@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{Segebarth2021,
  author    = {Segebarth, Dennis},
  title     = {Evaluation and validation of deep learning strategies for bioimage analyses},
  doi       = {10.25972/OPUS-24372},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-243728},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Significant advances in fluorescence imaging techniques enable life scientists today to gain insights into biological systems at an unprecedented scale. The interpretation of image features in such bioimage datasets and their subsequent quantitative analysis is referred to as bioimage analysis. A substantial proportion of bioimage analyses is still performed manually by a human expert - a tedious process that is long known to be subjective. Particularly in tasks that require the annotation of image features with a low signal-to-noise ratio, like in fluorescence images of tissue samples, the inter-rater agreement drops. However, like any other scientific analysis, also bioimage analysis has to meet the general quality criteria of quantitative research, which are objectivity, reliability, and validity. Thus, the automation of bioimage analysis with computer-aided approaches is highly desirable. Albeit conventional hard-coded algorithms are fully unbiased, a human user has to set its respective feature extraction parameters. Thus, also these approaches can be considered subjective. Recently, deep learning (DL) has enabled impressive advances in computer vision research. The predominant difference between DL and conventional algorithms is the capability of DL models to learn the respective task on base of an annotated training dataset, instead of following user-defined rules for feature extraction. This thesis hypothesized that DL can be used to increase the objectivity, reliability, and validity of bioimage analyses, thus going beyond mere automation. However, in absence of ground truth annotations, DL models have to be trained on manual and thus subjective annotations, which could cause the model to incorporate such a bias. Moreover, model training is stochastic and even training on the same data could result in models with divergent outputs. Consequently, both the training on subjective annotations and the model-to-model variability could impair the quality of DL-based bioimage analyses. This thesis systematically assessed the impacts of these two limitations experimentally by analyzing fluorescence signals of a protein called cFOS in mouse brain sections. Since the abundance of cFOS correlates with mouse behavior, behavioral analyses could be used for cross-validation of the bioimage analysis results. Furthermore, this thesis showed that pooling the input of multiple human experts during model training and integration of multiple trained models in a model ensemble can mitigate the impact of these limitations. In summary, the present study establishes guidelines for how DL can be used to increase the general quality of bioimage analyses.},
  subject      = {Deeplearning},
  language  = {en}
}
@phdthesis{Glaab2020,
  author    = {Glaab, Sabine},
  title     = {Green classroom at the wildlife park: Aspects of environmental, instructional and conceptual education of primary school children concerning the European wildcat.},
  doi       = {10.25972/OPUS-16949},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-169496},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {To foster sustainable environmentally friendly behavior in children it is important to provide an effective form of environmental education. In this context we studied three important factors: Attitude towards nature, environmental knowledge and advanced expert knowledge. Concerning attitude towards nature our first question was: "Is it possible to affect primary school children's environmental values during a one-day visit at a wildlife park?" As a control, the program was also conducted in schools, leading to two different learning settings- wildlife park and school. Regarding environmental knowledge, in our second question we wanted to know, if our modified teaching approach "guided learning at workstations" (G) combining instructional and constructivist elements would lead to good cognitive learning results of primary school children. Additionally, we compared it to a stronger teacher-centered (T) as well as to a stronger student-centered (S) approach. The third question we asked was "Is it possible to convey fascinating expert knowledge on a more advanced subject to primary school children using conceptual change theory?" After gathering primary school children's preconceptions, we defined different groups due to the heterogeneity of their pre-existing conceptions and the change in conceptions. Based on this research we designed a program along with an instrument to measure the impact of the conceptual change teaching method. After years of building a strong cooperation between the section Didactics of Biology at the Julius-Maximilians University W{\"u}rzburg, the nearby schools and the wildlife park "Wild-Park Klaushof" near Bad Kissingen in northern Bavaria it was time to evaluate the environmental education programs prepared and applied by undergraduate university students. As a model species we chose the European wildcat (Felis silvestris silvestris) which represents endangered wildlife in Europe and the need for human interaction for the sake of preserving a species by restoring or recreating the habitat conditions needed while maintaining current infrastructure. Drawing from our own as well as teachers' and university students' experiences, we built, implemented and evaluated a hands-on program following several workstations between the wildcat enclosure and the wildlife park's green classroom. The content of our intervention was presented as a problem-oriented lesson, where children were confronted with the need for human interaction in order to preserve the European wildcat. Not only on a theoretical basis, but very specific to their hometowns they were told where and when nature conservation groups met or where to donate money. 692 Bavarian third grade primary school children in 35 classes participated in the one-day intervention that took place between the months of april, 2014 and november, 2015 in the wildlife park or in their respective classrooms. The ages varied between 8 and 11 years with the mean age being 8.88 ± 0.56 years old. 48.6 \% of them were boys, 51.4 \% were girls. (1) To measure primary school children's environmental attitudes a questionnaire on two major environmental values- preservation and utilization of nature- was administered in a pre, post- and retention test design. It was possible to affect primary school children's environmental preservation values during our one-day program. This result could be found not only at the wildlife park but unexpectedly also in school, where we educated classes for control purposes. We also found this impact consistent in all used teaching approaches and were surprised to see the preservation values change in a way we did not expect from higher tendency towards preservation of nature to a lower one. We presume that children of this age group reflected on the contents of our intervention. This had an influence on their own values towards preservation which led to a more realistic marking behavior in the questionnaire. We therefore conclude that it is possible to affect primary school children's environmental values with a one-day program on environmental content. (2) We were interested in conveying environmental knowledge about the European wildcat; its morphology, ecology and behavior. We designed and applied a knowledge questionnaire also in a pre-, post- and retention test design, to find out, whether different forms of instruction made a difference in learning success of primary school children. We used two approaches with a teacher in the role of a didactic leader- our modified guided approach (G) as well as a stronger teacher-centered one (T) with a higher focus on instruction. The third approach was presented as a strong student-centered learning at workstations (S) without a didactic leader we also called "free learning at workstations". Overall, all children's knowledge scores changed significantly from pre- to post-test and from pre- to retention test, indicating learning success. Differences could only be found between the posttest values of both approaches with a didactic leader (G, T) in comparison to the strong student-centered (S) form. It appears that these primary school children gained knowledge at the out of school learning setting regardless of the used teaching approach. On the subject of short-term differences, we discuss, that the difference in learning success might have been consistent from post to retention test if a consolidation phase had been added in the days following the program as should be common practice after a visit to an out-of- school learning setting but was not part of our intervention. When comparing both approaches with a didactic leader (G, T), we prefer our modified guided learning at workstations (G) since constructivist phases can be implemented without losses concerning learning success. Moreover, the (at least temporary) presence of a teacher in the role of a didactic leader ensures maintained discipline and counteracts off-task behavior. To make sure, different emotional states did not factor in our program, we measured children's situational emotions directly after the morning intervention using a short scale that evaluated interest, wellbeing and boredom. We found, that these emotions remained consistent over both learning settings as well as different forms of instruction. While interest and wellbeing remained constantly high, boredom values remained low. We take this as a sign of high quality designing and conducting the intervention. (3) In the afternoon of the one-day intervention, children were given the opportunity to investigate the wildcat further, this time using the conceptual change theory in combination with a more complex and fascinating content: cats' vision in dusk and dawn. Children were confronted with their preconceptions which had been sampled prior to the study and turned into three distinctive topics reflected in a special questionnaire. In a pre-, post and retention test design we included the most common alternative conceptions, the scientifically correct conceptions as well as other preconceptions. We gathered a high heterogeneity of preconceptions and defined three groups based on conceptual change literature: "Conceptual change", "Synthetic Models" and "Conceptual Growth". In addition to these we identified two more groups after our data analysis: "Knowledge" and "Non-addressed Concepts". We found that instruction according to the conceptual change theory did not work with primary school children in our intervention. The conceptual change from the addressed alternative conceptions as well as from other preconceptions towards the scientifically correct conceptions was successfully achieved only on occasion. In our case and depending on the topic only one third to one fourth of the children actually held the addressed conception while the rest was not targeted by the instruction. Moreover, we conclude children holding other conceptions were rather confused than educated by the confrontation. We assume that children of this age group may be overchallenged by the conceptual change method.},
  subject      = {Biologie},
  language  = {en}
}
@phdthesis{Carstensen2018,
  author    = {Carstensen, Anne Carola},
  title     = {Identification of novel N-MYC interacting proteins reveals N-MYC interaction with TFIIIC},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143658},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {N-MYC is a member of the human MYC proto-oncogene family, which comprises three transcription factors (C-, N- and L-MYC) that function in multiple biological processes. Deregulated expression of MYC proteins is linked to tumour initiation, maintenance and progression. For example, a large fraction of neuroblastoma displays high N-MYC levels due to an amplification of the N-MYC encoding gene. MYCN-amplified neuroblastoma depend on high N-MYC protein levels, which are maintained by Aurora-A kinase. Aurora-A interaction with N-MYC interferes with degradation of N-MYC via the E3 ubiquitin ligase SCFFBXW7. However, the underlying mechanism of Aurora-A-mediated stabilisation of N-MYC remains to be elucidated. To identify novel N-MYC interacting proteins, which could be involved in N-MYC stabilisation by Aurora-A, a proteomic analysis of purified N-MYC protein complexes was conducted. Since two alanine mutations in MBI of N-MYC, T58A and S62A (N-MYC mut), disable Aurora-A-mediated stabilisation of N-MYC, N-MYC protein complexes from cells expressing either N-MYC wt or mut were analysed. Proteomic analysis revealed that N-MYC interacts with two deubiquitinating enzymes, USP7 and USP11, which catalyse the removal of ubiquitin chains from target proteins, preventing recognition by the proteasome and subsequent degradation. Although N-MYC interaction with USP7 and USP11 was confirmed in subsequent immunoprecipitation experiments, neither USP7, nor USP11 was shown to be involved in the regulation of N-MYC stability. Besides USP7/11, proteomic analyses identified numerous additional N-MYC interacting proteins that were not described to interact with MYC transcription factors previously. Interestingly, many of the identified N-MYC interaction partners displayed a preference for the interaction with N-MYC wt, suggesting a MBI-dependent interaction. Among these were several proteins, which are involved in three-dimensional organisation of chromatin domains and transcriptional elongation by POL II. Not only the interaction of N-MYC with proteins functioning in elongation, such as the DSIF component SPT5 and the PAF1C components CDC73 and CTR9, was validated in immunoprecipitation experiments, but also with the POL III transcription factor TFIIIC and topoisomerases TOP2A/B. ChIP-sequencing analysis of N-MYC and TFIIIC subunit 5 (TFIIIC5) revealed a large number of joint binding sites in POL II promoters and intergenic regions, which are characterised by the presence of a specific motif that is highly similar to the CTCF motif. Additionally, N-MYC was shown to interact with the ring-shaped cohesin complex that is known to bind to CTCF motifs and to assist the insulator protein CTCF. Importantly, individual ChIP experiments demonstrated that N-MYC, TFIIIC5 and cohesin subunit RAD21 occupy joint binding sites comprising a CTCF motif. Collectively, the results indicate that N-MYC functions in two biological processes that have not been linked to MYC biology previously. Furthermore, the identification of joint binding sites of N-MYC, TFIIIC and cohesin and the confirmation of their interaction with each other suggests a novel function of MYC transcription factors in three-dimensional organisation of chromatin.},
  subject      = {Biologie},
  language  = {en}
}
@phdthesis{May2011,
  author    = {May, Frauke},
  title     = {The role of the (hem)ITAM-coupled receptors C-type lectin-like receptor 2 (CLEC-2) and Glycoprotein (GP) VI for platelet function: in vitro and in vivo studies in mice},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-65383},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2011},
  abstract  = {Die Thrombozytenaktivierung und -adh{\"a}sion sowie die nachfolgende Thrombusbildung ist ein essentieller Prozess in der prim{\"a}ren H{\"a}mostase, der aber auch irreversible Gef{\"a}ßverschl{\"u}sse und damit Herzinfarkt oder Schlaganfall verursachen kann. Erst k{\"u}rzlich wurde beschrieben, dass der C-type lectin-like receptor 2 (CLEC-2) auf der Thrombozytenoberfl{\"a}che exprimiert wird, jedoch wurde f{\"u}r diesen Rezeptor noch keine Funktion in den Prozessen der H{\"a}mostase und Thrombose gezeigt. In der vorliegenden Arbeit wurde die Rolle von CLEC-2 in der Thrombozytenfunktion und Thrombusbildung im Mausmodel untersucht. In dem ersten Teil dieser Arbeit konnte gezeigt werden, dass die Behandlung von M{\"a}usen mit dem neu generierten monoklonalen Antik{\"o}rper INU1, der gegen murines CLEC-2 gerichtet ist, zu dem vollst{\"a}ndigen und hochspezifischen Verlust des Rezeptors in zirkulierenden Thrombozyten f{\"u}hrte, ein Prozess, der als „Immundepletion" bezeichnet wird. Die CLEC-2-defizienten Thrombozyten waren nicht mehr durch den CLEC-2-spezifischen Agonisten Rhodozytin aktivierbar, w{\"a}hrend die Aktivierung durch alle anderen getesteten Agonisten nicht beeintr{\"a}chtigt war. Dieser selektive Defekt f{\"u}hrte unter Flussbedingungen ex vivo zu stark verminderter Aggregatbildung der Thrombozyten. Außerdem zeigten in vivo-Thrombosestudien, dass die gebildeten Thromben instabil waren und vermehrt embolisierten. Infolgedessen war die CLEC-2 Defizienz mit einem deutlichen Schutz vor arterieller Thrombose verbunden. Außerdem ließ die in INU1-behandelten M{\"a}usen beobachtete variable Verl{\"a}ngerung der Blutungszeit auf einen moderaten h{\"a}mostatischen Defekt schließen. Diese Ergebnisse zeigen zum ersten Mal, dass CLEC-2 in vitro und in vivo signifikant zur Thrombusstabilit{\"a}t beitr{\"a}gt und eine essentielle Rolle in der H{\"a}mostase und arteriellen Thrombose spielt. Daher stellt CLEC-2 eine potentiell neue antithrombotische Zielstruktur dar, die in vivo inaktiviert werden kann. Diese in vivo-Herabregulierung von Thrombozytenoberfl{\"a}chenrezeptoren k{\"o}nnte einen vielversprechenden Ansatz f{\"u}r zuk{\"u}nftige antithrombotische Therapien darstellen. Der zweite Teil dieser Arbeit behandelte den Effekt einer Doppelimmundepletion der immunoreceptor tyrosine-based activation motiv (ITAM)- und hemITAM-gekoppelten Rezeptoren Glykoprotein (GP) VI und CLEC-2 auf H{\"a}mostase und Thrombose mittels einer Kombination der GPVI- beziehungsweise CLEC-2-spezifischen Antik{\"o}rper JAQ1 und INU1. Eine Einzeldepletion von GPVI oder CLEC-2 in vivo beeintr{\"a}chtigte nicht die Expression und Funktion des jeweils anderen Rezeptors. Eine gleichzeitige Behandlung mit beiden Antik{\"o}rpern f{\"u}hrte jedoch zu dem nachhaltigen Verlust der GPVI- und CLEC-2-vermittelten Signale in Thrombozyten, w{\"a}hrend andere Signalwege nicht betroffen waren. Im Gegensatz zu den Einzeldefizienzen, wiesen die GPVI/CLEC-2 doppeldefizienten M{\"a}use einen schwerwiegenden Blutungsph{\"a}notyp auf. Außerdem f{\"u}hrte die Behandlung zu einer starken Beeintr{\"a}chtigung der arteriellen Thrombusbildung, die die Effekte der Einzeldefizienzen weit {\"u}bertraf. Von Bedeutung ist auch, dass gleiche Ergebnisse in Gp6-/- M{\"a}usen gefunden wurden, die mittels INU1-Behandlung CLEC-2-depletiert wurden. Dies veranschaulicht, dass der Blutungsph{\"a}notyp nicht durch Sekund{\"a}reffekte der kombinierten Antik{\"o}rperbehandlung hervorgerufen wurde. Diese Daten deuten darauf hin, dass GPVI und CLEC-2 sowohl unabh{\"a}ngig voneinander als auch gleichzeitig in vivo von der Thrombozytenoberfl{\"a}che herabreguliert werden k{\"o}nnen und lassen unerwartete redundante Funktionen der beiden Rezeptoren in H{\"a}mostase und Thrombose erkennen. Da beide Rezeptoren, GPVI und CLEC-2, als neue antithrombotische Zielstrukturen diskutiert werden, k{\"o}nnten diese Ergebnisse wichtige Auswirkungen auf die Entwicklung von anti-GPVI oder anti-CLEC-2-basierenden Antithrombotika haben.},
  subject      = {Thrombozyt},
  language  = {en}
}
@phdthesis{Rabie2005,
  author    = {Rabie, Tamer},
  title     = {Cellular regulation of platelet glycoprotein VI : in vivo and in vitro studies in mice},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-14267},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2005},
  abstract  = {Platelet interaction with the subendothelium is essential to limit blood loss after tissue injury. However, upon rupture of atherosclerotic plaques, this interaction may result in blood vessel occlusion leading to life threatening diseases such as myocardial infarction or stroke. Among the subendothelial matrix proteins, collagen is considered to be the most thrombogenic component as it directly activates platelets. Platelets interact with collagen, either indirectly through glycoprotein (GP) Ib-V-IX receptor complex, or directly through the major collagen receptor on the platelet surface, GPVI. The work presented here focused on studying the cellular regulation of GPVI. In addition, a possible role for GPVI in thrombus formation induced by atherosclerotic plaque material was investigated and it was found that GPVI plays an important role in this process. Using a recently published mitochondrial injury model, it was found that GPVI contains a cleavage site for a platelet-expressed metalloproteinase. Further studies showed that platelet activation by CRP, or thrombin induced down-regulation of GPIb\&\#61537;, but not GPVI. In parallel, cellular regulation of GPV was studied and it was found that GPV is cleaved in vitro by the metalloproteinase ADAM17. In previous studies it was shown that injection of mice with the anti-GPVI mAb, JAQ1, induces GPVI down-regulation, which is associated with a strong, but transient, thrombocytopenia. Using new anti-GPVI mAbs, which bind different epitopes on the receptor, it is shown in this study that GPVI down-regulation occurs in an epitope-independent manner. Further experiments showed that antibody treatment induces a transient, but significant increase in bleeding time. Using different genetically modified mice, it is shown that, upon antibody injection, GPVI is both, shed from the platelet surface and internalized into the platelet. Signaling through the immunoreceptor tyrosine-based activation motif (ITAM) of the FcR\&\#61543; chain is essential for both processes, while LAT and PLC\&\#61543;2 are essential for the shedding process only. Antibody-induced increase in bleeding time and thrombocytopenia were absent in LAT deficient mice, showing that it is possible to uncouple the associated side effects from the down-regulation process. As antibody-induced GPVI internalization still occurs in LAT and PLC\&\#61543;2 deficient mice, this suggests a novel signaling pathway downstream of GPVI that has not been described so far.},
  subject      = {Maus},
  language  = {en}
}