@phdthesis{Lang2021,
  author    = {Lang, Konstantin},
  title     = {SLC6A2-regulierende microRNAs bei Angsterkrankungen: Genexpressions- und Assoziationsuntersuchungen},
  doi       = {10.25972/OPUS-23093},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-230939},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Angsterkrankungen sind h{\"a}ufige Krankheitsbilder mit bislang nicht vollst{\"a}ndig gekl{\"a}rter multifaktorieller {\"A}tiologie. Neben Umwelt- und psychosozialen Faktoren zeigen Studien eine signifikante famili{\"a}re H{\"a}ufung und lassen eine genetische Komponente mit einer Heritabilit{\"a}t in einem Bereich von 30-60 \% vermuten. Da hierbei am ehesten von einem komplexen Zusammenspiel verschiedenster Gene mit unterschiedlicher Relevanz auszugehen ist, stellen miRNAs eine bedeutende Gr{\"o}ße dar, da sie es verm{\"o}gen auf transkriptioneller Ebene Einfluss auf die Regulierung einer Vielzahl von Genen zu nehmen. Verschiedene Aspekte liefern Hinweise darauf, dass eine Neurotransmitterdysregulation eine wichtige Komponente in der Pathogenese von Angsterkrankungen einnimmt - insbesondere ver{\"a}nderte noradrenerge Signalwege sind hierbei entscheidend beteiligt. Dies macht den Noradrenalin-Transporter bzw. SLC6A2 zu einem interessanten Kandidatengen, und stellt die Bezugsgr{\"o}ße der angestellten Untersuchungen in dieser Arbeit dar. miRNAs, welche die SLC6A2-Expression modulieren, k{\"o}nnen somit Einfluss auf zentrale Verarbeitungswege von Angst nehmen. Im ersten Teil der vorliegenden Arbeit wurden potentielle miRNA-Regulatoren von SLC6A2 in silico ermittelt und in einem weiteren Schritt in vitro {\"u}berpr{\"u}ft. Zehn der miRNAs (hsa-miR-378g, hsa-miR-330-5p, hsa-miR-4781-5p, hsa-miR664b-3p, hsa-miR-4715-3p, hsa-miR-579-3p, hsa-miR-3921, hsa-miR-3622b-5p, hsa-miR-4773, hsa-miR-532-3p) zeigten hierbei eine relevante Abnahme der Luciferase-Aktivit{\"a}t als Hinweis auf ihre funktionelle Relevanz und stellen damit die Basis der nachfolgenden Untersuchungen dar. Im zweiten Teil der Arbeit wurden Einzelbasenpolymorphismen im Bereich der zuvor ermittelten miRNA-Gene sowie eines SNP innerhalb der 3'-UTR von SLC6A2 mittels Fall-Kontroll-Studie in einer Population von Patienten mit Panikst{\"o}rung und entsprechenden Kontrollen untersucht. Eine nominelle Assoziation ließ sich f{\"u}r das (minor) T-Allel von rs2910931 (stromaufw{\"a}rts von MIR579) (p-allel = 0,004) sowie das (major) A-Allel von rs2582372 (p-allel = 0,023) feststellen. In Einklang hiermit ließ sich weiterhin f{\"u}r rs2910931 eine signifikante Assoziation zwischen der Anzahl der (minor) T-Allele und dem ASI-Wert (β = 0,371, p = 0,029, 95 \%-CI 0,039-0,702) sowie dem ACQ-Wert (β = 0,012, p = 0,041, 95 \%-CI 0,000-0,023) ermitteln. Somit zeigt sich eine Einflussnahme der genetischen Variante um MIR579 auf die Feinmodulation der Noradrenalin-Hom{\"o}ostase als m{\"o}glichem {\"a}tiopathogenetischen Faktor von Angsterkrankungen.},
  subject      = {Angsterkrankungen},
  language  = {de}
}
@phdthesis{Kuhtz2015,
  author    = {Kuhtz, Juliane},
  title     = {Epimutationen humaner Keimzellen und Infertilit{\"a}t},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-108248},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2015},
  abstract  = {Infertilit{\"a}t stellt in unserer heutigen Gesellschaft ein zunehmendes Problem dar. Bei der Suche nach den der Infertilit{\"a}t zugrunde liegenden Ursachen ger{\"a}t immer mehr die Epigenetik in den Fokus. Epigenetische Prozesse sind nicht nur in die Embryo-nalentwicklung und Wachstumsprozesse des Kindes involviert, sondern auch in korrekte Funktionsweisen von Gameten. St{\"o}rungen k{\"o}nnen die Fertilit{\"a}t beeintr{\"a}ch-tigen. Eine besondere Rolle spielen gepr{\"a}gte Gene, die auf einem ihrer Allele, je nach parentaler Herkunft, ein Imprint in Form von DNA-Methylierung tragen. Fehl-regulationen solcher gepr{\"a}gter Gene k{\"o}nnen zu Imprinting-Erkrankungen f{\"u}hren. Seit Einf{\"u}hrung der In-vitro-Fertilisation (IVF) wurden verschiedene assistierte Re-produktionstechniken (ART) entwickelt, um infertilen Paaren zu helfen. Die Sicher-heit dieser Techniken ist nicht abschließend gekl{\"a}rt. Immer wieder wird von nach ART-Behandlung geh{\"a}uft auftretenden Imprinting-Erkrankungen berichtet. Diese Erkrankungen stehen jedoch eher in Zusammenhang mit der zugrunde liegenden Infertilit{\"a}t, als mit ART selbst. Dennoch ist es notwendig zu untersuchen inwieweit sich ART eventuell auf den Gesundheitszustand dieser Kinder auswirken k{\"o}nnte. In der hier vorgelegten Arbeit wurde der Zusammenhang von Epigenetik, Infertilit{\"a}t und ART von verschiedenen Standpunkten aus beleuchtet. In humanen Spermien wurde die DNA-Methylierung verschiedener gepr{\"a}gter Gene hinsichtlich Epimutationen untersucht. ICSI (intracytoplasmatic sperm injection) und IMSI (intracytoplasmic morphologically selected sperm injection) sind verschiedene Techniken zur Selektion von Spermien f{\"u}r eine ART-Behandlung. Hier wurde un-tersucht, ob IMSI epigenetisch bessere Spermien selektiert als die konventionelle ICSI-Methode. Außerdem ist bekannt, dass in Spermienk{\"o}pfen fertiler und infertiler M{\"a}nner Vakuolen vorkommen k{\"o}nnen, deren epigenetische Bedeutung jedoch un-bekannt ist. Ob diese Vakuolen in Zusammenhang mit Epimutationen stehen k{\"o}nn-ten, wurde ebenfalls {\"u}berpr{\"u}ft. Dazu wurde bisulfitkonvertierte DNA weniger Sper-mien (11 je Probe) mithilfe der Limiting Dilution (LD)-Technik und Pyrosequenzie-rung analysiert. Insgesamt standen 880 Spermien f{\"u}r diese Untersuchung zur Ver-f{\"u}gung. Es konnte kein Unterschied zwischen IMSI- und ICSI-selektierten Spermien gefunden werden. Vorhandene Vakuolen im Spermienkopf beeintr{\"a}chtigten nicht die DNA-Methylierung der Gene hGTL2, hLIT1 und hPEG3. Ein weiteres Projekt befasste sich mit der Frage, inwieweit die Technik der In-vitro-Maturation (IVM) DNA-Methylierung in humanen Oocyten beeinflussen k{\"o}nnte. Bisulfitkonvertierte DNA einzelner humaner Oocyten wurde mit LD und Pyrose-quenzierung analysiert. Verglichen wurden IVM und in vivo gereifte Oocyten. Hier-f{\"u}r standen 139 Oocyten zur Verf{\"u}gung, wovon 90 mittels IVM und 49 in vivo gereift waren. Untersucht wurden vier gepr{\"a}gte Gene (hGTL2, hLIT1, hPEG3 und hSNRPN) und drei nicht gepr{\"a}gte Gene (hDNMT3Lo, hNANOG und hOCT4). Es konnten keine IVM-bedingten Epimutationen gefunden werden. Im dritten Projekt wurde untersucht, ob sich die DNA-Methylierung normaler Sper-mien von Spermien aus Oligozoospermie-Asthenozoospermie-Teratozoospermie (OAT)-Syndrom-Patienten unterscheidet. Eine weitere Frage war, ob Epimutationen einen Einfluss auf den ART-Ausgang haben. Untersucht wurden 54 Spermienpro-ben von Paaren in ART-Behandlung. Zur Untersuchung der DNA-Methylierungsmuster der gepr{\"a}gten Gene hGTL2 und hPEG3 sowie der beiden nicht gepr{\"a}gten Pluripotenzgene hNANOG und hOCT4 wurde die Methode Deep Bisulfite Sequencing (DBS) verwendet. Dies ist eine Next Generation Sequencing (NGS)-Technik, angewandt an bisulfitkonvertierter DNA. Diese Technik erm{\"o}glicht es mehrere Proben sowie Gene gleichzeitig zu analysieren. Es zeigte sich, dass OAT-Spermien, die zu einer Lebendgeburt gef{\"u}hrt hatten, sich epigenetisch nicht von normalen Spermien unterschieden. Besonders viele Epimutationen konnten hingegen in OAT-Spermien gefunden werden, die zu keiner Schwangerschaft ge-f{\"u}hrt hatten. Zwischen Spermien die zu einer Lebendgeburt oder keiner Schwan-gerschaft gef{\"u}hrt hatten, zeigten sich Unterschiede in der H{\"a}ufigkeit von hGTL2-Epimutationen. {\"U}ber die H{\"a}ufigkeit von Epimutationen konnte eine pr{\"a}diktive Aus-sage zum ART-Ausgang getroffen werden. Zusammenfassend konnte in dieser Arbeit festgestellt werden, dass sich eine H{\"a}u-fung von Epimutationen darauf auswirkt, ob eine Schwangerschaft erreicht werden kann oder nicht. Diese Epimutationen liegen bereits im parentalen Genom vor. Sie werden nicht durch ART verursacht. Allerdings muss man Techniken finden, mit denen man Gameten mit m{\"o}glichst wenig Epimutationen selektiert, um eine {\"U}ber-tragung solcher auf das Kind zu verhindern.},
  subject      = {Epigenetik},
  language  = {de}
}
@phdthesis{Fraune2014,
  author    = {Fraune, Johanna},
  title     = {The evolutionary history of the mammalian synaptonemal complex},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-100043},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2014},
  abstract  = {Der Synaptonemalkomplex (SC) ist eine hochkonservierte Proteinstruktur. Er weist eine dreiteili-ge, leiter{\"a}hnliche Organisation auf und ist f{\"u}r die stabile Paarung der homologen Chromosomen w{\"a}hrend der Prophase der ersten meiotischen Teilung verantwortlich, die auch als Synpase be-zeichnet wird. Fehler w{\"a}hrend der Synpase f{\"u}hren zu Aneuploidie oder Apoptose der sich entwi-ckelnden Keimzellen. Seit 1956 ist der SC Gegenstand intensiver Forschung. Seine Existenz wurde in zahlreichen Orga-nismen von der Hefe bis zum Menschen beschrieben. Seine Struktur aus zwei parallel verlaufen-den Lateralelementen (LE), die durch eine Vielzahl von sogenannten Transversalfilamenten (TF) verbunden werden und dem Zentralen Element (CE) in der Mitte des SC ist dabei offensichtlich {\"u}ber die Millionen von Jahren der Evolution erhalten geblieben. Einzelne Proteinkomponenten des SC wurden jedoch nur in wenigen Modelorganismen charakterisiert, darunter Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster, Ceanorhabditis elegans und Mus mus-culus. Unerwarteter Weise gelang es bei dieser Charakterisierung nicht, eine evolution{\"a}re Ver-wandtschaft, d.h. eine Homologie zwischen den Proteinsequenzen der verschiedenen SCs nach-zuweisen. Diese Tatsache sprach gegen die grunds{\"a}tzliche Annahme, dass der SC in der Evolution nur einmal entstanden sei. Diese Arbeit hat sich nun der Aufgabe gewidmet, die Diskrepanz zwischen der hochkonservierten Struktur des SC und seiner augenscheinlich nicht-homologen Proteinzusammensetzung zu l{\"o}sen. Dabei beschr{\"a}nkt sie sich auf die Analyse des Tierreichs. Es ist die erste Studie zur Evolution des SC in Metazoa und demonstriert die Monophylie der S{\"a}uger SC Proteinkomponenten im Tierreich. Die Arbeit zeigt, dass mindestens vier von sieben SC Proteinen der Maus sp{\"a}testens im letzten gemeinsamen Vorfahren der Gewebetiere (Eumetazoa) enstanden sind und auch damals Teil ei-nes urspr{\"u}nglichen SC waren, wie er heute in dem Nesseltier Hydra zu finden ist. Dieser SC weist die typische Struktur auf und besitzt bereits alle notwendigen Komponenten, um die drei Dom{\"a}-nen - LE, TF und CE - zu assemblieren. Dar{\"u}ber hinaus ergaben die einzelnen Phylogenien der verschiedenen SC Proteine der Maus, dass der SC eine sehr dynamische Evolutionsgeschichte durchlaufen hat. Zus{\"a}tzliche Proteine wurden w{\"a}hrend der Entstehung der Bilateria und der Wir-beltiere in den SC integriert, w{\"a}hrend andere urspr{\"u}ngliche Komponenten m{\"o}glicherweise Gen-Duplikationen erfuhren bzw. besonders in der Linie der H{\"a}utungstiere verloren gingen oder sich stark ver{\"a}nderten. Es wird die These aufgestellt, dass die auf den ersten Blick nicht-homologen SC Proteine der Fruchtfliege und des Fadenwurms tats{\"a}chlich doch von den urspr{\"u}nglichen Prote-inenkomponenten abstammen, sich aber aufgrund der rasanten Evolution der Arthropoden und der Nematoden bis zu deren Unkenntlichkeit diversifizierten. Zus{\"a}tzlich stellt die Arbeit Hydra als alternatives wirbelloses Modellsystem f{\"u}r die Meiose- und SC-Forschung zu den {\"u}blichen Modellen D. melanogaster und C. elegans vor. Die k{\"u}rzlich gewon-nenen Erkenntnisse {\"u}ber den Hydra SC sowie der Einsatz der Standard-Methoden in diesem Orga-nismus werden in dem abschließenden Kapitel zusammengefasst und diskutiert.},
  subject      = {Synaptinemal-Komplex},
  language  = {en}
}
@phdthesis{Beer2021,
  author    = {Beer, Katharina},
  title     = {A Comparison of the circadian clock of highly social bees (\(Apis\) \(mellifera\)) and solitary bees (\(Osmia\) \(spec.\)): Circadian clock development, behavioral rhythms and neuroanatomical characterization of two central clock components (PER and PDF)},
  doi       = {10.25972/OPUS-15976},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-159765},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {Summary Bees, like many other organisms, evolved an endogenous circadian clock, which enables them to foresee daily environmental changes and exactly time foraging flights to periods of floral resource availability. The social lifestyle of a honey bee colony has been shown to influence circadian behavior in nurse bees, which do not exhibit rhythmic behavior when they are nursing. On the other hand, forager bees display strong circadian rhythms. Solitary bees, like the mason bee, do not nurse their offspring and do not live in hive communities, but face the same daily environmental changes as honey bees. Besides their lifestyle mason and honey bees differ in their development and life history, because mason bees overwinter after eclosion as adults in their cocoons until they emerge in spring. Honey bees do not undergo diapause and have a relatively short development of a few weeks until they emerge. In my thesis, I present a comparison of the circadian clock of social honey bees (Apis mellifera) and solitary mason bees (Osmia bicornis and Osmia cornuta) on the neuroanatomical level and behavioral output level. I firstly characterized in detail the localization of the circadian clock in the bee brain via the expression pattern of two clock components, namely the clock protein PERIOD (PER) and the neuropeptide Pigment Dispersing Factor (PDF), in the brain of honey bee and mason bee. PER is localized in lateral neuron clusters (which we called lateral neurons 1 and 2: LN1 and LN2) and dorsal neuron clusters (we called dorsal lateral neurons and dorsal neurons: DLN, DN), many glia cells and photoreceptor cells. This expression pattern is similar to the one in other insect species and indicates a common ground plan of clock cells among insects. In the LN2 neuron cluster with cell bodies located in the lateral brain, PER is co-expressed with PDF. These cells build a complex arborization network throughout the brain and provide the perfect structure to convey time information to brain centers, where complex behavior, e.g. sun-compass orientation and time memory, is controlled. The PDF arborizations centralize in a dense network (we named it anterio-lobular PDF hub: ALO) which is located in front of the lobula. In other insects, this fiber center is associated with the medulla (accessory medulla: AME). Few PDF cells build the ALO already in very early larval development and the cell number and complexity of the network grows throughout honey bee development. Thereby, dorsal regions are innervated first by PDF fibers and, in late larval development, the fibers grow laterally to the optic lobe and central brain. The overall expression pattern of PER and PDF are similar in adult social and solitary bees, but I found a few differences in the PDF network density in the posterior protocerebrum and the lamina, which may be associated with evolution of sociality in bees. Secondly, I monitored activity rhythms, for which I developed and established a device to monitor locomotor activity rhythms of individual honey bees with contact to a mini colony in the laboratory. This revealed new aspects of social synchronization and survival of young bees with indirect social contact to the mini colony (no trophalaxis was possible). For mason bees, I established a method to monitor emergence and locomotor activity rhythms and I could show that circadian emergence rhythms are entrainable by daily temperature cycles. Furthermore, I present the first locomotor activity rhythms of solitary bees, which show strong circadian rhythms in their behavior right after emergence. Honey bees needed several days to develop circadian locomotor rhythms in my experiments. I hypothesized that honey bees do not emerge with a fully matured circadian system in the hive, while solitary bees, without the protection of a colony, would need a fully matured circadian clock right away after emergence. Several indices in published work and preliminary studies support my hypothesis and future studies on PDF expression in different developmental stages in solitary bees may provide hard evidence.},
  subject      = {Chronobiologie},
  language  = {en}
}
@phdthesis{ReuterWeissenberger2022,
  author    = {Reuter-Weissenberger, Philipp},
  title     = {The role of a fungal-specific transcription regulator on vacuolar biology and host interaction in \(Candida\) \(albicans\)},
  doi       = {10.25972/OPUS-25928},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-259287},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2022},
  abstract  = {Microorganisms that colonize the human body face large fluctuations in their surroundings. Therefore, those microbes developed sophisticated mechanisms that allow them to adapt their cell biology and maintain cellular homeostasis. One organelle vital to preserve cell physiology is the vacuole. The vacuole exhibits a wide range of functions and is able to adjust itself in response to both external and internal stimuli. Moreover, it plays an important role in host interaction and virulence in fungi such as Candida albicans. Despite this connection, only a few regulatory proteins have been described to modulate vacuolar biology in fungal pathogens. Furthermore, whether such regulation alters fungus-host interplay remains largely unknown. This thesis focuses on the characterization of ZCF8, a fungus-specific transcription regulator in the human-associated yeast C. albicans. To this end, I combined genome-wide protein-DNA interaction assays and gene expression analysis that identified genes regulated by Zcf8p. Fluorescence microscopy uncovered that several top targets of Zcf8p localize to the fungal vacuole. Moreover, deletion and overexpression of ZCF8 resulted in alterations in vacuolar morphology and in luminal pH and rendered the fungus resistant or susceptible to a vacuole-disturbing drug. Finally, in vitro adherence assays showed that Zcf8p modulates the attachment of C. albicans to human epithelial cells in a vacuole-dependent manner. Given those findings, I posit that the previously uncharacterized transcription regulator Zcf8p modulates fungal attachment to epithelial cells in a manner that depends on the status of the fungal vacuole. Furthermore, the results highlight that vacuolar physiology is a substantial factor influencing the physical interaction between Candida cells and mammalian mucosal surfaces.},
  subject      = {Vakuole},
  language  = {en}
}
@phdthesis{Leimbach2017,
  author    = {Leimbach, Andreas},
  title     = {Genomics of pathogenic and commensal \(Escherichia\) \(coli\)},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-154539},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2017},
  abstract  = {High-throughput sequencing (HTS) has revolutionized bacterial genomics. Its unparalleled sensitivity has opened the door to analyzing bacterial evolution and population genomics, dispersion of mobile genetic elements (MGEs), and within-host adaptation of pathogens, such as Escherichia coli. One of the defining characteristics of intestinal pathogenic E. coli (IPEC) pathotypes is a specific repertoire of virulence factors (VFs). Many of these IPEC VFs are used as typing markers in public health laboratories to monitor outbreaks and guide treatment options. Instead, extraintestinal pathogenic E. coli (ExPEC) isolates are genotypically diverse and harbor a varied set of VFs -- the majority of which also function as fitness factors (FFs) for gastrointestinal colonization. The aim of this thesis was the genomic characterization of pathogenic and commensal E. coli with respect to their virulence- and antibiotic resistance-associated gene content as well as phylogenetic background. In order to conduct the comparative analyses, I created a database of E. coli VFs, ecoli_VF_collection, with a focus on ExPEC virulence-associated proteins (Leimbach, 2016b). Furthermore, I wrote a suite of scripts and pipelines, bac-genomics-scripts, that are useful for bacterial genomics (Leimbach, 2016a). This compilation includes tools for assembly and annotation as well as comparative genomics analyses, like multi-locus sequence typing (MLST), assignment of Clusters of Orthologous Groups (COG) categories, searching for protein homologs, detection of genomic regions of difference (RODs), and calculating pan-genome-wide association statistics. Using these tools we were able to determine the prevalence of 18 autotransporters (ATs) in a large, phylogenetically heterogeneous strain panel and demonstrate that many AT proteins are not associated with E. coli pathotypes. According to multivariate analyses and statistics the distribution of AT variants is instead significantly dependent on phylogenetic lineages. As a consequence, ATs are not suitable to serve as pathotype markers (Zude et al., 2014). During the German Shiga toxin-producing E. coli (STEC) outbreak in 2011, the largest to date, we were one of the teams capable of analyzing the genomic features of two isolates. Based on MLST and detection of orthologous proteins to known E. coli reference genomes the close phylogenetic relationship and overall genome similarity to enteroaggregative E. coli (EAEC) 55989 was revealed. In particular, we identified VFs of both STEC and EAEC pathotypes, most importantly the prophage-encoded Shiga toxin (Stx) and the pAA-type plasmid harboring aggregative adherence fimbriae. As a result, we could show that the epidemic was caused by an unusual hybrid pathotype of the O104:H4 serotype. Moreover, we detected the basis of the antibiotic multi-resistant phenotype on an extended-spectrum beta-lactamase (ESBL) plasmid through comparisons to reference plasmids. With this information we proposed an evolutionary horizontal gene transfer (HGT) model for the possible emergence of the pathogen (Brzuszkiewicz et al., 2011). Similarly to ExPEC, E. coli isolates of bovine mastitis are genotypically and phenotypically highly diverse and many studies struggled to determine a positive association of putative VFs. Instead the general E. coli pathogen-associated molecular pattern (PAMP), lipopolysaccharide (LPS), is implicated as a deciding factor for intramammary inflammation. Nevertheless, a mammary pathogenic E. coli (MPEC) pathotype was proposed presumably encompassing strains more adapted to elicit bovine mastitis with virulence traits differentiating them from commensals. We sequenced eight E. coli isolates from udder serous exudate and six fecal commensals (Leimbach et al., 2016). Two mastitis isolate genomes were closed to a finished-grade quality (Leimbach et al., 2015). The genomic sequence of mastitis-associated E. coli (MAEC) strain 1303 was used to elucidate the biosynthesis gene cluster of its O70 LPS O-antigen. We analyzed the phylogenetic genealogy of our strain panel plus eleven bovine-associated E. coli reference strains and found that commensal or MAEC could not be unambiguously allocated to specific phylogroups within a core genome tree of reference E. coli. A thorough gene content analysis could not identify functional convergence of either commensal or MAEC, instead both have only very few gene families enriched in either pathotype. Most importantly, gene content and ecoli_VF_collection analyses showed that no virulence determinants are significantly associated with MAEC in comparison to bovine fecal commensals, disproving the MPEC hypothesis. The genetic repertoire of bovine-associated E. coli, again, is dominated by phylogenetic background. This is also mostly the case for large virulence-associated E. coli gene cluster previously associated with mastitis. Correspondingly, MAEC are facultative and opportunistic pathogens recruited from the bovine commensal gastrointestinal microbiota (Leimbach et al., 2017). Thus, E. coli mastitis should be prevented rather than treated, as antibiotics and vaccines have not proven effective. Although traditional E. coli pathotypes serve a purpose for diagnostics and treatment, it is clear that the current typing system is an oversimplification of E. coli's genomic plasticity. Whole genome sequencing (WGS) revealed many nuances of pathogenic E. coli, including emerging hybrid or heteropathogenic pathotypes. Diagnostic and public health microbiology need to embrace the future by implementing HTS techniques to target patient care and infection control more efficiently.},
  subject      = {Escherichia coli},
  language  = {en}
}
@phdthesis{Wedel2018,
  author    = {Wedel, Carolin},
  title     = {The impact of DNA sequence and chromatin on transcription in \(Trypanosoma\) \(brucei\)},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-173438},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {For cellular viability, transcription is a fundamental process. Hereby, the DNA plays the most elemental and highly versatile role. It has long been known that promoters contain conserved and often well-defined motifs, which dictate the site of transcription initiation by providing binding sites for regulatory proteins. However, research within the last decade revealed that it is promoters lacking conserved promoter motifs and transcribing constitutively expressed genes that constitute the majority of promoters in eukaryotes. While the process of transcription initiation is well studied, whether defined DNA sequence motifs are required for the transcription of constitutively expressed genes in eukaryotes remains unknown. In the highly divergent protozoan parasite Trypanosoma brucei, most of the proteincoding genes are organized in large polycistronic transcription units. The genes within one polycistronic transcription unit are generally unrelated and transcribed by a common transcription start site for which no RNA polymerase II promoter motifs have been identified so far. Thus, it is assumed that transcription initiation is not regulated but how transcription is initiated in T. brucei is not known. This study aimed to investigate the requirement of DNA sequence motifs and chromatin structures for transcription initiation in an organism lacking transcriptional regulation. To this end, I performed a systematic analysis to investigate the dependence of transcription initiation on the DNA sequence. I was able to identify GT-rich promoter elements required for directional transcription initiation and targeted deposition of the histone variant H2A.Z, a conserved component during transcription initiation. Furthermore, nucleosome positioning data in this work provide evidence that sites of transcription initiation are rather characterized by broad regions of open and more accessible chromatin than narrow nucleosome depleted regions as it is the case in other eukaryotes. These findings highlight the importance of chromatin during transcription initiation. Polycistronic RNA in T. brucei is separated by adding an independently transcribed miniexon during trans-splicing. The data in this work suggest that nucleosome occupancy plays an important role during RNA maturation by slowing down the progressing polymerase and thereby facilitating the choice of the proper splice site during trans-splicing. Overall, this work investigated the role of the DNA sequence during transcription initiation and nucleosome positioning in a highly divergent eukaryote. Furthermore, the findings shed light on the conservation of the requirement of DNA motifs during transcription initiation and the regulatory potential of chromatin during RNA maturation. The findings improve the understanding of gene expression regulation in T. brucei, a eukaryotic parasite lacking transcriptional Regulation.},
  subject      = {Transkription},
  language  = {en}
}
@article{KuenstnerHoffmannFraseretal.2016,
  author    = {K{\"u}nstner, Axel and Hoffmann, Margarete and Fraser, Bonnie A. and Kottler, Verena A. and Sharma, Eshita and Weigel, Detlef and Dreyer, Christine},
  title     = {The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population},
  series = {PLoS ONE},
  volume    = {11},
  journal   = {PLoS ONE},
  number    = {12},
  doi       = {10.1371/journal.pone.0169087},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166755},
  pages     = {e0169087},
  year      = {2016},
  abstract  = {For over a century, the live bearing guppy, Poecilia reticulata, has been used to study sexual selection as well as local adaptation. Natural guppy populations differ in many traits that are of intuitively adaptive significance such as ornamentation, age at maturity, brood size and body shape. Water depth, light supply, food resources and predation regime shape these traits, and barrier waterfalls often separate contrasting environments in the same river. We have assembled and annotated the genome of an inbred single female from a high-predation site in the Guanapo drainage. The final assembly comprises 731.6 Mb with a scaffold N50 of 5.3 MB. Scaffolds were mapped to linkage groups, placing 95\% of the genome assembly on the 22 autosomes and the X-chromosome. To investigate genetic variation in the population used for the genome assembly, we sequenced 10 wild caught male individuals. The identified 5 million SNPs correspond to an average nucleotide diversity (π) of 0.0025. The genome assembly and SNP map provide a rich resource for investigating adaptation to different predation regimes. In addition, comparisons with the genomes of other Poeciliid species, which differ greatly in mechanisms of sex determination and maternal resource allocation, as well as comparisons to other teleost genera can begin to reveal how live bearing evolved in teleost fish.},
  language  = {en}
}
@phdthesis{Vikuk2020,
  author    = {Vikuk, Veronika},
  title     = {Epichlo{\"e} endophyte-grass symbioses in Germany - Infection rates, alkaloid concentrations and possible intoxication risks},
  doi       = {10.25972/OPUS-21389},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213895},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {Endophytes live in partial symbiosis inside a plant and have been detected in all tested plants. They belong to the group of fungi or bacteria and their ecological function is mostly unknown. The fungal endophytes of the genus Epichlo{\"e} belong to a special group of endophytes. Epichlo{\"e} endophytes live symbiotically inside cool season grass species and some of them are able to produce alkaloids toxic to vertebrates and insects. Their symbiosis is seen as mutualistic for the following reasons: the fungus provides the plant herbivore resistance by producing alkaloids, and it increases the plant's drought tolerance as well as its biomass production. In return, the grass provides the fungus shelter, nutrients and dispersal. Epichlo{\"e} endophytes are host specific and the ability to produce alkaloids differs between species. In order to estimate intoxication risks in grasslands, it is necessary to detect infection rates of different grass species with Epichlo{\"e} endophytes, and to determine the genotypes and chemotypes of the Epichlo{\"e} species as well as the produced alkaloid concentrations. Factors like land-use intensity or season may have an influence on infection rates and alkaloid concentrations. Also, different methodological approaches may lead to different results. In this doctoral thesis my general aim was to evaluate intoxication risks in German grasslands caused by Epichlo{\"e} endophytes. For that I investigated infection rates of different grass species and the genotypes and chemotypes of their Epichlo{\"e} endophytes in German grasslands (Chapter II). Furthermore, I compared alkaloid concentrations detected with dry and fresh plant weight and different analytical methods. I also detected possible changes on the influence of season or land-use intensity (Chapter III). Additionally, I examined infections with Epichlo{\"e} endophytes and alkaloid concentrations in commercially available grass seed mixtures and determined how that influences the intoxication risk of grazing animals in Europe (Chapter IV). It is of agricultural interest to estimate intoxication risks for grazing livestock on German grasslands due to Epichlo{\"e} infected grass species. Therefore, it is important to investigate which grasses are infected with the Epichlo{\"e} endophyte, if the endophytes have the ability to produce vertebrate and invertebrate toxic alkaloids and if the alkaloids are indeed produced. I showed that Epichlo{\"e} festucae var. lolii infecting agriculturally important Lolium perenne lacked the starting gene for ergovaline biosynthesis. Hence, vertebrate toxic ergovaline was not detected in the majority of the collected L. perenne plants. The detection of alkaloid concentrations is an important tool to estimate intoxication risk for vertebrates, but also invertebrates. My studies showed that the usage of dry plant material is crucial to quantify the correct alkaloid concentrations, and that alkaloid concentrations can vary depending on the detection method. Hence, the usage of validated, similar detection methods is important to be able to compare alkaloid concentrations from different studies. Nevertheless, the trends of seasonal changes and the influence of land-use intensity stayed the same, regardless if dry or fresh plant weight was used. Also, alkaloid concentrations were below toxicity thresholds on population level, regardless of the method used. Two commercially available forage grass and two commercially available turf grass seed mixtures were infected with Epichlo{\"e} endopyhtes and alkaloids were detected. This might contribute to the spreading of Epichlo{\"e} endopyhtes in Germany, therefore seed mixtures should be tested for Epichlo{\"e} infections. My results indicate that the intoxication risk is generally low in Germany at the moment, although that might change due to climate change, an increase of monocultural land-use, or the seeding of Epichlo{\"e} infected grass seeds.},
  subject      = {Endophytische Pilze},
  language  = {en}
}
@phdthesis{Maistrenko2021,
  author    = {Maistrenko, Oleksandr},
  title     = {Pangenome analysis of bacteria and its application in metagenomics},
  doi       = {10.25972/OPUS-21499},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-214996},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2021},
  abstract  = {The biosphere harbors a large quantity and diversity of microbial organisms that can thrive in all environments. Estimates of the total number of microbial species reach up to 1012, of which less than 15,000 have been characterized to date. It has been challenging to delineate phenotypically, evolutionary and ecologically meaningful lineages such as for example, species, subspecies and strains. Even within recognized species, gene content can vary considerably between sublineages (for example strains), a problem that can be addressed by analyzing pangenomes, defined as the non-redundant set of genes within a phylogenetic clade, as evolutionary units. Species considered to be ecologically and evolutionary coherent units, however to date it is still not fully understood what are primary habitats and ecological niches of many prokaryotic species and how environmental preferences drive their genomic diversity. Majority of comparative genomics studies focused on a single prokaryotic species in context of clinical relevance and ecology. With accumulation of sequencing data due to genomics and metagenomics, it is now possible to investigate trends across many species, which will facilitate understanding of pangenome evolution, species and subspecies delineation. The major aims of this thesis were 1) to annotate habitat preferences of prokaryotic species and strains; 2) investigate to what extent these environmental preferences drive genomic diversity of prokaryotes and to what extent phylogenetic constraints limit this diversification; 3) explore natural nucleotide identity thresholds to delineate species in bacteria in metagenomics gene catalogs; 4) explore species delineation for applications in subspecies and strain delineation in metagenomics. The first part of the thesis describes methods to infer environmental preferences of microbial species. This data is a prerequisite for the analyses performed in the second part of the thesis which explores how the structure of bacterial pangenomes is predetermined by past evolutionary history and how is it linked to environmental preferences of the species. The main finding in this subchapter that habitat preferences explained up to 49\% of the variance for pangenome structure, compared to 18\% by phylogenetic inertia. In general, this trend indicates that phylogenetic inertia does not limit evolution of pangenome size and diversity, but that convergent evolution may overcome phylogenetic constraints. In this project we show that core genome size is associated with higher environmental ubiquity of species. It is likely this is due to the fact that species need to have more versatile genomes and most necessary genes need to be present in majority of genomes of that species to be highly prevalent. Taken together these findings may be useful for future predictive analyses of ecological niches in newly discovered species. The third part of the thesis explores data-driven, operational species boundaries. I show that homologous genes from the same species from different genomes tend to share at least 95\% of nucleotide identity, while different species within the same genus have lower nucleotide identity. This is in line with other studies showing that genome-wide natural species boundary might be in range of 90-95\% of nucleotide identity. Finally, the fourth part of the thesis discusses how challenges in species delineation are relevant for the identification of meaningful within-species groups, followed by a discussion on how advancements in species delineation can be applied for classification of within-species genomic diversity in the age of metagenomics.},
  subject      = {Pangenom},
  language  = {en}
}