@phdthesis{WasgebHouben2023,
  author    = {Was [geb. Houben], Nina},
  title     = {Die Rolle der nicht-kodierenden RNAs miR-26 und \(Malat1\) bei der \(in\) \(vitro\) Differenzierung zu Neuronen},
  doi       = {10.25972/OPUS-30371},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-303714},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {W{\"a}hrend der embryonalen Neurogenese spielt die Repression neuraler Gene in nicht neuralen Zellen, sowie in neuralen Vorl{\"a}uferzellen durch den REST (repressor element silencing transcription factor)-Komplex eine wichtige Rolle. Durch die schrittweise Inaktivierung diese Komplexes im Verlauf der Differenzierung werden neurale Genexpressionsprogramme gesteuert. Zus{\"a}tzlich kommt bei der Kontrolle der r{\"a}umlichen und zeitlichen Regulation der Genexpression w{\"a}hrend der Neurogenese verschiedenen miRNAs eine wichtige Rolle zu. So konnte in vorangegangenen Arbeiten im Zebrafischen gezeigt werden, dass miR-26b die Transkription eines wichtigen Effektorproteins des REST-Komplexes, CTDSP2 (C-terminal domain small phosphatases), w{\"a}hrend der Neurogenese negativ reguliert. Da dar{\"u}ber hinaus die miR-26 Repression zu einer stark verminderten neuronalen Differenzierung f{\"u}hrte, kommt diesem regulatorischen Schaltkreis eine zentrale Rolle bei der Neurogenese im Zebrafisch zu. Die zusammen mit ihren Ctdsp-Wirtsgenen koexprimierte miR-26 Familie liegt in Vertebraten evolution{\"a}r hoch konserviert vor. Analog zum Zebrafisch konnte im murinen in vitro ES-Zell Differenzierungssystem gezeigt werden, dass miR-26 die Expression von Ctdsp2 reprimiert. Weiterhin konnte in diesem System gezeigt werden, dass auch Rest ein miR-26 Zielgen ist und dass der Verlust der miR-26 zu einem Arrest der differenzierenden Zellen im neuronalen Vorl{\"a}uferstadium f{\"u}hrt. Zusammengenommen deuten diese vorangegangenen Arbeiten auf eine zentrale Rolle der miR-26 w{\"a}hrend der Neurogenese hin. Die hier vorgestellte Arbeit zielte zun{\"a}chst darauf ab die Regulation des REST-Komplexes durch die miR-26 auf molekularer Ebene besser zu verstehen. Der Verlust der miR-26 Bindestelle in der Ctdsp2 mRNA f{\"u}hrte zu einer erh{\"o}hten Ctdsp2 Expression, beeinflusste aber nicht die terminale Differenzierung zu Neuronen. Im Gegensatz hierzu f{\"u}hrte der Verlust der miR-26 Bindestelle in der Rest mRNA zu einem Arrest der Differenzierung im neuralen Vorl{\"a}uferzellstadium. Zellen in denen die miR-26 Bindestelle in Rest deletiert war, zeigten zudem, genau wie miR-26 knockout (KO) Zellen, eine erh{\"o}hte Expression von REST-Komplex Komponenten, sowie eine verringerte Expression von REST-regulierten miRNAs. Zusammengenommen weisen diese Daten daraufhin, dass w{\"a}hrend der Neurogenese im S{\"a}ugersystem die Inaktivierung von Rest durch miR-26 f{\"u}r die Maturierung von Neuronen eine zentrale Rolle spielt. Ein weiterer Fokus dieser Arbeit lag auf der Regulation der miR-26 Expression w{\"a}hrend der Neurogenese. Vorangegangene Arbeiten in nicht-neuronalen Zelltypen identifizierten die lnc (long-non-coding) RNA Malat1 als eine ce (competitive endogenous) RNA der miR-26. Um den Einfluss von Malat1 auf die miR-26 Expression w{\"a}hrend der Neurogenese zu untersuchen, wurde zun{\"a}chst mittels CRISPR/Cas9 der vollst{\"a}ndige Malat1-Lokus in ESCs deletiert. Der Verlust von Malat1 f{\"u}hrte zu einer erh{\"o}hten Expression der miR-26 Familienmitglieder sowie deren Ctdsp-Wirtsgene. Weiterhin war die Proliferation von Malat1 KO neuronalen Vorl{\"a}uferzellen stark vermindert, was mit einer Erh{\"o}hung der Frequenz seneszenter Zellen einherging. Durch die Inaktivierung von miR-26 in differenzierenden Malat1 KO ESCs konnte dieser proliferative Ph{\"a}notyp aufgehoben werden. Dar{\"u}ber hinaus konnte eine verst{\"a}rkte neuronale Differenzierung dieser Zellen beobachtet werden. Zusammenfassend zeigen diese Daten, dass neben der Regulation des REST-Komplexes durch miR-26 auch die Kontrolle des Zellzyklus {\"u}ber die Malat1-vermittelte Regulation der miR-26 in neuronalen Vorl{\"a}uferzellen einen kritischen Schritt bei der Differenzierung von neuronalen Vorl{\"a}uferzellen zu maturen Neuronen darstellt.},
  subject      = {Neurogenese},
  language  = {de}
}
@phdthesis{Sauerwein2023,
  author    = {Sauerwein, Till},
  title     = {Implementation and application of bioinformatical software for the analysis of dual RNA sequencing data of host and pathogen during infection},
  doi       = {10.25972/OPUS-30307},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-303075},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Since the advent of high-throughput sequencing technologies in the mid-2010s, RNA se- quencing (RNA-seq) has been established as the method of choice for studying gene expression. In comparison to microarray-based methods, which have mainly been used to study gene expression before the rise of RNA-seq, RNA-seq is able to profile the entire transcriptome of an organism without the need to predefine genes of interest. Today, a wide variety of RNA-seq methods and protocols exist, including dual RNA sequenc- ing (dual RNA-seq) and multi RNA sequencing (multi RNA-seq). Dual RNA-seq and multi RNA-seq simultaneously investigate the transcriptomes of two or more species, re- spectively. Therefore, the total RNA of all interacting species is sequenced together and only separated in silico. Compared to conventional RNA-seq, which can only investi- gate one species at a time, dual RNA-seq and multi RNA-seq analyses can connect the transcriptome changes of the species being investigated and thus give a clearer picture of the interspecies interactions. Dual RNA-seq and multi RNA-seq have been applied to a variety of host-pathogen, mutualistic and commensal interaction systems. We applied dual RNA-seq to a host-pathogen system of human mast cells and Staphylo- coccus aureus (S. aureus). S. aureus, a commensal gram-positive bacterium, can become an opportunistic pathogen and infect skin lesions of atopic dermatitis (AD) patients. Among the first immune cells S. aureus encounters are mast cells, which have previously been shown to be able to kill the bacteria by discharging antimicrobial products and re- leasing extracellular traps made of protein and deoxyribonucleic acid (DNA). However, S. aureus is known to evade the host's immune response by internalizing within mast cells. Our dual RNA-seq analysis of different infection settings revealed that mast cells and S. aureus need physical contact to influence each other's gene expression. We could show that S. aureus cells internalizing within mast cells undergo profound transcriptome changes to adjust their metabolism to survive in the intracellular niche. On the host side, we found out that infected mast cells elicit a type-I interferon (IFN-I) response in an autocrine manner and in a paracrine manner to non-infected bystander-cells. Our study provides the first evidence that mast cells are capable to produce IFN-I upon infection with a bacterial pathogen.},
  subject      = {Biologie},
  language  = {en}
}
@phdthesis{FetivaMora2023,
  author    = {Fetiva Mora, Maria Camila},
  title     = {Changes in chromatin accessibility by oncogenic YAP and its relevance for regulation of cell cycle gene expression and cell migration},
  doi       = {10.25972/OPUS-30291},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-302910},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Various types of cancer involve aberrant cell cycle regulation. Among the pathways responsible for tumor growth, the YAP oncogene, a key downstream effector of the Hippo pathway, is responsible for oncogenic processes including cell proliferation, and metastasis by controlling the expression of cell cycle genes. In turn, the MMB multiprotein complex (which is formed when B-MYB binds to the MuvB core) is a master regulator of mitotic gene expression, which has also been associated with cancer. Previously, our laboratory identified a novel crosstalk between the MMB-complex and YAP. By binding to enhancers of MMB target genes and promoting B-MYB binding to promoters, YAP and MMB co-regulate a set of mitotic and cytokinetic target genes which promote cell proliferation. This doctoral thesis addresses the mechanisms of YAP and MMB mediated transcription, and it characterizes the role of YAP regulated enhancers in transcription of cell cycle genes. The results reported in this thesis indicate that expression of constitutively active, oncogenic YAP5SA leads to widespread changes in chromatin accessibility in untransformed human MCF10A cells. ATAC-seq identified that newly accessible and active regions include YAP-bound enhancers, while the MMB-bound promoters were found to be already accessible and remain open during YAP induction. By means of CRISPR-interference (CRISPRi) and chromatin immuniprecipitation (ChIP), we identified a role of YAP-bound enhancers in recruitment of CDK7 to MMB-regulated promoters and in RNA Pol II driven transcriptional initiation and elongation of G2/M genes. Moreover, by interfering with the YAP-B-MYB protein interaction, we can show that binding of YAP to B-MYB is also critical for the initiation of transcription at MMB-regulated genes. Unexpectedly, overexpression of YAP5SA also leads to less accessible chromatin regions or chromatin closing. Motif analysis revealed that the newly closed regions contain binding motifs for the p53 family of transcription factors. Interestingly, chromatin closing by YAP is linked to the reduced expression and loss of chromatin-binding of the p53 family member Np63. Furthermore, I demonstrate that downregulation of Np63 following expression of YAP is a key step in driving cellular migration. Together, the findings of this thesis provide insights into the role of YAP in the chromatin changes that contribute to the oncogenic activities of YAP. The overexpression of YAP5SA not only leads to the opening of chromatin at YAP-bound enhancers which together with the MMB complex stimulate the expression of G2/M genes, but also promotes the closing of chromatin at ∆Np63 -bound regions in order to lead to cell migration.},
  subject      = {Chromatin},
  language  = {en}
}
@phdthesis{Schardt2023,
  author    = {Schardt, Simon},
  title     = {Agent-based modeling of cell differentiation in mouse ICM organoids},
  doi       = {10.25972/OPUS-30194},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-301940},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Mammalian embryonic development is subject to complex biological relationships that need to be understood. However, before the whole structure of development can be put together, the individual building blocks must first be understood in more detail. One of these building blocks is the second cell fate decision and describes the differentiation of cells of the inner cell mass of the embryo into epiblast and primitive endoderm cells. These cells then spatially segregate and form the subsequent bases for the embryo and yolk sac, respectively. In organoids of the inner cell mass, these two types of progenitor cells are also observed to form, and to some extent to spatially separate. This work has been devoted to these phenomena over the past three years. Plenty of studies already provide some insights into the basic mechanics of this cell differentiation, such that the first signs of epiblast and primitive endoderm differentiation, are the expression levels of transcription factors NANOG and GATA6. Here, cells with low expression of GATA6 and high expression of NANOG adopt the epiblast fate. If the expressions are reversed, a primitive endoderm cell is formed. Regarding the spatial segregation of the two cell types, it is not yet clear what mechanism leads to this. A common hypothesis suggests the differential adhesion of cell as the cause for the spatial rearrangement of cells. In this thesis however, the possibility of a global cell-cell communication is investigated. The approach chosen to study these phenomena follows the motto "mathematics is biology's next microscope". Mathematical modeling is used to transform the central gene regulatory network at the heart of this work into a system of equations that allows us to describe the temporal evolution of NANOG and GATA6 under the influence of an external signal. Special attention is paid to the derivation of new models using methods of statistical mechanics, as well as the comparison with existing models. After a detailed stability analysis the advantages of the derived model become clear by the fact that an exact relationship of the model parameters and the formation of heterogeneous mixtures of two cell types was found. Thus, the model can be easily controlled and the proportions of the resulting cell types can be estimated in advance. This mathematical model is also combined with a mechanism for global cell-cell communication, as well as a model for the growth of an organoid. It is shown that the global cell-cell communication is able to unify the formation of checkerboard patterns as well as engulfing patterns based on differently propagating signals. In addition, the influence of cell division and thus organoid growth on pattern formation is studied in detail. It is shown that this is able to contribute to the formation of clusters and, as a consequence, to breathe some randomness into otherwise perfectly sorted patterns.},
  subject      = {Mathematische Modellierung},
  language  = {en}
}
@article{DhillonDahmsKuebertFlocketal.2023,
  author    = {Dhillon, Maninder Singh and Dahms, Thorsten and Kuebert-Flock, Carina and Rummler, Thomas and Arnault, Joel and Steffan-Dewenter, Ingolf and Ullmann, Tobias},
  title     = {Integrating random forest and crop modeling improves the crop yield prediction of winter wheat and oil seed rape},
  series = {Frontiers in Remote Sensing},
  volume    = {3},
  journal   = {Frontiers in Remote Sensing},
  issn      = {2673-6187},
  doi       = {10.3389/frsen.2022.1010978},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-301462},
  year      = {2023},
  abstract  = {The fast and accurate yield estimates with the increasing availability and variety of global satellite products and the rapid development of new algorithms remain a goal for precision agriculture and food security. However, the consistency and reliability of suitable methodologies that provide accurate crop yield outcomes still need to be explored. The study investigates the coupling of crop modeling and machine learning (ML) to improve the yield prediction of winter wheat (WW) and oil seed rape (OSR) and provides examples for the Free State of Bavaria (70,550 km2), Germany, in 2019. The main objectives are to find whether a coupling approach [Light Use Efficiency (LUE) + Random Forest (RF)] would result in better and more accurate yield predictions compared to results provided with other models not using the LUE. Four different RF models [RF1 (input: Normalized Difference Vegetation Index (NDVI)), RF2 (input: climate variables), RF3 (input: NDVI + climate variables), RF4 (input: LUE generated biomass + climate variables)], and one semi-empiric LUE model were designed with different input requirements to find the best predictors of crop monitoring. The results indicate that the individual use of the NDVI (in RF1) and the climate variables (in RF2) could not be the most accurate, reliable, and precise solution for crop monitoring; however, their combined use (in RF3) resulted in higher accuracies. Notably, the study suggested the coupling of the LUE model variables to the RF4 model can reduce the relative root mean square error (RRMSE) from -8\% (WW) and -1.6\% (OSR) and increase the R 2 by 14.3\% (for both WW and OSR), compared to results just relying on LUE. Moreover, the research compares models yield outputs by inputting three different spatial inputs: Sentinel-2(S)-MOD13Q1 (10 m), Landsat (L)-MOD13Q1 (30 m), and MOD13Q1 (MODIS) (250 m). The S-MOD13Q1 data has relatively improved the performance of models with higher mean R 2 [0.80 (WW), 0.69 (OSR)], and lower RRMSE (\%) (9.18, 10.21) compared to L-MOD13Q1 (30 m) and MOD13Q1 (250 m). Satellite-based crop biomass, solar radiation, and temperature are found to be the most influential variables in the yield prediction of both crops.},
  language  = {en}
}
@phdthesis{Helmerich2023,
  author    = {Helmerich, Dominic Andreas},
  title     = {Einfl{\"u}sse der Photophysik und Photochemie von Cyaninfarbstoffen auf die Lokalisationsmikroskopie},
  doi       = {10.25972/OPUS-24716},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-247161},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {In den letzten Jahren haben sich hochaufl{\"o}sende Fluoreszenzmikroskopiemethoden, basierend auf der Lokalisation einzelner Fluorophore, zu einem leistungsstarken Werkzeug etabliert, um Fluoreszenzbilder weit unterhalb der Aufl{\"o}sungsgrenze zu generieren. Hiermit k{\"o}nnen r{\"a}umliche Aufl{\"o}sungen von ~ 20 nm erzielt werden, was weit unterhalb der Beugungsgrenze liegt. Dabei haben zahlreiche Optimierungen und Entwicklungen neuer Methoden in der Einzelmolek{\"u}l-Lokalisationsmikroskopie die Genauigkeit der orstspezifischen Bestimmung einzelner Fluorophore auf bis zu ~ 1 - 3 nm erh{\"o}ht. Eine Aufl{\"o}sung im molekularen Bereich, weit unterhalb von ~ 10 nm bleibt allerdings herausfordernd, da die Lokalisationsgenauigkeit nur ein Kriterium hierf{\"u}r ist. Allerdings wurde sich in den letzten Jahren {\"u}berwiegend auf die Verbesserung dieses Parameters konzentriert. Weitere Kriterien f{\"u}r die fluoreszenzmikroskopische Aufl{\"o}sung sind dabei unter anderem die Markierungsdichte und die Kopplungseffizienz der Zielstruktur, sowie der Kopplungsfehler (Abstand zur Zielstruktur nach Farbstoffkopplung), die sich herausfordernd f{\"u}r eine molekulare Aufl{\"o}sung darstellen. Auch wenn die Kopplungseffizienz und -dichte hoch und der Kopplungsfehler gering ist, steigt bei Interfluorophordistanzen < 5nm, abh{\"a}ngig von den Farbstoffen, die Wahrscheinlichkeit von starken und schwachen Farbstoffwechselwirkungen und damit von Energie{\"u}bertragungsprozessen zwischen den Farbstoffen, stark an. Daneben sollten Farbstoffe, abh{\"a}nging von der Lokalisationsmikroskopiemethode, spezifische Kriterien, wie beispielsweise die Photoschaltbarkeit bei dSTORM, erf{\"u}llen, was dazu f{\"u}hrt, dass diese Methoden h{\"a}ufig nur auf einzelne Farbstoffe beschr{\"a}nkt sind. In dieser Arbeit konnte mithilfe von definierten DNA-Origami Konstrukten gezeigt werden, dass das Blinkverhalten von Cyaninfarbstoffen unter dSTORM-Bedingungen einer Abstandsabh{\"a}ngigkeit aufgrund von spezifischen Energie{\"u}bertragungsprozessen folgt, womit Farbstoffabst{\"a}nde im sub-10 nm Bereich charakterisiert werden konnten. Dar{\"u}ber hinaus konnte diese Abstandsabh{\"a}ngigkeit an biologischen Proben gezeigt werden. Hierbei konnten verschiedene zellul{\"a}re Rezeptoren effizient und mit geringem Abstandsfehler zur Zielstruktur mit Cyaninfarbstoffen gekoppelt werden. Diese abstandsabh{\"a}nigen Prozesse und damit Charakterisierungen k{\"o}nnten dabei nicht nur spezifisch f{\"u}r die h{\"a}ufig unter dSTORM-Bedingungen verwendeten Cyaninfarbstoffen g{\"u}ltig sein, sondern auch auf andere Farbstoffklassen, die einen Auszustand zeigen, {\"u}bertragbar sein. Dar{\"u}ber hinaus konnte gezeigt werden, dass hochaufl{\"o}sende dSTORM Aufnahmen unabh{\"a}ngig vom Farbstoffkopplungsgrad der Antik{\"o}rpern sind, welche h{\"a}ufig f{\"u}r Standardf{\"a}rbungen von zellul{\"a}ren Strukturen verwendet werden. Dabei konnte durch Photonenkoinzidenzmessungen dargelegt werden, dass aufgrund komplexer Farbstoffwechselwirkungen im Mittel nur ein Farbstoff aktiv ist, wobei h{\"o}here Kopplungsgrade ein komplexes Blinkverhalten zu Beginn der Messung zeigen. Durch die undefinierten Farbstoffabst{\"a}nde an Antik{\"o}rpern konnte hier kein eindeutiger Energie{\"u}bertragungsmechanismus entschl{\"u}sselt werden. Dennoch konnte gezeigt werden, dass Farbstoffaggregate bzw. H-Dimere unter dSTORM-Bedingungen destabilisiert werden. Durch die zuvor erw{\"a}hnten DNA-Origami Konstrukte definierter Interfluorophordistanzen konnten Energie{\"u}bertragungsmechanismen entschl{\"u}sselt werden, die auch f{\"u}r die Antik{\"o}rper diverser Kopplungsgrade g{\"u}ltig sind. Des Weiteren konnten, ausgel{\"o}st durch komplexe Energie{\"u}bertragungsprozesse h{\"o}herer Kopplungsgrade am Antik{\"o}rper, Mehrfarbenaufnahmen zellul{\"a}rer Strukturen generiert werden, die {\"u}ber die spezifische Fluoreszenzlebenszeit separiert werden konnten. Dies stellt hier eine weitere M{\"o}glichkeit dar, unter einfachen Bedingungen, schnelle Mehrfarbenaufnahmen zellul{\"a}rer Strukturen zu generieren. Durch die Verwendung des selben Farbstoffes unterschiedlicher Kopplungsgrade kann hier nur mit einer Anregungswellenl{\"a}nge und frei von chromatischer Aberration gearbeitet werden. Neben den photophysikalischen Untersuchungen der Cyaninfarbstoffe Cy5 und Alexa Fluor 647 wurden diese ebenso photochemisch n{\"a}her betrachtet. Dabei konnte ein neuartiger chemischer Mechanismus entschl{\"u}sselt werden. Dieser Mechanismus f{\"u}hrt, ausgel{\"o}st durch Singulett-Sauerstoff (1O2), zu einer Photozerschneidung des konjugierten Doppelbindungssystems um zwei Kohlenstoffatome, was zu strukturellen und spektroskopischen Ver{\"a}nderungen dieser Farbstoffe f{\"u}hrt. Auf Grundlage dieses Mechanismus konnte eine neue DNA-PAINT Methode entwickelt werden, die zu einer Beschleunigung der Aufnahmezeit f{\"u}hrt.},
  subject      = {Einzelmolek{\"u}lmikroskopie},
  language  = {de}
}
@unpublished{Dandekar2023,
  author    = {Dandekar, Thomas},
  title     = {Analysing the phase space of the standard model and its basic four forces from a qubit phase transition perspective: implications for large-scale structure generation and early cosmological events},
  doi       = {10.25972/OPUS-29858},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-298580},
  pages     = {42},
  year      = {2023},
  abstract  = {The phase space for the standard model of the basic four forces for n quanta includes all possible ensemble combinations of their quantum states m, a total of n**m states. Neighbor states reach according to transition possibilities (S-matrix) with emergent time from entropic ensemble gradients. We replace the "big bang" by a condensation event (interacting qubits become decoherent) and inflation by a crystallization event - the crystal unit cell guarantees same symmetries everywhere. Interacting qubits solidify and form a rapidly growing domain where the n**m states become separated ensemble states, rising long-range forces stop ultimately further growth. After that very early events, standard cosmology with the hot fireball model takes over. Our theory agrees well with lack of inflation traces in cosmic background measurements, large-scale structure of voids and filaments, supercluster formation, galaxy formation, dominance of matter and life-friendliness. We prove qubit interactions to be 1,2,4 or 8 dimensional (agrees with E8 symmetry of our universe). Repulsive forces at ultrashort distances result from quantization, long-range forces limit crystal growth. Crystals come and go in the qubit ocean. This selects for the ability to lay seeds for new crystals, for self-organization and life-friendliness. We give energy estimates for free qubits vs bound qubits, misplacements in the qubit crystal and entropy increase during qubit decoherence / crystal formation. Scalar fields for color interaction and gravity derive from the permeating qubit-interaction field. Hence, vacuum energy gets low only inside the qubit crystal. Condensed mathematics may advantageously model free / bound qubits in phase space.},
  language  = {en}
}