+)-Hom{\"o}ostase, mitochondrialer oxidativer Stress und metabolische St{\"o}rungen. Ziel dieser Studie ist es, die mitochondriale Energetik und die Ca2+ -Hom{\"o}ostase in kardio-restriktiven PKP2-Knockout-M{\"a}usen (KO) im Alter von 4, 8 und 12 Wochen sowie in PG-Knockout- M{\"a}usen im Alter von 6 Wochen zu untersuchen. Vier Wochen alte PKP2-KO-M{\"a}use zeigten fr{\"u}he Anzeichen von ACM, w{\"a}hrend alle anderen Altersgruppen typische Kennzeichen von ACM rekapitulierten. Kontraktilit{\"a}t, die damit verbundenen Ca2+ - Transienten, der Redoxstatus und das mitochondriale Membranpotenzial (ΔΨm) isolierter Kardiomyozyten wurden mit einem IonOptix-System bei elektrischer und β- adrenerger Stimulation untersucht. Alle desmosomalen KO-Kardiomyozyten zeigten eine verringerte diastolische Sarkomerl{\"a}nge, was auf eine diastolische Dysfunktion hinwies. In allen PKP2 KO Kardiomyozyten lag außerdem ein erh{\"o}hter intrazellul{\"a}rer Ca2+ -Spiegel vor, w{\"a}hrend in den PG KO-Kardiomyozyten das intrazellul{\"a}rer Ca2+ unver{\"a}ndert war. PKP2 KO- und PG KO-Kardiomyozyten wiesen keine Ca2+ - Sensibilisierung der Myofilamente auf. Zur weiteren Bewertung der mitochondrialen Funktion wurde eine hochaufl{\"o}sende Respirometrie in isolierten Herzmitochondrien bei gleichzeitiger {\"U}berwachung von ΔΨm in PKP2 KO und PG KO M{\"a}usen durchgef{\"u}hrt, welche in allen Versuchs- und Kontrollgruppen vergleichbar war. Im Verlauf der Versuche blieb der Redoxstatus stabil und es konnte kein Exzess reaktiver Sauerstoffspezies (ROS) festgestellt werden. Daraus konnte gefolgert werden, dass weder PKP2 KO noch PG KO-M{\"a}use eine beeintr{\"a}chtigte mitochondriale Atmung aufwiesen. Diese Studie zeigt, dass isolierte PKP2 KO- oder PG KO-Kardiomyozyten EC-Kopplungsdefekte ohne mitochondriale Dysfunktion aufwiesen. Eine mitochondriale Dysfunktion konnte als treibender Faktor f{\"u}r die Progression des ACM- Ph{\"a}notyps in den vorgestellten Mausmodellen ausgeschlossen werden. Weitere Studien sind erforderlich, um die mitochondriale Funktion im Zusammenhang mit ACM zu entschl{\"u}sseln.},
  subject      = {Herzmuskelkrankheit},
  language  = {de}
}
@phdthesis{Eckert2024,
  author    = {Eckert, Lisa Doreen},
  title     = {Multimodale Verfahren zum Eisenstoffwechsel bei ADHS - Vergleichende Bildgebung},
  doi       = {10.25972/OPUS-34829},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-348295},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {Die Aufmerksamkeitsdefizit-/Hyperaktivit{\"a}tsst{\"o}rung (ADHS) geh{\"o}rt weltweit zu den bedeutendsten psychiatrischen Erkrankungen des Kinder- und Jugendalters. Die Pathomechanismen sind aktuell noch nicht vollst{\"a}ndig gekl{\"a}rt, wobei es deutliche Hinweise auf hirnorganische Ver{\"a}nderungen gibt. Die transkranielle Sonographie stellt eine nicht-invasive Methode dar, strukturelle Unterschiede tiefer Hirnstrukturen zu untersuchen. Bereits in vorangegangenen Studien konnte mit der Methode eine Ver{\"a}nderung der Echogenit{\"a}t der Substantia nigra (SN) bei Kindern mit ADHS im Vergleich zu gesunden Kontrollprobanden nachgewiesen werden. In dieser Studie sollen nun die m{\"o}glichen physiologischen Hintergr{\"u}nde der erh{\"o}hten Echogenit{\"a}t der Substantia Nigra in Zusammenschau mit bildgebenden Verfahren betrachtet werden. Hierzu wurde in der vorliegenden multimodalen Studie bei 20 m{\"a}nnlichen Kindern mit ADHS im Alter zwischen 8 und 12 Jahren eine transkranielle Ultraschalluntersuchung (TCS) zur Bestimmung der echogenen Fl{\"a}che der Substantia Nigra sowie ein neuromelaninsensitives cMRT zur Bestimmung des neuromelaninassoziierten Volumens der SN, sowie des neuromelaninassoziierten Kontrastes SN/Cb durchgef{\"u}hrt. Als Kennwerte des peripheren Eisenhaushalts wurden die Konzentrationen von Eisen, Ferritin und Transferrin im Blut bestimmt. In die Auswertung gingen außerdem die St{\"a}rke der ADHS-Symptomatik (Strength and Difficulties Questionaire, SDQ; Fremdbeurteilungsbogen bei ADHS, FBB-ADHS), die kognitive Begabung ({\"u}ber CFT-20-R) und das Alter der Probanden ein. Psychiatrische Komorbidit{\"a}t wurde mit Hilfe der Child Behaviour Checklist (CBCL) erhoben.},
  subject      = {Aufmerksamkeitsdefizit-Syndrom},
  language  = {de}
}
@phdthesis{Goepfert2024,
  author    = {G{\"o}pfert, Dennis},
  title     = {Evaluation des psychischen Belastungserlebens von Gesundheitspersonal w{\"a}hrend der Sars-CoV-2 Pandemie - Eine Beurteilung anhand von Umfrageergebnissen der an{\"a}sthesiologischen Abteilung am Universit{\"a}tsklinikum W{\"u}rzburg},
  doi       = {10.25972/OPUS-34816},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-348164},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {Die Evaluation des psychischen Belastungserlebens bei Intensivpersonal zeigte w{\"a}hrend der ersten Covid-19 Welle eine stabile psychosoziale Situation mit Angst um Angeh{\"o}rige und soziale Isolierung als Hauptbelastungsfaktoren. Weiterhin konnten bestimmte vulnerable Gruppen identifiziert werden.},
  subject      = {Psychosoziale Belastung},
  language  = {de}
}
@phdthesis{Ibrahim2024,
  author    = {Ibrahim, Eslam Samir Ragab},
  title     = {Unraveling the function of the old yellow enzyme OfrA in \(Staphylococcus\) \(aureus\) stress response},
  doi       = {10.25972/OPUS-28960},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-289600},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {Biological systems are in dynamic interaction. Many responses reside in the core concepts of biological systems interplay (competition and cooperation). In infection situation, the competition between a bacterial system and a host is shaped by many stressors at spatial and temporal determinants. Reactive chemical species are universal stressors against all biological systems since they potentially damage the basic requirements of these systems (nucleic acids, proteins, carbohydrates, and lipids). Either produced endogenously or exogenously, reactive chemical species affect the survival of pathogens including the gram-positive Staphylococcus aureus (S. aureus). Therefore, bacteria developed strategies to overcome the toxicity of reactive species. S. aureus is a widely found opportunistic pathogen. In its niche, S. aureus is in permanent contact with surrounding microbes and host factors. Deciphering the deterministic factors in these interactions could facilitate pinpointing novel bacterial targets. Identifying the aforementioned targets is crucial to develop new strategies not only to kill the pathogenic organisms but also to enhance the normal flora to minimize the pathogenicity and virulence of potential pathogens. Moreover, targeting S. aureus stress response can be used to overcome bacterial resistance against host-derived factors. In this study, I identify a novel S. aureus stress response factor against reactive electrophilic, oxygen, and hypochlorite species to better understand its resilience as a pathogen. Although bacterial stress response is an active research field, gene function is a current bottleneck in characterizing the understudied bacterial strategies to mediate stress conditions. I aimed at understanding the function of a novel protein family integrated in many defense systems of several biological systems. In bacteria, fungi, and plants, old yellow enzymes (OYEs) are widely found. Since the first isolation of the yellow flavoprotein, OYEs are used as biocatalysts for decades to reduce activated C=C bonds in α,β-unsaturated carbonyl compounds. The promiscuity of the enzymatic catalysis is advantageous for industrial applications. However, the physiological function of OYEs, especially in bacteria, is still puzzling. Moreover, the relevance of the OYEs in infection conditions remained enigmatic.   Here, I show that there are two groups of OYEs (OYE flavin oxidoreductase, OfrA and OfrB) that are encoded in staphylococci and some firmicutes. OfrA (SAUSA300_0859) is more conserved than OfrB (SAUSA300_0322) in staphylococci and is a part of the staphylococcal core genome. A reporter system was established to report for ofrA in S. aureus background. The results showed that ofrA is induced under electrophilic, oxidative, and hypochlorite stress. OfrA protects S. aureus against quinone, methylglyoxal, hydrogen peroxide, and hypochlorite stress. Additionally, the results provide evidence that OfrA supports thiol-dependent redox homeostasis. At the host-pathogen interface, OfrA promotes S. aureus fitness in murine macrophage cell line. In whole human blood, OfrA is involved in S. aureus survival indicating a potential clinical relevance to bacteraemia. In addition, ofrA mutation affects the production of the virulence factor staphyloxanthin via the upper mevalonate pathway. In summary, decoding OfrA function and its proposed mechanism of action in S. aureus shed the light on a conserved stress response within multiple organisms.},
  subject      = {Staphylococcus aureus},
  language  = {en}
}
@phdthesis{Pres2024,
  author    = {Pres, Sebastian},
  title     = {Detection of a plasmon-polariton quantum wave packet by coherent 2D nanoscopy},
  doi       = {10.25972/OPUS-34824},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-348242},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {Plasmonic nanostructures are considered promising candidates for essential components of integrated quantum technologies because of their ability to efficiently localize broad-band electromagnetic fields on the nanoscale. The resulting local near field can be understood as a spatial superposition of spectrally different plasmon-polariton modes due to the spectrally broad optical excitation, and thus can be described as a classical wave packet. Since plasmon polaritons, in turn, can transmit and receive non-classical light states, the exciting question arises to what extent they have to be described as quantum mechanical wave packets, i.e. as a superposition of different quantum states. But how to probe, characterize and eventually manipulate the quantum state of such plasmon polaritons? Up to now, probing at room temperatures relied completely on analyzing quantum optical properties of the corresponding in-going and out-going far-field photon modes. However, these methods so far only allow a rather indirect investigation of the plasmon-polariton quantum state by means of transfer into photons. Moreover, these indirect methods lack spatial resolution and therefore do not provide on-site access to the plasmon-polariton quantum state. However, since the spectroscopic method of coherent two-dimensional (2D) nanoscopy offers the capability to follow the plasmon- polariton quantum state both in Hilbert space and in space and time domain a complete characterization of the plasmon polariton is possible. In this thesis a versatile coherent 2D nanoscopy setup is presented combining spectral tunability and femtosecond time resolution with spatial resolution on the nanometer scale due to the detection of optically excited nonlinear emitted electrons via photoemission electron microscopy (PEEM). Optical excitation by amplitude- and phase-shaped, systematically-modified and interferometric-stable multipulse sequences is realized, and characterized via Fourier-transform spectral interferometry (FTSI). This linear technique enables efficient data acquisition in parallel to a simultaneously performed experiment. The full electric-field reconstruction of every generated multipulse sequence is used to analyze the effect of non-ideal pulse sequences on the two-dimensional spectral data of population-based multidimensional spectroscopy methods like, e.g., the coherent 2D nanoscopy applied in this thesis. Investigation of the spatially-resolved nonlinear electron emission yield from plasmonic gold nanoresonators by coherent 2D nanoscopy requires a quasi-particle treatment of the addressed plasmon-polariton mode and development of a quantum model to adequately describe the plasmon-assisted multi-quantum electron emission from nanostructures. Good agreement between simulated and experimental data enables to connect certain spectral features to superpositions of non-adjacent plasmon-polariton quantum states, i.e, non-adjacent occupation-number states of the underlying quantized, harmonic oscillator, thus direct probing of the plasmon-polariton quantum wave packet at the location of the nanostructure. This is a necessary step to locally control and manipulate the plasmon-polariton quantum state and thus of general interest for the realization of nanoscale quantum optical devices.},
  subject      = {Coherent Multidimensional Spectroscopy},
  language  = {en}
}
@phdthesis{Neitz2024,
  author    = {Neitz, Hermann},
  title     = {Hydrophobic recognition motifs in functionalized DNA},
  doi       = {10.25972/OPUS-34838},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-348382},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {In w{\"a}ssriger Umgebung spielen hydrophobe Wechselwirkungen eine wichtige Rolle f{\"u}r die DNA. Die Einf{\"u}hrung von Modifikationen, die auf hydrophoben aromatischen Einheiten basieren, kann die Erkennung und Reaktivit{\"a}t von funktionellen Gruppen in der DNA steuern. Modifikationen k{\"o}nnen durch ein k{\"u}nstliches R{\"u}ckgrat oder in Form einer Erweiterung der Nukleobasen eingebracht werden und so zu zus{\"a}tzlichen Eigenschaften der DNA f{\"u}hren. Diese Dissertation befasst sich mit der Verwendung von hydrophoben Einheiten zur Funktionalisierung von DNA. Im ersten Teil der Arbeit wurde das Tolanmotiv (Diphenylacetylen) in Kombination mit dem acyclischen R{\"u}ckgrat von GNA und BuNA verwendet, um Erkennungseinheiten im DNA-Kontext zu erzeugen. Die gezielte Fluorierung der aromatischen Ringe des Tolan-Bausteins bildete die Grundlage f{\"u}r eine supramolekulare Sprache, die auf Aren-Fluoroaren-Wechselwirkungen basiert. Die spezifische Erkennung wurde mittels thermodynamischer, kinetischer und NMR-spektroskopischer Methoden untersucht. Im zweiten Teil der Arbeit wurden Desoxyuridin-Derivate mit einer hydrophoben aromatischen Modifikation hergestellt und in die DNA-Doppelhelix eingebaut. Die Bestrahlung mit UV-Licht f{\"u}hrte zu einer [2+2]-Cycloaddition zwischen zwei modifizierten Nukleosiden in der DNA. Das Reaktionsprodukt wurde strukturell charakterisiert und die Reaktion in verschiedenen biochemischen und nanotechnologischen DNA-Anwendungen eingesetzt.},
  subject      = {Supramolekulare Chemie},
  language  = {en}
}
@phdthesis{Lu2024,
  author    = {Lu, Jinping},
  title     = {The vacuolar TPC1 channel and its luminal calcium sensing site in the luminal pore entrance},
  doi       = {10.25972/OPUS-25135},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-251353},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {The slowly activating vacuolar SV/TPC1 channel is ubiquitously expressed in plants and provides a large cation conductance in the vacuolar membrane. Thereby, monovalent (K+, Na+) and in principle also divalent cations, such as Ca2+, can pass through the channel. The SV/TPC1 channel is activated upon membrane depolarization and cytosolic Ca2+ but inhibited by luminal calcium. With respect to the latter, two luminal Ca2+ binding sites (site 1 Asp240/Asp454/Glu528, site 2 Glu239/Asp240/Glu457) were identified to coordinate luminal Ca2+. In this work, the characteristics of the SV/TPC1 channels in terms of regulation and function were further elucidated, focusing on the TPC1s of Arabidopsis thaliana and Vicia faba. For electrophysiological analysis of the role of distinct pore residues for channel gating and luminal Ca2+ sensing, TPC1 channel variants were generated by site-directed mutagenesis and transiently expressed as eGFP/eYFP-fusion constructs in Arabidopsis thaliana mesophyll protoplasts of the TPC1 loss-of-function mutant attpc1-2. 1. As visualized by confocal fluorescence laser-scanning microscopy, all AtTPC1 (WT, E605A/Q, D606N, D607N, E605A/D606N, E605Q/D606N/D607N, E457N/E605A/D606N) and VfTPC1 channel variants (WT, N458E/A607E/ N608D) were correctly targeted to the vacuole membrane. 2. Patch-clamp studies revealed that removal of one of the negative charges at position Glu605 or Asp606 was already sufficient to promote voltage-dependent channel activation with higher voltage sensitivity. The combined neutralization of these residues (E605A/D606N), however, was required to additionally reduce the luminal Ca2+ sensitivity of the AtTPC1 channel, leading to hyperactive AtTPC1 channels. Thus, the residues Glu605/Asp606 are functionally coupled with the voltage sensor of AtTPC1 channel, thereby modulating channel gating, and form a novel luminal Ca2+ sensing site 3 in AtTPC1 at the luminal entrance of the ion transport pathway. 3. Interestingly, this novel luminal Ca2+ sensing site 3 (Glu605/Asp606) and Glu457 from the luminal Ca2+ sensing site 2 of the luminal Ca2+-sensitive AtTPC1 channel were neutralized by either asparagine or alanine in the TPC1 channel from Vicia faba and many other Fabaceae. Moreover, the VfTPC1 was validated to be a hyperactive TPC1 channel with higher tolerance to luminal Ca2+ loads which was in contrast to the AtTPC1 channel features. As a result, VfTPC1 but not AtTPC1 conferred the hyperexcitability of vacuoles. When AtTPC1 was mutated for the three VfTPC1-homologous polymorphic site residues, the AtTPC1 triple mutant (E457N/E605A/D606N) gained VfTPC1-like characteristics. However, when VfTPC1 was mutated for the three AtTPC1-homologous polymorphic site residues, the VfTPC1 triple mutant (N458E/A607E/N608D) still sustained VfTPC1-WT-like features. These findings indicate that the hyperactivity of VfTPC1 is achieved in part by the loss of negatively charged amino acids at positions that - as part of the luminal Ca2+ sensing sites 2 and 3 - are homologous to AtTPC1-Glu457/Glu605/Asp606 and are likely stabilized by other unknown residues or domains. 4.The luminal polymorphic pore residues (Glu605/Asp606 in AtTPC1) apparently do not contribute to the unitary conductance of TPC1. Under symmetrical K+ conditions, a single channel conductance of about 80 pS was determined for AtTPC1 wild type and the AtTPC1 double mutant E605A/D606A. This is in line with the three-fold higher unitary conductance of VfTPC1 (232 pS), which harbors neutral luminal pore residues at the homologous sites to AtTPC1. In conclusion, by studying TPC1 channel from Arabidopsis thaliana and Vicia faba, the present thesis provides evidence that the natural TPC1 channel variants exhibit differences in voltage gating, luminal Ca2+ sensitivity and luminal Ca2+ binding sites.},
  language  = {en}
}
@phdthesis{Okorn2024,
  author    = {Okorn, Alexander},
  title     = {Synthese und Reaktivit{\"a}t von PAH-substituierten Diborenen und Dihydroanthracendiyl-verbr{\"u}ckten Diborverbindungen},
  doi       = {10.25972/OPUS-34836},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-348368},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {Die vorliegende Arbeit besch{\"a}ftig sich mit der Synthese und Reaktivit{\"a}t von Phosphan-stabilisierten Diborenen, die auf Grund ihres Substitutionsmusters {\"u}ber ein erh{\"o}htes Reaktivit{\"a}tsverm{\"o}gen verf{\"u}gen. Der erste Teil dieser Arbeit beschreibt die Synthese von polycyclischen aromatischen Kohlenwasserstoff (PAH)-substituierten, Trimethylphosphan-stabilisierten Diborenen. Im zweiten Abschnitt dieser Arbeit wird die Synthese von Diborenen beschrieben, welche in einer Dihydroanthracendiyl-verbr{\"u}ckten Ringstruktur eingebunden sind.},
  language  = {de}
}
@phdthesis{Pekarek2024,
  author    = {Pek{\´a}rek, Luk{\´a}š},
  title     = {Single-Molecule Approaches To Study Frameshifting Mechanisms},
  doi       = {10.25972/OPUS-34611},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-346112},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {The RNAs of many viruses contain a frameshift stimulatory element (FSE) that grants access to an alternate reading frame via -1 programmed ribosomal frameshifting (PRF). This -1PRF is essential for effective viral replication. The -1PRF efficiency relies on the presence of conserved RNA elements within the FSE, such as a slippery sequence, spacer, and a downstream secondary structure - often a hairpin or a pseudoknot. The PRF efficiency is also affected by trans-acting factors such as proteins, miRNAs and metabolites. The interactions of these factors with the RNA and the translation machinery have not yet been completely understood. Traditional ensemble methods used previously to study these events focus on the whole population of molecular species. This results in innate averaging of the molecular behavior and a loss of heterogeneity information. Here, we first established the experimental workflow to study the RNA structures and the effect of potential trans-acting factors using single-molecule force spectroscopy technique, optical tweezers. Additionally, to streamline the data analysis, we developed an algorithm for automatized data processing. Next, we harnessed this knowledge to study viral RNA elements responsible for stimulation of PRF and how the presence of trans-acting factors affects the RNA behavior. We further complemented these single-molecule structural data with ensemble functional assays to gain a complex view on the dynamics behind the programmed ribosomal frameshifting. Specifically, two different viral RNA elements have been studied in the presented work. First, the dynamics of SARS-CoV-2 FSE and the role of extended sequences have been explored. Then, the mode of action of the host-encoded trans-acting factor ZAP-S inhibition of SARS-CoV-2 PRF has been examined. Finally, the mechanism of the trans-acting viral factor induced PRF in Encephalomyocarditis virus (EMCV) has been uncovered.},
  language  = {en}
}