@phdthesis{Dugar2016, author = {Dugar, Gaurav}, title = {Comparative transcriptomics and post-transcriptional regulation in \(Campylobacter\) \(jejuni\)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146180}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {The transcriptome is defined as the set of all RNA molecules transcribed in a cell. These include protein-coding messenger RNAs (mRNAs) as well as non-coding RNAs, such as ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), and small non-coding RNAs (sRNAs). sRNAs are known to play an important role in regulating gene expression and virulence in pathogens. In this thesis, the transcriptome of the food-borne pathogen Campylobacter jejuni was characterized at single nucleotide resolution by use of next-generation sequencing approaches. The first genome of a C. jejuni strain was published in the year 2000. However, its transcriptome remained uncharacterized at large. C. jejuni can survive in a variety of ecological niches and hosts. However, how strain-specific transcriptional changes contribute to such adaptation is not known. In this study, the global transcriptome maps of four closely related C. jejuni strains were defined using a differential RNA-seq (dRNA-seq) approach. This analysis also included a novel automated method to annotate the transcriptional start sites (TSS) at a genome-wide scale. Next, the transcriptomes of four strains were simultaneously mapped and compared by the use of a common coordinate system derived from whole-genome alignment, termed as SuperGenome. This approach helped to refine the promoter maps by comparison of TSS within strains. Most of the TSS were found to be conserved among all four strains, but some single-nucleotide-polymorphisms (SNPs) around promoter regions led to strain-specific transcriptional output. Most of these SNPs altered transcription only slightly, but some others led to a complete abrogation of transcription leading to differential molecular phenotypes. These in turn might help the strains to adapt to their specific host or microniche. The transcriptome also unveiled a plethora of sRNAs, some of which were conserved among the four strains while others were strain specific. Furthermore, a Cas9-dependent minimal type-II CRISPR-Cas system with only three Cas genes and multiple promoters to drive the transcription of the CRISPR locus was also characterized in C. jejuni using the dRNA-seq dataset. Apart from sRNAs, the role of global RNA binding proteins (RBPs) is also unclear in C. jejuni. Aided by the global transcriptome data, the role of RBPs in post-transcriptional regulation of C. jejuni was studied at a global scale. Two of the most widely studied RNA binding proteins in bacteria are Hfq and CsrA. The RNA interactome of the translational regulator CsrA was defined using another global deep-sequencing technique that combines co-immunoprecipitation (coIP) with RNA sequencing (RIP-seq). Using this interactome dataset, the direct targets of this widespread global post-transcriptional regulator were defined, revealing a significant enrichment for mRNAs encoding genes involved in flagella biosynthesis. Unlike Gammaproteobacteria, where sRNAs such as CsrB/C, antagonize CsrA activity, no sRNAs were enriched in the CsrA-coIP in C. jejuni, indicating absence of any sRNA antagonists and novel modes of CsrA activity regulation. Instead, the CsrA regulatory pathway revealed flaA mRNA, encoding the major flagellin, as a dual-function mRNA. flaA mRNA was the main target of CsrA but it also served to antagonize CsrA activity along with the protein antagonist FliW previously identified in the Gram-positive bacterium Bacillus subtilis. Furthermore, this regulatory mRNA was also shown in this thesis to localize to the poles of elongating C. jejuni cells in a translation-dependent manner. It was also shown that this localization is dependent on the CsrA-FliW regulon, which controls the translation of flaA mRNA. The role and mechanism of flaA mRNA localization or mRNA localization in general is not yet clear in bacteria when compared to their eukaryotic counterparts. Overall, this study provides first insights into riboregulation of the bacterial pathogen C. jejuni. The work presented in this thesis unveils several novel modes of riboregulation in C. jejuni, which could be applicable more generally. Moreover, this study also lays out several unsolved intriguing questions, which may pave the way for interesting studies to come.}, subject = {Campylobacter jejuni}, language = {en} } @phdthesis{Guan2016, author = {Guan, Chonglin}, title = {Functional and genetic dissection of mechanosensory organs of \(Drosophila\) \(melanogaster\)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146220}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {In Drosophila larvae and adults, chordotonal organs (chos) are highly versatile mechanosensors that are essential for proprioception, touch sensation and hearing. Chos share molecular, anatomical and functional properties with the inner ear hair cells of mammals. These multiple similarities make chos powerful models for the molecular study of mechanosensation. In the present study, I have developed a preparation to directly record from the sensory neurons of larval chos (from the lateral chos or lch5) and managed to correlate defined mechanical inputs with the corresponding electrical outputs. The findings of this setup are described in several case studies. (1) The basal functional lch5 parameters, including the time course of response during continuous mechanical stimulation and the recovery time between successive bouts of stimulation, was characterized. (2) The calcium-independent receptor of α-latrotoxin (dCIRL/Latrophilin), an Adhesion class G protein-coupled receptor (aGPCR), is identified as a modulator of the mechanical signals perceived by lch5 neurons. The results indicate that dCIRL/Latrophilin is required for the perception of external and internal mechanical stimuli and shapes the sensitivity of neuronal mechanosensation. (3) By combining this setup with optogenetics, I have confirmed that dCIRL modulates lch5 neuronal activity at the level of their receptor current (sensory encoding) rather than their ability to generate action potentials. (4) dCIRL´s structural properties (e.g. ectodomain length) are essential for the mechanosensitive properties of chordotonal neurons. (5) The versatility of chos also provides an opportunity to study multimodalities at multiple levels. In this context, I performed an experiment to directly record neuronal activities at different temperatures. The results show that both spontaneous and mechanically evoked activity increase in proportion to temperature, suggesting that dCIRL is not required for thermosensation in chos. These findings, from the development of an assay of sound/vibration sensation, to neuronal signal processing, to molecular aspects of mechanosensory transduction, have provided the first insights into the mechanosensitivity of dCIRL. In addition to the functional screening of peripheral sensory neurons, another electrophysiological approach was applied in the central nervous system: dCIRL may impact the excitability of the motor neurons in the ventral nerve cord (VNC). In the second part of my work, whole-cell patch clamp recordings of motor neuron somata demonstrated that action potential firing in the dCirl\(^K\)\(^O\) did not differ from control samples, indicating comparable membrane excitability.}, subject = {Taufliege}, language = {en} } @phdthesis{Leinders2016, author = {Leinders, Mathias}, title = {microRNAs in chronic pain}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-144395}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Chronic pain is a common problem in clinical practice, not well understood clinically, and frequently tough to satisfactorily diagnose. Because the pathophysiology is so complex, finding effective treatments for people with chronic pain has been overall less than successful and typically reduced to an unsatisfactory trial-and-error process, all of which translates into a significant burden to society. Knowledge of the mechanisms underlying the development of chronic pain, and moreover why some patients experience pain and others not, may aid in developing specific treatment regimens. Although nerve injuries are major contributors to pain chronification, they cannot explain the entire phenomenon. Considerable research has underscored the importance of the immune system for the development and maintenance of chronic pain, albeit the exact factors regulating inflammatory reactions remain unclear. Understanding the putative molecular and cellular regulator switches of inflammatory reactions will open novel opportunities for immune modulatory analgesics with putatively higher specificity and less adverse effects. It has become clear that small, non- coding RNA molecules known as microRNAs are in fact potent regulators of many thousands of genes and possibly cross-communicate between cellular pathways in multiple systems acting as so-called "master-switches". Aberrant expression of miRNAs is now implicated in numerous disorders, including nerve injuries as well as in inflammatory processes. Moreover, compelling evidence supports the idea that miRNAs also regulate pain, and in analogy to the oncology field aid in the differential diagnosis of disease subtypes. In fact, first reports describing characteristic miRNA expression profiles in blood or cerebrospinal fluid of patients with distinct pain conditions are starting to emerge, however evidence linking specific miRNA expression profiles to specific pain disorders is still insufficient. The present thesis aimed at first, identifying specific miRNA signatures in two distinct chronic pain conditions, namely peripheral neuropathies of different etiologies and fibromyalgia syndrome. Second, it aimed at identifying miRNA profiles to better understand potential factors that differentiate painful from painless neuropathies and third, study the mechanistic role of miRNAs in the pathophysiology of pain, to pave the way for new druggable targets. Three studies were conducted in order to identify miRNA expression signatures that are characteristic for the given chronic pain disorder. The first study measured expression of miR-21, miR-146a and miR-155 in white blood cells, skin and nerve biopsies of patients with peripheral neuropathies. It shows that peripheral neuropathies of different etiologies are associated with increased peripheral miR-21 and miR-146a, but decreased miR-155 expression. More importantly, it was shown that painful neuropathies have increased sural nerve miR-21 and miR-155 expression, but reduced miR-146a and miR-155 expression in distal skin of painful neuropathies. These results point towards the potential use of miRNAs profiles to stratify painful neuropathies. The seconds study extends these findings and first analyzed the role of miR-132-3p in patients and subsequently in an animal model of neuropathic pain. Interestingly, miR-132-3p was upregulated in white blood cells and sural nerve biopsies of patients with painful neuropathies and in animals after spared nerve injury. Pharmacologically modulating the expression of miR-132-3p dose-dependently reversed pain behavior and pain aversion, indicating the pro-nociceptive effect of miR-132-3p in chronic pain. This study thus demonstrates the potential analgesic impact by modulating miRNA expression. Fibromyalgia is associated with chronic widespread pain and, at least in a subgroup, impairment in small nerve fiber morphology and function. Interestingly, the disease probably comprises subgroups with different underlying pathomechanisms. In accordance with this notion, the third study shows that fibromyalgia is associated with both aberrant white blood cell and cutaneous miRNA expression. Being the first of its kind, this study identified miR-let-7d and its downstream target IGF-1R as potential culprit for impaired small nerve fiber homeostasis in a subset of patients with decreased intra-epidermal nerve fiber density. The work presented in this thesis is a substantial contribution towards the goal of better characterizing chronic pain based on miRNA expression signatures and thus pave the way for new druggable targets.}, subject = {miRNS}, language = {en} } @phdthesis{HoppKraemer2016, author = {Hopp-Kr{\"a}mer, Sarah}, title = {Untersuchungen zur Pathophysiologie und therapeutischer Relevanz des Blutgerinnungsfaktors XII nach experimentellem Sch{\"a}del-Hirn-Trauma}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-144421}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Das Sch{\"a}del-Hirn-Trauma (SHT) entsteht durch {\"a}ußere Gewalteinwirkung auf den Kopf und verursacht mechanisch eine Sch{\"a}digung des Hirngewebes. Zus{\"a}tzlich tragen sekund{\"a}re Pathomechanismen, wie Entz{\"u}ndungsprozesse und die Sch{\"a}digung der Blut-Hirn-Schranke (BHS), dazu bei, dass sich das initial gesch{\"a}digte L{\"a}sionsareal im Laufe der Zeit vergr{\"o}ßert. Vor allem bei jungen Erwachsenen ist das SHT eine der h{\"a}ufigsten Ursachen f{\"u}r bleibende Behinderungen und Todesf{\"a}lle. Aufgrund der schweren Auswirkungen des SHT und der bislang fehlenden Therapieoptionen ist die Identifizierung neuer Zielstrukturen f{\"u}r eine kausale Therapie von gr{\"o}ßter Bedeutung. Ausgehend von tierexperimentellen Studien ist das Kallikrein-Kinin-System (KKS) ein besonders erfolgversprechender Angriffspunkt zur Behandlung des SHT. Die Aktivierung des KKS {\"u}ber den Gerinnungsfaktor XII (FXII) und die darauf folgende Bildung von Bradykinin sind mit dem Entstehen von Hirn{\"o}demen und Entz{\"u}ndungsreaktionen assoziiert. Vorangegangene Studien haben weiterhin die Frage aufgeworfen, ob und in welchem Maße thrombotische Prozesse einen Einfluss auf die Pathophysiologie und die sekund{\"a}ren Hirnsch{\"a}digungen nach SHT haben. Da FXII sowohl das KKS als auch die intrinsische plasmatische Gerinnungskaskade initiiert und somit zur Fibrinbildung beitr{\"a}gt, stand FXII im Mittelpunkt der Untersuchungen dieser Dissertation. Die vorliegende Arbeit besch{\"a}ftigt sich mit den Fragen, (I) inwiefern FXII eine Rolle bei der sekund{\"a}ren Hirnsch{\"a}digung nach Trauma spielt und (II) ob thrombotische Prozesse ein pathophysiologisches Merkmal nach Trauma darstellen. In zwei unterschiedlichen Trauma-Modellen wurden FXII-defiziente Tiere und mit einem spezifischen Inhibitor des aktivierten FXII (FXIIa) behandelte Tiere gegen Kontrolltiere nach SHT verglichen. Die Analyse der funktionellen Ausfallerscheinungen und des Ausmaßes an neuronaler Degeneration zeigte, dass FXII-Defizienz und FXIIa-Inhibition vor den Auswirkungen eines SHT sch{\"u}tzen. Als zugrundeliegende Mechanismen wurden die Reduktion von thrombotisch verschlossenen Gef{\"a}ßen in der Mikrovaskulatur des Gehirns sowie der Schutz vor BHS-St{\"o}rungen und verringerte inflammatorische Prozesse identifiziert. Weiterhin wurde festgestellt, dass eine Blockade der intrinsischen Gerinnungskaskade {\"u}ber FXII keine intrazerebralen Blutungen ausl{\"o}st. In Gewebeproben von Patienten mit SHT wurde gezeigt, dass Thrombozytenaggregate auch im klinischen Verlauf auftreten und sich somit die tierexperimentellen Befunde auf die humane Situation {\"u}bertragen lassen. Insgesamt tragen die Ergebnisse dazu bei, die komplexen und vielf{\"a}ltigen Pathomechanismen nach SHT besser zu verstehen und vor allem die Relevanz thrombo-inflammatorischer Prozesse nach SHT aufzuzeigen. Die gezielte Blockade des FXII(a) k{\"o}nnte als therapeutisches Prinzip zur Abschw{\"a}chung der Sekund{\"a}rschaden nach SHT geeignet sein.}, subject = {Sch{\"a}del-Hirn-Trauma}, language = {de} } @phdthesis{Endres2016, author = {Endres, Marcel Matthias}, title = {LASP1 reguliert die Genexpression und Sekretion von Matrix-Metalloproteasen in Brustkrebszellen}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-136733}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Migration und Tumorzellinvasion erfordern die vorhergehende Degradation der umliegenden Extrazellul{\"a}rmartrix (EZM). Dieser Umbauprozess erfolgt prim{\"a}r durch proteolytische Endopeptidasen, sog. Matrix-Metalloproteasen (MMPs). Damit diese ihre funktionelle Aktivit{\"a}t aus{\"u}ben k{\"o}nnen, m{\"u}ssen sie zun{\"a}chst rekrutiert und mit Hilfe podosomaler bzw. invadopodialer Strukturen in die EZM sezerniert werden. Das LIM und SH3 Dom{\"a}nen Protein 1 (LASP1), ein neu in Podosomen von Makrophagen identifiziertes regulatorisches Ger{\"u}stprotein, beeinflusst, neben Gr{\"o}ße, Anzahl und Best{\"a}ndigkeit von Podosomen, in hohem Maße die Matrixdegradationskapazit{\"a}t der Zelle. Auch in invasiven Brustkrebszellen wurde eine Lokalisation von LASP1 an Invadopodien, den Podosomen-{\"a}quivalenten Strukturen, detektiert. Das prim{\"a}re Ziel der vorliegenden Arbeit war daher die funktionelle Charakterisierung von LASP1 in Invadopodien. Unter Etablierung eines Matrix-Degradations-Assays konnte gezeigt werden, dass eine Herunterregulation von LASP1 auch in der humanen Brustkrebszelllinie MDA-MB-231, die zuvor schon f{\"u}r Makrophagen gezeigte Matrixdegradation nachhaltig beeintr{\"a}chtig. Durch Analyse und Verifikation von zug{\"a}nglichen Mikroarraydaten mittels qRT-PCR und Western Blot konnte ferner belegt werden, dass LASP1 in den Brustkrebszellen die Genexpression und Proteintranslation von MMP1, -3 und -9 positiv moduliert und somit das gesamt-invasive Potential der Zelle steigert. Dar{\"u}ber hinaus deuten Zymogramme und die Analyse des konditionierten Mediums darauf hin, dass LASP1 als Strukturprotein die vesikul{\"a}re Sekretion der inaktiven Zymogene (proMMPs) in die EZM f{\"o}rdert. Demzufolge modifiziert LASP1 w{\"a}hrend der Krebsprogression die zellul{\"a}re Mikroumgebung zugunsten einer erh{\"o}hten Metastasierungsrate. Die neu identifizierte regulatorische Funktion von LASP1 auf die Transkription sowie Sekretion von Matrix-Metalloproteasen erkl{\"a}rt die in fr{\"u}heren Arbeiten beobachtete Korrelation zwischen einer erh{\"o}hten LASP1 Konzentration im Gewebe und dem vermehrten Auftreten von Metastasen, und damit einhergehend, schlechteren {\"U}berleben der Patientinnen.}, subject = {Brustkrebs}, language = {de} } @phdthesis{Wiegner2016, author = {Wiegner, Armin}, title = {Auswirkungen der gepaarten Stimulation des H{\"o}rnerven und des Nervus vagus auf die spektrale Plastizit{\"a}t im auditorischen Kortex der mongolischen W{\"u}stenrennmaus}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-135887}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Das Cochlea-Implantat (CI) erm{\"o}glichte bereits >300 000 hochgradig h{\"o}rgesch{\"a}digten Menschen weltweit eine grunds{\"a}tzlich wiederhergestellte H{\"o}rfunktion. Es wird angenommen, dass sich das Sprachverst{\"a}ndnis von CI-Tr{\"a}gern verbessert, wenn die funktionale Trennung der CI-Kan{\"a}le erh{\"o}ht wird. Neben verschiedenen auf die auditorische Peripherie beschr{\"a}nkten Ans{\"a}tzen gibt es {\"U}berlegungen, eine verbesserte Kanaltrennung durch die Rehabilitation taubheitsinduzierter Degenerationen in der spektralen Verarbeitung im zentralen auditorischen System zu erreichen. Es konnte in ertaubten Tieren bislang allerdings kein ad{\"a}quates CI-Stimulationsmuster beschrieben werden, dass es erlaubte, eine gezielte neuronale Plastizit{\"a}t in der spektralen Verarbeitung zu induzieren. Die Arbeitsgruppe um M.P. Kilgard (UT Dallas, USA) zeigte in mehreren Studien in h{\"o}renden Tieren, dass auditorische Stimulation gepaart mit elektrischer Vagusnerv-Stimulation (VNS) zu einer gezielten kortikalen Plastizit{\"a}t f{\"u}hrt. Diese gepaarte Stimulation konnte die spektrale Verarbeitung von Signalen im auditorischen Kortex (AC) gezielt beeinflussen und so z.B. pathologisch verbreiterte Repr{\"a}sentationen von T{\"o}nen wieder verfeinern. Dieses hochgradige Potential f{\"u}r gezielte Plastizit{\"a}t im AC durch die gepaarte VNS scheint eine vielversprechende L{\"o}sung darzustellen, um die durch verbreiterte Repr{\"a}sentation im ertaubten AC verminderte CI-Kanaltrennung zu verbessern. Vor diesem Hintergrund sollte in der vorliegenden Promotion die {\"U}bertragbarkeit dieses hochgradigen Potentials auf das ertaubte und CI-stimulierte auditorische System evaluiert werden. Um die CI-Kanaltrennung zu untersuchen, wurde ein Multikanal-CI f{\"u}r die Mongolische W{\"u}stenrennmaus (Gerbil) entwickelt. Trotz der kleinen Ausmaße von Cochlea und AC im Gerbil und der generell breiten neuronalen Erregung durch intracochle{\"a}re elektrische Stimulation konnte eine tonotop organisierte und selektive Repr{\"a}sentation der neuronalen Antworten f{\"u}r mehrere CI-Kan{\"a}le im AC nachgewiesen werden. F{\"u}r die gepaarte CI/VN-Stimulation wurden die Tiere zus{\"a}tzlich mit einer Manschettenelektrode um den linken zervikalen Nervus vagus (VN) implantiert. Die chronischen Implantate erlaubten {\"u}ber mehrere Wochen hinweg eine stabile und zuverl{\"a}ssige elektrische Stimulation im frei-beweglichen Gerbil. Damit kombiniert das in dieser Promotion entwickelte Multikanal-CI-VNS-Modell die Vorteile einer tonotop selektiven und stabilen neuronalen Aktivierung mit den ethischen, kostenrelevanten und entwicklungsbezogenen Vorteilen, die der Einsatz von Kleinnagern bietet. Als n{\"a}chster Schritt wurde das grunds{\"a}tzliche Potential der gepaarten CI/VN-Stimulation f{\"u}r gezielte plastische Ver{\"a}nderungen im AC des Gerbils getestet. Engineer et al. (2011) hatten bereits in akustischen Studien in h{\"o}renden Ratten die kortikale {\"U}berrepr{\"a}sentation eines einzelnen chronisch mit VNS gepaarten Tones gezeigt. In der vorliegenden Promotion wurde versucht, die Ergebnisse aus der akustischen Studie in h{\"o}renden Ratten in zwei verschiedenen Studien im Gerbil zu reproduzieren. Analog zur gepaarten Ton/VN-Stimulation in der Ratte untersuchten wir zuerst in ertaubten Gerbils die Auswirkungen einkanaliger CI-Stimulation gepaart mit VNS. Im AC des Gerbils konnten keine Ver{\"a}nderung der zentralen Repr{\"a}sentation des VNS gepaarten CI-Kanals festgestellt werden. Um speziesspezifische (Ratte vs. Gerbil) und stimulusspezifische (akustisch vs. elektrisch) Unterschiede zwischen den Studien als m{\"o}gliche Gr{\"u}nde f{\"u}r das Ausbleiben der VNS induzierten Plastizit{\"a}t auszuschließen, wurde nun die gepaarte Ton/VN-Stimulation (Engineer et al., 2011) im h{\"o}renden Gerbil wiederholt. Eine kortikale {\"U}berrepr{\"a}sentation des VNS gepaarten Signals konnte aber auch im h{\"o}renden Gerbil nicht reproduziert werden. M{\"o}gliche Gr{\"u}nde f{\"u}r die Diskrepanz zwischen unseren Ergebnissen im Gerbil und den publizierten Ergebnissen in der Ratte werden diskutiert. Die generelle Funktionsf{\"a}higkeit der VNS in den chronisch stimulierten Tieren wurde durch die Ableitung VNS evozierter Potentiale (VNEP) kontrolliert. Ein speziesspezifischer Unterschied erscheint bei der biologischen N{\"a}he von Ratte und mongolischer W{\"u}stenrennmaus unwahrscheinlich, kann allerdings durch die vorliegenden Studien nicht vollst{\"a}ndig ausgeschlossen werden. Eine Abh{\"a}ngigkeit des plastischen Potentials der gepaarten VNS von der Stimulationsintensit{\"a}t ist bekannt. Da Ratten und Gerbils {\"a}hnliche VNEP-Schwellen zeigten und mit identischen VNS-Amplituden stimuliert wurden, gehen wir davon aus, dass Unterschiede im plastischen Potential gepaarter VNS zwischen beiden Spezies nicht auf die verwendete Stimulationsintensit{\"a}t zur{\"u}ckzuf{\"u}hren sind. Die beschriebene Diskrepanz im Potential f{\"u}r kortikale Plastizit{\"a}t durch gepaarte VNS weckt Zweifel an der {\"U}bertragbarkeit des f{\"u}r die Ratte publizierten Potentials auf andere Spezies, einschließlich des Menschen.}, subject = {H{\"o}rrinde}, language = {de} } @phdthesis{Rosenbaum2016, author = {Rosenbaum, Corinna}, title = {The role of enteric glial cells under inflammatory conditions of the intestine}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-138946}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {The enteric nervous system (ENS) innervates the gastrointestinal (GI) tract and controls central aspects of GI physiology including contractility of the intestinal musculature, glandular secretion and intestinal blood flow. The ENS is composed of neurons that conduct electrical signals and of enteric glial cells (EGCs). EGCs resemble central nervous system (CNS) astrocytes in their morphology and in the expression of shared markers such as the intermediate filament protein glial fibrillary acidic protein (GFAP). They are strategically located at the interface of ENS neurons and their effector cells to modulate intestinal motility, epithelial barrier stability and inflammatory processes. The specific contributions of EGCs to the maintenance of intestinal homeostasis are subject of current research. From a clinical point of view EGC involvement in pathophysiological processes such as intestinal inflammation is highly relevant. Like CNS astrocytes ECGs can acquire a reactive, tissue-protective phenotype in response to intestinal injury. In patients with chronic inflammatory bowel diseases (IBD) such as Crohn's disease and ulcerative colitis, alterations in the EGC network are well known, particularly a differential expression of GFAP, which is a hallmark of reactive gliosis in the CNS. With increasing recognition of the role of EGCs in intestinal health and disease comes the need to study the glial population in its complexity. The overall aim of this thesis was to comprehensively study EGCs with focus on the reactive GFAP-expressing subpopulation under inflammatory conditions in vivo and in vitro. In a first step, a novel in vivo rat model of acute systemic inflammation mimicking sepsis was employed to investigate rapidly occuring responses of EGCs to inflammation. This study revealed that within a short time frame of a few hours, EGCs responded to the inflammation with an upregulation of Gfap gene expression. This inflammation-induced upregulation was confined to the myenteric plexus and varied in intensity along the intestinal rostro-caudal axis. This highly responsive myenteric GFAP-expressing EGC population was further characterized in vivo andin vitro using a transgenic mouse model (hGFAP-eGFP mice). Primary purified murine GFAP-EGC cultures in vitro were established and it was assessed how the transcriptomic and proteomic profiles of these cells change upon inflammatory stimulation. Here, myenteric GFAP-EGCs were found to undergo a shift in gene expression profile that predominantly affects expression of genes associated with inflammatory responses. Further, a secretion of inflammatory mediators was validated on protein level. The GFAP+ subpopulation is hence an active participant in inflammatory pathophysiology. In an acute murine IBD model in vivo, GFAP-EGCs were found to express components of the major histocompatibility complex (MHC) class II in inflamed tissue, which also indicates a crosstalk of EGCs with the innate and the adaptive lamina propria immune system in acute inflammation. Taken together, this work advances our knowledge on EGC (patho-)physiology by identifying and characterizing an EGC subpopulation rapidly responsive to inflammation. This study further provides the transcriptomic profile of this population in vivo and in vitro, which can be used to identify targets for therapeutic intervention. Due to the modulating influence of EGCs on the intestinal microenvironment, the study further underlines the importance of integrating EGCs into in vitro test systems that aim to model intestinal tissues in vitro and presents an outlook on a potential strategy.}, subject = {Darmwandnervensystem}, language = {en} } @phdthesis{Ulrich2016, author = {Ulrich, Natalie}, title = {Processing of Near Outcomes and Outcome Sequences in Gambling: Implications for the Biopsychological Basis of Problem Gambling}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-139612}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Gambling is a popular activity in Germany, with 40\% of a representative sample reporting having gambled at least once in the past year (Bundeszentrale f{\"u}r gesundheitliche Aufkl{\"a}rung, 2014). While the majority of gamblers show harmless gambling behavior, a subset develops serious problems due to their gambling, affecting their psychological well-being, social life and work. According to recent estimates, up to 0.8\% of the German population are affected by such pathological gambling. People in general and pathological gamblers in particular show several cognitive distortions, that is, misconceptions about the chances of winning and skill involvement, in gambling. The current work aimed at elucidating the biopsychological basis of two such kinds of cognitive distortions, the illusion of control and the gambler's and hot hand fallacies, and their modulation by gambling problems. Therefore, four studies were conducted assessing the processing of near outcomes (used as a proxy for the illusion of control) and outcome sequences (used as a proxy for the gambler's and hot hand fallacies) in samples of varying degrees of gambling problems, using a multimethod approach. The first study analyzed the processing and evaluation of near outcomes as well as choice behavior in a wheel of fortune paradigm using electroencephalography (EEG). To assess the influence of gambling problems, a group of problem gamblers was compared to a group of controls. The results showed that there were no differences in the processing of near outcomes between the two groups. Near compared to full outcomes elicited smaller P300 amplitudes. Furthermore, at a trend level, the choice behavior of participants showed signs of a pattern opposite to the gambler's fallacy, with longer runs of an outcome color leading to increased probabilities of choosing this color again on the subsequent trial. Finally, problem gamblers showed smaller feedback-related negativity (FRN) amplitudes relative to controls. The second study also targeted the processing of near outcomes in a wheel of fortune paradigm, this time using functional magnetic resonance imaging and a group of participants with varying degrees of gambling problems. The results showed increased activity in the bilateral superior parietal cortex following near compared to full outcomes. The third study examined the peripheral physiology reactions to near outcomes in the wheel of fortune. Heart period and skin conductance were measured while participants with varying degrees of gambling problems played on the wheel of fortune. Near compared to full outcomes led to increased heart period duration shortly after the outcome. Furthermore, heart period reactions and skin conductance responses (SCRs) were modulated by gambling problems. Participants with high relative to low levels of gambling problems showed increased SCRs to near outcomes and similar heart period reactions to near outcomes and full wins. The fourth study analyzed choice behavior and sequence effects in the processing of outcomes in a coin toss paradigm using EEG in a group of problem gamblers and controls. Again, problem gamblers showed generally smaller FRN amplitudes compared to controls. There were no differences between groups in the processing of outcome sequences. The break of an outcome streak led to increased power in the theta frequency band. Furthermore, the P300 amplitude was increased after a sequence of previous wins. Finally, problem gamblers compared to controls showed a trend of switching the outcome symbol relative to the previous outcome symbol more often. In sum, the results point towards differences in the processing of near compared to full outcomes in brain areas and measures implicated in attentional and salience processes. The processing of outcome sequences involves processes of salience attribution and violation of expectations. Furthermore, problem gamblers seem to process near outcomes as more win-like compared to controls. The results and their implications for problem gambling as well as further possible lines of research are discussed.}, subject = {Spielsucht}, language = {en} } @phdthesis{Costea2016, author = {Costea, Paul Igor}, title = {Stratification and variation of the human gut microbiota}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-139649}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {The microbial communities that live inside the human gastrointestinal tract -the human gut microbiome- are important for host health and wellbeing. Characterizing this new "organ", made up of as many cells as the human body itself, has recently become possible through technological advances. Metagenomics, the high-throughput sequencing of DNA directly from microbial communities, enables us to take genomic snapshots of thousands of microbes living together in this complex ecosystem, without the need for isolating and growing them. Quantifying the composition of the human gut microbiome allows us to investigate its properties and connect it to host physiology and disease. The wealth of such connections was unexpected and is probably still underestimated. Due to the fact that most of our dietary as well as medicinal intake affects the microbiome and that the microbiome itself interacts with our immune system through a multitude of pathways, many mechanisms have been proposed to explain the observed correlations, though most have yet to be understood in depth. An obvious prerequisite to characterizing the microbiome and its interactions with the host is the accurate quantification of its composition, i.e. determining which microbes are present and in what numbers they occur. Historically, standard practices have existed for sample handling, DNA extraction and data analysis for many years. However, these were generally developed for single microbe cultures and it is not always feasible to implement them in large scale metagenomic studies. Partly because of this and partly because of the excitement that new technology brings about, the first metagenomic studies each took the liberty to define their own approach and protocols. From early meta-analysis of these studies it became clear that the differences in sample handling, as well as differences in computational approaches, made comparisons across studies very difficult. This restricts our ability to cross-validate findings of individual studies and to pool samples from larger cohorts. To address the pressing need for standardization, we undertook an extensive comparison of 21 different DNA extraction methods as well as a series of other sample manipulations that affect quantification. We developed a number of criteria for determining the measurement quality in the absence of a mock community and used these to propose best practices for sampling, DNA extraction and library preparation. If these were to be accepted as standards in the field, it would greatly improve comparability across studies, which would dramatically increase the power of our inferences and our ability to draw general conclusions about the microbiome. Most metagenomics studies involve comparisons between microbial communities, for example between fecal samples from cases and controls. A multitude of approaches have been proposed to calculate community dissimilarities (beta diversity) and they are often combined with various preprocessing techniques. Direct metagenomics quantification usually counts sequencing reads mapped to specific taxonomic units, which can be species, genera, etc. Due to technology-inherent differences in sampling depth, normalizing counts is necessary, for instance by dividing each count by the sum of all counts in a sample (i.e. total sum scaling), or by subsampling. To derive a single value for community (dis-)similarity, multiple distance measures have been proposed. Although it is theoretically difficult to benchmark these approaches, we developed a biologically motivated framework in which distance measures can be evaluated. This highlights the importance of data transformations and their impact on the measured distances. Building on our experience with accurate abundance estimation and data preprocessing techniques, we can now try and understand some of the basic properties of microbial communities. In 2011, it was proposed that the space of genus level variation of the human gut microbial community is structured into three basic types, termed enterotypes. These were described in a multi-country cohort, so as to be independent of geography, age and other host properties. Operationally defined through a clustering approach, they are "densely populated areas in a multidimensional space of community composition"(source) and were proposed as a general stratifier for the human population. Later studies that applied this concept to other datasets raised concerns about the optimum number of clusters and robustness of the clustering approach. This heralded a long standing debate about the existence of structure and the best ways to determine and capture it. Here, we reconsider the concept of enterotypes, in the context of the vastly increased amounts of available data. We propose a refined framework in which the different types should be thought of as weak attractors in compositional space and we try to implement an approach to determining which attractor a sample is closest to. To this end, we train a classifier on a reference dataset to assign membership to new samples. This way, enterotypes assignment is no longer dataset dependent and effects due to biased sampling are minimized. Using a model in which we assume the existence of three enterotypes characterized by the same driver genera, as originally postulated, we show the relevance of this stratification and propose it to be used in a clinical setting as a potential marker for disease development. Moreover, we believe that these attractors underline different rules of community assembly and we recommend they be accounted for when analyzing gut microbiome samples. While enterotypes describe structure in the community at genus level, metagenomic sequencing can in principle achieve single-nucleotide resolution, allowing us to identify single nucleotide polymorphisms (SNPs) and other genomic variants in the gut microbiome. Analysis methodology for this level of resolution has only recently been developed and little exploration has been done to date. Assessing SNPs in a large, multinational cohort, we discovered that the landscape of genomic variation seems highly structured even beyond species resolution, indicating that clearly distinguishable subspecies are prevalent among gut microbes. In several cases, these subspecies exhibit geo-stratification, with some subspecies only found in the Chinese population. Generally however, they present only minor dispersion limitations and are seen across most of our study populations. Within one individual, one subspecies is commonly found to dominate and only rarely are several subspecies observed to co-occur in the same ecosystem. Analysis of longitudinal data indicates that the dominant subspecies remains stable over periods of more than three years. When interrogating their functional properties we find many differences, with specific ones appearing relevant to the host. For example, we identify a subspecies of E. rectale that is lacking the flagellum operon and find its presence to be significantly associated with lower body mass index and lower insulin resistance of their hosts; it also correlates with higher microbial community diversity. These associations could not be seen at the species level (where multiple subspecies are convoluted), which illustrates the importance of this increased resolution for a more comprehensive understanding of microbial interactions within the microbiome and with the host. Taken together, our results provide a rigorous basis for performing comparative metagenomics of the human gut, encompassing recommendations for both experimental sample processing and computational analysis. We furthermore refine the concept of community stratification into enterotypes, develop a reference-based approach for enterotype assignment and provide compelling evidence for their relevance. Lastly, by harnessing the full resolution of metagenomics, we discover a highly structured genomic variation landscape below the microbial species level and identify common subspecies of the human gut microbiome. By developing these high-precision metagenomics analysis tools, we thus hope to contribute to a greatly improved understanding of the properties and dynamics of the human gut microbiome.}, subject = {Mensch}, language = {en} } @phdthesis{Ratz2016, author = {Ratz, Valentin}, title = {Entwicklung einer funktionellen 3D Magnetresonanz-Def{\"a}kographie}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-139762}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Epidemiologische Studien sch{\"a}tzen die Inzidenz chronischer Obstipation auf bis zu 27\% der Gesamtbev{\"o}lkerung. Betroffenen Patienten ist die Stuhlentleerung nicht oder nur unter großer Anstrengung und nicht selten nur unter Zuhilfenahme der Hand m{\"o}glich. H{\"a}ufig sind funktionelle Pathologien, welche sich nur w{\"a}hrend der Def{\"a}kation ausbilden, hierf{\"u}r verantwortlich. Daher ist f{\"u}r die Diagnose und Evaluation dieser Pathologien ein bildgebendes Verfahren notwendig, welches die dynamische Darstellung der Def{\"a}kation erm{\"o}glicht. Der Goldstandard zur Untersuchung von Patienten mit funktionellen Beckenbodenst{\"o}rungen ist die Entero-Colpo-Cysto-Def{\"a}kographie (ECCD). Diese Durchleuchtungsmethode erfordert die Applikation ionisierender Strahlung im Bereich des Beckens. Außerdem m{\"u}ssen f{\"u}r die Untersuchung Rektum und Vagina mit bariumhaltigem Kontrastmittel, der D{\"u}nndarm mit barium- und iodhaltigem Kontrastmittel und zus{\"a}tzlich die Blase mit iodhaltigem Kontrastmittel gef{\"u}llt werden. Bei der MR-Def{\"a}kographie hingegen ist keine ionisierende Strahlung notwendig und nur eine rektale F{\"u}llung mit Ultraschallgel als Kontrastmittel erforderlich. Zudem erm{\"o}glichen statische Aufnahmen aufgrund des hohen Weichteilkontrasts der MR-Bildgebung eine detaillierte Darstellung des gesamten Beckenbodens. Die MR-Bildgebung ist jedoch im Vergleich zu anderen Bildgebungsmodalit{\"a}ten, wie beispielsweise der radiographischen Durchleuchtung, langsam. Besonders zur Darstellung dynamischer Prozesse ist daher eine starke Beschleunigung des Akquisitionsprozesses notwendig. Bei der Standard 2D MR-Def{\"a}kographie wird f{\"u}r die Beschleunigung der Datenakquisition eine regelm{\"a}ßige zweifache Unterabtastung des k-Raums vorgenommen. Hierdurch lassen sich aber nur drei r{\"a}umlich voneinander getrennte 68 2D Schichten mit einer zeitlichen Aktualisierungsrate der drei Schichten von ca. 1s akquirieren. Dadurch ist aber besonders die Diagnose lateral lokalisierter Pathologien eingeschr{\"a}nkt oder gar nicht m{\"o}glich. Daher wurde in dieser Arbeit eine 3D MR-Def{\"a}kographie zur dynamischen Darstellung der Def{\"a}kation innerhalb eines vollst{\"a}ndigen 3D Volumens entwickelt, implementiert und anhand von 9 Patientenmessungen optimiert. Die letzten 4 Patienten wurden mit den optimierten Sequenzparametern untersucht. Ausgehend von der kartesischen Datenakquisition der bestehenden 2D MRDef{\"a}kographie wurden zun{\"a}chst dreidimensionale kartesische Trajektorien zur Datenakquisition und daf{\"u}r geeignete Algorithmen zur Datenrekonstruktion untersucht. In diesem Zusammenhang wurde ein GRAPPA Centric-Out Akquisitionsschema in Kombination mit einer GRAPPA Datenrekonstruktion vorgestellt. Es zeigte sich jedoch, dass eine Stack-of-Stars Trajektorie in Bezug auf die stabile, rauscharme, dynamische Darstellung der Def{\"a}kation, vorteilhaft gegen{\"u}ber der untersuchten kartesischen GRAPPA Centric-Out Trajektorie ist. Zur weiteren Optimierung der Messsequenz wurden daher drei radiale Stackof-Stars Akquisitionsschemata untersucht: Das Standard Stack-of-Stars Schema sowie zwei mit View-Sharing und zwei unterschiedlichen Dichtegewichtungen modifizierte Stack-of-Stars Schemata (DW-Sampling 1 und DW-Sampling 2). Das View-Sharing erm{\"o}glicht durch die Umstellung der Reihenfolge der akquirierten Partitionen nahezu eine Verdopplung der rekonstruierten Zeitpunkte der dynamisch gemessenen Zeitserie. Die Dichtegewichtung bewirkt, dass in den zentralen Partitionen mehr radiale Speichen gemessen werden und damit das k-Raum Zentrum dichter abgetastet wird als in den {\"a}ußeren Partitionen. Beim Dichtegewichtungsschema DW-Sampling 2 ist der Abfall der Anzahl der innerhalb einer Partition gemessenen Speichen st{\"a}rker als beim DW-Sampling 1. Trotzdem f{\"u}hrte das mit View-Sharing und DW-Sampling 2 modifizierte Stackof-Stars Akquisitionsschema in Verbindung mit der FISTA Compressed Sensing Datenrekonstruktion zum besten Kompromiss zwischen erreichbarer r{\"a}umlicher 69 und zeitlicher Aufl{\"o}sung. Dieses optimierte Setup erm{\"o}glicht die dynamische Darstellung der Def{\"a}kation in 7 Schichten eines vollst{\"a}ndigen 3D Volumens mit einer Volumenaktualisierungsrate von 1,3s. Im Vergleich zur standardm{\"a}ßig durchgef{\"u}hrten 2D MR-Def{\"a}kographie ist daher eine mehr als doppelt so große Abdeckung mit einer vergleichbaren zeitlichen Aktualisierungsrate und einer etwas geringeren r{\"a}umlichen Aufl{\"o}sung gew{\"a}hrleistet. Hierdurch lassen sich zus{\"a}tzlich zu den gew{\"o}hnlichen zentral gelegenen Pathologien auch lateral ausgepr{\"a}gte Pathologien besser abdecken und diagnostizieren.}, subject = {Kernspintomografie}, language = {de} }