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Humans are continuously exposed to airborne spores of the saprophytic fungus Aspergillus fumigatus. However, in healthy individuals pulmonary host defense mechanisms efficiently eliminate the fungus. In contrast, A. fumigatus causes devastating infections in immunocompromised patients. Host immune responses against A. fumigatus lung infections in immunocompromised conditions have remained largely elusive. Given the dynamic changes in immune cell subsets within tissues upon immunosuppressive therapy, we dissected the spatiotemporal pulmonary immune response after A. fumigatus infection to reveal basic immunological events that fail to effectively control invasive fungal disease. In different immunocompromised murine models, myeloid, notably neutrophils, and macrophages, but not lymphoid cells were strongly recruited to the lungs upon infection. Other myeloid cells, particularly dendritic cells and monocytes, were only recruited to lungs of corticosteroid treated mice, which developed a strong pulmonary inflammation after infection. Lymphoid cells, particularly CD4\(^+\) or CD8\(^+\) T-cells and NK cells were highly reduced upon immunosuppression and not recruited after A. fumigatus infection. Moreover, adoptive CD11b\(^+\) myeloid cell transfer rescued cyclophosphamide immunosuppressed mice from lethal A. fumigatus infection but not cortisone and cyclophosphamide immunosuppressed mice. Our findings illustrate that CD11b\(^+\) myeloid cells are critical for anti-A. fumigatus defense under cyclophosphamide immunosuppressed conditions.
G-quadruplex structures are highly stable alternative DNA structures that can, when not properly regulated, impede replication fork progression and cause genome instability (Castillo Bosch et al, 2014; Crabbe et al, 2004; Koole et al, 2014; Kruisselbrink et al, 2008; London et al, 2008; Lopes et al, 2011; Paeschke et al, 2013; Paeschke et al, 2011; Piazza et al, 2015; Piazza et al, 2010; Piazza et al, 2012; Ribeyre et al, 2009; Sabouri et al, 2014; Sarkies et al, 2012; Sarkies et al, 2010; Schiavone et al, 2014; Wu & Spies, 2016; Zimmer et al, 2016). The aim of this thesis was to identify novel G-quadruplex interacting proteins in Saccharomyces cerevisiae and to unravel their regulatory function at these structures to maintain genome integrity. Mms1 and Rtt101 were identified as G-quadruplex binding proteins in vitro via a pull-down experiment with subsequent mass spectrometry analysis. Rtt101, Mms1 and Mms22, which are all components of an ubiquitin ligase (Rtt101Mms1/Mms22), are important for the progression of the replication fork following fork stalling (Luke et al, 2006; Vaisica et al, 2011; Zaidi et al, 2008). The in vivo binding of endogenously tagged Mms1 to its target regions was analyzed genome-wide using chromatin-immunoprecipitation followed by deep-sequencing. Interestingly, Mms1 bound independently of Mms22 and Rtt101 to G-rich regions that have the potential to form G-quadruplex structures. In vitro, formation of G-quadruplex structures could be shown for the G-rich regions Mms1 bound to. This binding was observed throughout the cell cycle. Furthermore, the deletion of MMS1 caused replication fork stalling as evidenced by increased association of DNA Polymerase 2 at Mms1 dependent sites. A gross chromosomal rearrangement assay revealed that deletion of MMS1 results in a significantly increased genome instability at G-quadruplex motifs compared to G-rich or non-G-rich regions. Additionally, binding of the helicase Pif1, which unwinds G4 structures in vitro (Paeschke et al, 2013; Ribeyre et al, 2009; Sanders, 2010; Wallgren et al, 2016), to Mms1 binding sites was reduced in mms1 cells. The data presented in this thesis, together with published data, suggests a novel mechanistic model in which Mms1 binds to G-quadruplex structures and enables Pif1 association. This allows for replication fork progression and genome integrity.
MYC is a transcription factor, whose expression is elevated or deregulated in many human cancers (up to 70%) and is often associated with aggressive and poorly differentiated tumors. Although MYC is extensively studied, discrepancies have emerged about how this transcription factor works. In primary lymphocytes, MYC promotes transcriptional amplification of virtually all genes with an open promoter, whereas in tumor cells MYC regulates specific sets of genes that have significant prognostic value. Furthermore, the set of target genes that distinguish MYC’s physiological function from the pathological/oncogenic one, whether it exists or not, has not been fully understood yet.
In this study, it could be shown that MYC protein levels within a cell and promoter affinity (determined by E-box presence or interaction with other proteins) of target genes toward MYC are important factors that influence MYC activity. At low levels, MYC can amplify a certain transcriptional program, which includes high affinity binding sites, whereas at high levels MYC leads to the specific up- and down regulation of genes with low affinity. Moreover, the promoter affinity characterizes different sets of target genes which can be distinguished in the physiological or oncogenic MYC signatures.
MYC-mediated repression requires higher MYC levels than activation and formation of a complex with MIZ1 is necessary for inhibiting expression of a subset of MYC target genes.
Wilms tumor protein 1 (WT1) is a suitable target to develop an immunotherapeutic approach against high risk acute myeloid leukemia (AML), particularly their relapse after allogeneic hematopoietic stem cell transplantation (HSCT). As an intracellular protein traversing between nucleus and cytoplasm, recombinant expression of WT1 is difficult. Therefore, an induction of WT1-specific T-cell responses is mostly based on peptide vaccination as well as dendritic cell (DC) electroporation with mRNA encoding full-length protein to mount WT1-derived peptide variations presented to T cells. Alternatively, the WT1 peptide presentation could be broadened by forcing receptor-mediated endocytosis of DCs.
In this study, antibody fusion proteins consisting of an antibody specific to the human DEC205 endocytic receptor and various fragments of WT1 (anti-hDEC205-WT1) were generated for a potential DC-targeted recombinant WT1 vaccine. Anti-hDEC205-WT1 antibody fusion proteins containing full-length or major parts of WT1 were not efficiently expressed and secreted due to their poor solubility and secretory capacity. However, small fragment-containing variants: anti-hDEC205-WT110-35, anti-hDEC205-WT191-138, anti-hDEC205-WT1223-273, and anti-hDEC205-WT1324-371 were obtained in good yields.
Since three of these fusion proteins contain the most of the known immunogenic epitopes in their sequences, the anti-hDEC205-WT191-138, anti-hDEC205-WT1223-273, and anti-hDEC205-WT1324-371 were tested for their T-cell stimulatory capacities. Mature monocyte-derived DCs loaded with anti-hDEC205-WT191-138 could induce ex vivo T-cell responses in 12 of 16 blood samples collected from either healthy or HSC transplanted individuals compared to included controls (P < 0.01). Furthermore, these T cells could kill WT1-overexpressing THP-1 leukemia cells in vitro after expansion.
In conclusion, alongside proving the difficulty in expression and purification of intracellular WT1 as a vaccine protein, our results from this work introduce an alternative therapeutic vaccine approach to improve an anti-leukemia immune response in the context of allogeneic HSCT and potentially beyond.
Beyond the state of the art, towards intuitive and reliable non-visual Brain-Computer-Interfacing
(2016)
For the present work three main goals were formulated:
goal 1 To design a tactile BCI used for mobility which is
intuitive (G1.1), reliable and fast while being usable
by participants aged 50 years and above.
goal 2 To design an auditory BCI used for communication
which is intuitive and reliable.
goal 3 To examine the effects of training on tactile and
auditory BCI performance.
Three studies were performed to achieve these goals.
In the first study nine participants aged above 50 years
performed a five-session training after which eight participants
were able to navigate a virtual wheelchair with
mean accuracy above 95% and an ITR above 20 bits / min.
In the second study 15 participants, four of them endusers
with motor-impairment, were able to communicate
meaningful with high accuracies using an auditory BCI.
In the third study nine healthy and nine visually impaired
participants (regarded as sensory experts for non-visual
perception) performed tactile, auditory and visual (for
healthy participants only) copy tasks. Participants with
trained perception significantly outperformed control
participants for tactile but not for auditory performance.
Tactile performance of sensory experts was on equal levels
as the visual performance of control participants.
We were able to demonstrate viability of intuitive gazeindependent
tactile and auditory BCI. Our tactile BCI performed
on levels similar to those of visual BCI, outperforming
current tactile BCI protocols. Furthermore, we were
able to demonstrate significant beneficial effect of training
on tactile BCI performance. Our results demonstrate previously
untapped potential for tactile BCI and avenues for
future research in the field of gaze-independent BCI.
Eclosion is the emergence of an adult insect from the pupal case at the end of development. In the fruit fly Drosophila melanogaster, eclosion is a circadian clock-gated event and is regulated by various peptides. When studied on the population level, eclosion reveals a clear rhythmicity with a peak at the beginning of the light-phase that persists also under constant conditions. It is a long standing hypothesis that eclosion gating to the morning hours with more humid conditions is an adaption to reduce water loss and increase the survival. Eclosion behavior, including the motor pattern required for the fly to hatch out of the puparium, is orchestrated by a well-characterized cascade of peptides. The main components are ecdysis-triggering hormone (ETH), eclosion hormone (EH) and crustacean cardioactive peptide (CCAP). The molt is initiated by a peak level and pupal ecdysis by a subsequent decline of the ecdysteroid ecdysone. Ecdysteroids are produced by the prothoracic gland (PG), an endocrine tissue that contains a peripheral clock and degenerates shortly after eclosion. Production and release of ecdysteroids are regulated by the prothoracicotropic hormone (PTTH).
Although many aspects of the circadian clock and the peptidergic control of the eclosion behavior are known, it still remains unclear how both systems are interconnected. The aim of this dissertation research was to dissect this connection and evaluate the importance of different Zeitgebers on eclosion rhythmicity under natural conditions.
Potential interactions between the central clock and the peptides regulating ecdysis motor behavior were evaluated by analyzing the influence of CCAP on eclosion rhythmicity. Ablation and silencing of CCAP neurons, as well as CCAP null-mutation did not affect eclosion rhythmicity under either light or temperature entrainment nor under natural conditions.
To dissect the connection between the central and the peripheral clock, PTTH neurons were ablated. Monitoring eclosion under light and temperature entrainment revealed that eclosion became arrhythmic under constant conditions. However, qPCR expression analysis revealed no evidence for cycling of Ptth mRNA in pharate flies. To test for a connection with pigment-dispersing factor (PDF)-expressing neurons, the PDF receptor (PDFR) and short neuropeptide F receptor (sNPFR) were knocked down in the PTTH neurons. Knockdown of sNPFR, but not PDFR, resulted in arrhythmic eclosion under constant darkness conditions. PCR analysis of the PTTH receptor, Torso, revealed its expression in the PG and the gonads, but not in the brain or eyes, of pharate flies. Knockdown of torso in the PG lead to arrhythmicity under constant conditions, which provides strong evidence for the specific effect of PTTH on the PG. These results suggest connections from the PDF positive lateral neurons to the PTTH neurons via sNPF signaling, and to the PG via PTTH and Torso. This interaction presumably couples the period of the peripheral clock in the PG to that of the central clock in the brain.
To identify a starting signal for eclosion and possible further candidates in the regulation of eclosion behavior, chemically defined peptidergic and aminergic neurons were optogenetically activated in pharate pupae via ChR2-XXL. This screen approach revealed two candidates for the regulation of eclosion behavior: Dromyosuppressin (DMS) and myo-inhibitory peptides (MIP). However, ablation of DMS neurons did not affect eclosion rhythmicity or success and the exact function of MIP must be evaluated in future studies.
To assess the importance of the clock and of possible Zeitgebers in nature, eclosion of the wildtype Canton S and the clock mutant per01 and the PDF signaling mutants pdf01 and han5304 was monitored under natural conditions. For this purpose, the Würzburg eclosion monitor (WEclMon) was developed, which is a new open monitoring system that allows direct exposure of pupae to the environment. A general decline of rhythmicity under natural conditions compared to laboratory conditions was observed in all tested strains. While the wildtype and the pdf01 and han5304 mutants stayed weakly rhythmic, the per01 mutant flies eclosed mostly arrhythmic. PDF and its receptor (PDFR encoded by han) are required for the synchronization of the clock network and functional loss can obviously be compensated by a persisting synchronization to external Zeitgebers. The loss of the central clock protein PER, however, lead to a non-functional clock and revealed the absolute importance of the clock for eclosion rhythmicity. To quantitatively analyze the effect of the clock and abiotic factors on eclosion rhythmicity, a statistical model was developed in cooperation with Oliver Mitesser and Thomas Hovestadt. The modelling results confirmed the clock as the most important factor for eclosion rhythmicity. Moreover, temperature was found to have the strongest effect on the actual shape of the daily emergence pattern, while light has only minor effects. Relative humidity could be excluded as Zeitgeber for eclosion and therefore was not further analyzed.
Taken together, the present dissertation identified the so far unknown connection between the central and peripheral clock regulating eclosion. Furthermore, a new method for the analysis of eclosion rhythms under natural conditions was established and the necessity of a functional clock for rhythmic eclosion even in the presence of multiple Zeitgebers was shown.
Staphylococcus aureus is a prevalent commensal bacterium which represents one of the leading causes in health care-associated bacterial infections worldwide and can cause a variety of different diseases ranging from simple abscesses to severe and life threatening infections including pneumonia, osteomyelitis and sepsis.
In recent times multi-resistant strains have emerged, causing severe problems in nosocomial as well as community-acquired (CA) infection settings, especially in the United States (USA). Therefore S. aureus has been termed as a superbug by the WHO, underlining the severe health risk originating from it. Today, infections in the USA are dominated by S. aureus genotypes which are classified as USA300 and USA400, respectively. Strains of genotype USA300 are responsible for about 70% of the CA infections.
The molecular mechanisms which render S. aureus such an effective pathogen are still not understood in its entirety. For decades S. aureus was thought to be a strictly extracellular pathogen relying on pore-forming toxins like α-hemolysin to damage human cells and tissue. Only recently it has been shown that S. aureus can enter non-professional phagocytes, using adhesins like the fibronectin-binding proteins which mediate an endocytotic uptake into the host cells. The bacteria are consequently localized to endosomes, where the degradation of enclosed bacterial cells through phagosome maturation would eventually occur.
S. aureus can avoid degradation, and translocate to the cellular cytoplasm, where it can replicate. The ability to cause this so-called phagosomal escape has mainly been attributed to a family of amphiphilic peptides called phenol soluble modulins (PSMs), but as studies have shown, they are not sufficient.
In this work I used a transposon mutant library in combination with automated fluorescence microscopy to screen for genes involved in the phagosomal escape process and intracellular survival of S. aureus. I thereby identified a number of genes, including a non-ribosomal peptide synthetase (NRPS). The NRPS, encoded by the genes ausA and ausB, produces two types of small peptides, phevalin and tyrvalin. Mutations in the ausAB genes lead to a drastic decrease in phagosomal escape rates in epithelial cells, which were readily restored by genetic complementation in trans as well as by supplementation of synthetic phevalin. In leukocytes, phevalin interferes with calcium fluxes and activation of neutrophils and promotes cytotoxicity of intracellular bacteria in both, macrophages and neutrophils. Further ausAB is involved in survival and virulence of the bacterium during mouse lung pneumoniae.
The here presented data demonstrates the contribution of the bacterial cyclic dipeptide phevalin to S. aureus virulence and suggests, that phevalin directly acts on a host cell target to promote cytotoxicity of intracellular bacteria.
A large fraction of human tumors exhibits aberrant expression of the oncoprotein MYC. As a transcription factor regulating various cellular processes, MYC is also crucially involved in normal development. Direct targeting of MYC has been a major challenge for molecular cancer drug discovery. The proof of principle that its inhibition is nevertheless feasible came from in vivo studies using a dominant-negative allele of MYC termed OmoMYC. Systemic expression of OmoMYC triggered long-term tumor regression with mild and fully reversible side effects on normal tissues.
In this study, OmoMYC’s mode of action was investigated combining methods of structural biology and functional genomics to elucidate how it is able to preferentially affect oncogenic functions of MYC.
The crystal structure of the OmoMYC homodimer, both in the free and the E-box-bound state, was determined, which revealed that OmoMYC forms a stable homodimer, and as such, recognizes DNA via the same base-specific DNA contacts as the MYC/MAX heterodimer. OmoMYC binds DNA with an equally high affinity as MYC/MAX complexes. RNA-sequencing showed that OmoMYC blunts both MYC-dependent transcriptional activation and repression. Genome-wide DNA-binding studies using chromatin immunoprecipitation followed by high-throughput sequencing revealed that OmoMYC competes with MYC/MAX complexes on chromatin, thereby reducing their occupancy at consensus DNA binding sites. The most prominent decrease in MYC binding was seen at low-affinity promoters, which were invaded by MYC at oncogenic levels. Strikingly, gene set enrichment analyses using OmoMYC-regulated genes enabled the identification of tumor subgroups with high MYC levels in multiple tumor entities. Together with a targeted shRNA screen, this identified novel targets for the eradication of MYC-driven tumors, such as ATAD3A, BOP1, and ADRM1.
In summary, the findings suggest that OmoMYC specifically inhibits tumor cell growth by attenuating the expression of rate-limiting proteins in cellular processes that respond to elevated levels of MYC protein using a DNA-competitive mechanism. This opens up novel strategies to target oncogenic MYC functions for tumor therapy.
Anxiety disorders (AD) are common, disabling mental disorders, which constitute the most prevalent mental health condition conveying a high individual and socioeconomic burden. Social anxiety disorder (SAD), i.e. fear in social situations particularly when subjectively scrutinized by others, is the second most common anxiety disorder with a life time prevalence of 10%. Panic disorder (PD) has a life time prevalence of 2-5% and is characterized by recurrent and abrupt surges of intense fear and anticipatory anxiety, i.e. panic attacks, occurring suddenly and unexpected without an apparent cue.
In recent years, psychiatric research increasingly focused on epigenetic mechanisms such as DNA methylation as a possible solution for the problem of the so-called “hidden heritability”, which conceptualizes the fact that the genetic risk variants identified so far only explain a small part of the estimated heritability of mental disorders.
In the first part of this thesis, oxytocin receptor (OXTR) gene methylation was investigated regarding its role in the pathogenesis of social anxiety disorder. In summary, OXTR methylation patterns were implicated in different phenotypes of social anxiety disorder on a categorical, neuropsychological, neuroendocrinological as well as on a neural network level. The results point towards a multilevel role of OXTR gene hypomethylation particularly at one CpG site (CpG3, Chr3: 8 809 437) within the protein coding region of the gene in SAD.
The second part of the thesis investigated monoamine oxidase A (MAOA) gene methylation regarding its role in the pathogenesis of panic disorder as well as – applying a psychotherapy-epigenetic approach – its dynamic regulation during the course of cognitive behavioural therapy (CBT) in PD patients. First, MAOA hypomethylation was shown to be associated with panic disorder as well as with panic disorder severity. Second, in patients responding to treatment MAOA hypomethylation was shown to be reversible up to the level of methylation in healthy controls after the course of CBT. This increase in MAOA methylation along with successful psychotherapeutic treatment was furthermore shown to be associated with symptom improvement regarding agoraphobic avoidance in an independent replication sample of non-medicated patients with PD.
Taken together, in the future the presently identified epigenetic patterns might contribute to establishing targeted preventive interventions and personalized treatment options for social anxiety disorder or panic disorder, respectively.
Functional and genetic dissection of mechanosensory organs of \(Drosophila\) \(melanogaster\)
(2016)
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.
Comparative transcriptomics and post-transcriptional regulation in \(Campylobacter\) \(jejuni\)
(2016)
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.
microRNAs in chronic pain
(2016)
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.
To simplify a judgment, people often base it on easily accessible information. One cue that is usually readily available is processing fluency – a metacognitive feeling of ease of cognitive processing. Consequently, processing fluency is used as a cue for many different types of judgment, such as judgment of truth, confidence, and novelty. The present work describes results of three studies investigating various aspects of processing fluency effects on judgment.
Processing fluency has been sometimes equated with speed of a cognitive process. Therefore, response times have been used for evaluation of processing fluency. However, response times in experimental tasks often do not encompass only the time needed for a given process, but also the time needed for a decision based on the resulting information. The study described in Chapter II uses a novel experimental method that enables separation of reading and decision times. The results show that people make a decision about liking of pseudowords faster when the pseudowords are hard-to-pronounce (i.e., disfluent) than when they are moderate in pronounceability. This suggests that response times cannot be used as a proxy for processing fluency when they include the time needed to make a decision.
One of the studies of judgmental effects of processing fluency showed that food additives with easier pronounceable names are judged to be less harmful than those with hard-to-pronounce names. While people encounter food additives that are safe more often, this environmental association may be in the opposite direction for some categories of objects. For example, people are more likely to see names of especially dangerous criminals in the news. Chapter III describes a study which initially tested whether the fluency-safety association may be in the opposite direction for some categories of objects as a consequence of this selective exposure to especially dangerous exemplars. The results did not show support for this hypothesis. Furthermore, subsequent studies suggest that the previously found association between fluency and safety is replicable with the original stimuli used in the previous research, but not with newly constructed stimuli.
Chapter IV describes a study which applied a finding from the processing fluency literature to a positive psychology exercise in order to increase its effectiveness. Namely, the experiment manipulated the number of good things that participants listed daily for two weeks as part of the exercise. While listing more things was considered harder, the number of things listed each day had no effect on effectiveness of the exercise.
Traditional species identification based on morphological characters is laborious
and requires expert knowledge. It is further complicated in the case of
species assemblages or degraded and processed material. DNA-barcoding,
species identification based on genetic data, has become a suitable alternative,
yet species assemblages are still difficult to study. In the past decade
meta-barcoding has widely been adopted for the study of species communities,
due to technological advances in modern sequencing platforms and
because manual separation of individual specimen is not required. Here,
meta-barcoding is put into context and applied to the study of bee-collected
pollen as well as bacterial communities. These studies provide the basis
for a critical evaluation of the powers and limitations of meta-barcoding. Advantages
identified include species identification without the need for expert
knowledge as well as the high throughput of samples and sequences. In
microbiology, meta-barcoding can facilitate directed cultivation of taxa of interest
identified with meta-barcoding data. Disadvantages include insufficient
species resolution due to short read lengths and incomplete reference
databases, as well as limitations in abundance estimation of taxa and functional
profiling. Despite these, meta-barcoding is a powerful method for the
analysis of species communities and holds high potential especially for automated
biomonitoring.
Attention-Deficit/Hyperactivity Disorder (ADHD) is characterized by symptoms of inattentiveness and hyperactivity/impulsivity. Besides, increasing evidence points to ADHD patients showing emotional dysfunctions and concomitant problems in social life. However, systematic research on emotional dysfunctions in ADHD is still rare, and to date most studies lack conceptual differentiation between emotion processing and emotion regulation. The aim of this thesis was to systematically investigate emotion processing and emotion regulation in adult ADHD in a virtual reality paradigm implementing social interaction. Emotional reactions were assessed on experiential, physiological, and behavioral levels.
Experiment 1 was conducted to develop a virtual penalty kicking paradigm implying social feedback and to test it in a healthy sample. This paradigm should then be applied in ADHD patients later on. Pleasant and unpleasant trials in this paradigm consisted of hits respectively misses and subsequent feedback from a virtual coach. In neutral trials, participants were teleported to different spots of the virtual stadium. Results indicated increased positive affectivity (higher valence and arousal ratings, higher zygomaticus activations, and higher expression rates of positive emotional behavior) in response to pleasant compared to neutral trials. Reactions to unpleasant trials were contradictory, indicating increased levels of both positive and negative affectivity, compared to neutral trials. Unpleasant vs. neutral trials revealed lower valence ratings, higher arousal ratings, higher zygomaticus activations, slightly lower corrugator activations, and higher expression rates of both positive and negative emotional behavior. The intensity of emotional reactions correlated with experienced presence in the virtual reality.
To better understand the impact of hits or misses per se vs. hits or misses with coach feedback healthy participants’ emotional reactions, only 50% of all shots were followed by coach feedback in experiment 2. Neutral trials consisted of shots over the free soccer field which were followed by coach feedback in 50 % of all trials. Shots and feedback evoked more extreme valence and arousal ratings, higher zygomaticus activations, lower corrugator activations, and higher skin conductance responses than shots alone across emotional conditions. Again, results speak for the induction of positive emotions in pleasant trials whereas the induction of negative emotions in unpleasant trials seems ambiguous. Technical improvements of the virtual reality were reflected in higher presence ratings than in experiment 1.
Experiment 3 investigated emotional reactions of adult ADHD patients and healthy controls after emotion processing and response-focused emotion regulation. Participants successively
went through an ostensible online ball-tossing game (cyber ball) inducing negative emotions, and an adapted version of the virtual penalty kicking game. Throughout cyber ball, participants were included or ostracized by two other players in different experimental blocks. Participants were instructed to explicitly show, not regulate, or hide their emotions in different experimental blocks. Results provided some evidence for deficient processing of positive emotions in ADHD. Patients reported slightly lower positive affect than controls during cyber ball, gave lower valence ratings than controls in response to pleasant penalty kicking trials, and showed lower zygomaticus activations than controls especially during penalty kicking. Patients in comparison with controls showed slightly increased processing of unpleasant events during cyber ball (higher ratings of negative affect, especially in response to ostracism), but not during penalty kicking. Patients showed lower baseline skin conductance levels than controls, and impaired skin conductance modulations. Compared to controls, patients showed slight over-expression of positive as well as negative emotional behavior. Emotion regulation analyses revealed no major difficulties of ADHD vs. controls in altering their emotional reactions through deliberate response modulation. Moreover, patients reported to habitually apply adaptive emotion regulation strategies even more frequently than controls. The analyses of genetic high-risk vs. low-risk groups for ADHD across the whole sample revealed similar results as analyses for patients vs. controls for zygomaticus modulations during emotion processing, and for modulations of emotional reactions due to emotion regulation.
To sum up, the virtual penalty kicking paradigm proved to be successful for the induction of positive, but not negative emotions. The importance of presence in virtual reality for the intensity of induced emotions could be replicated. ADHD patients showed impaired processing of primarily positive emotions. Aberrations in negative emotional responding were less clear and need further investigation. Results point to adult ADHD in comparison to healthy controls suffering from baseline deficits in autonomic arousal and deficits in arousal modulation. Deficits of ADHD in the deliberate application of response-focused emotion regulation could not be found.
Frontal asymmetry, a construct invented by Richard Davidson, linking positive and negative valence as well as approach and withdrawal motivation to lateralized frontal brain activation has been investigated for over thirty years. The frontal activation patterns described as relevant were measured via alpha-band frequency activity (8-13 Hz) as a measurement of deactivation in electroencephalography (EEG) for homologous electrode pairs, especially for the electrode position F4/ F3 to account for the frontal relative lateralized brain activation.
Three different theories about frontal activation patterns linked to motivational states were investigated in two studies. The valence theory of Davidson (1984; 1998a; 1998b) and its extension to the motivational direction theory by Harmon-Jones and Allen (1998) refers to the approach motivation with relative left frontal brain activity (indicated by relative right frontal alpha activity) and to withdrawal motivation with relative right frontal brain activation (indicated by relative left frontal alpha activity). The second theory proposed by Hewig and colleagues (2004; 2005; 2006) integrates the findings of Davidson and Harmon – Jones and Allen with the reinforcement sensitivity theory of Jeffrey A. Gray (1982, 1991). Hewig sees the lateralized frontal approach system and withdrawal system proposed by Davidson as subsystems of the behavioral activation system proposed by Gray and bilateral frontal activation as a biological marker for the behavioral activation system. The third theory investigated in the present studies is the theory from Wacker and colleagues (2003; 2008; 2010) where the frontal asymmetrical brain activation patterns are linked to the revised reinforcement sensitivity theory of Gray and McNaughton (2000). Here, right frontal brain activity (indicated by lower relative right frontal alpha activity) accounts for conflict, behavioral inhibition and activity of the revised behavioral inhibition system, while left frontal brain activation (indicated by lower relative left frontal alpha activity) stands for active behavior and the activity of the revised behavioral activation system as well as the activation of the revised flight fight freezing system. In order to investigate these three theories, a virtual reality T-maze paradigm was introduced to evoke motivational states in the participants, offering the opportunity to measure frontal brain activation patterns via EEG and behavior simultaneously in the first study. In the second study the virtual reality paradigm was additionally compared to mental imagery and a movie paradigm, two well-known state inducing paradigms in the research field of frontal asymmetry.
In the two studies, there was confirming evidence for the theory of Hewig and colleages (2004; 2005; 2006), showing higher bilateral frontal activation for active behavior and lateralized frontal activation patterns for approach (left frontal brain activation) and avoidance (right frontal brain activation) behavior. Additionally a limitation for the capability model of anterior brain asymmetry proposed by Coan and colleagues (2006), where the frontal asymmetry should be dependent on the relevant traits driving the frontal asymmetry pattern if a relevant situation occurs, could be found. As the very intense virtual reality paradigm did not lead to a difference of frontal brain activation patterns compared to the mental imagery paradigm or the movie paradigm for the traits of the participants, the trait dependency of the frontal asymmetry in a relevant situation might not be given, if the intensity of the situation exceeds a certain level. Nevertheless there was an influence of the traits in the virtual reality T-maze paradigm, because the shown behavior in the maze was trait-dependent.
The implications of the findings are multifarious, leading from possible objective personality testing via diversification of the virtual reality paradigm to even clinical implications for depression treatments based on changes in the lateralized frontal brain activation patterns for changes in the motivational aspects, but also for changes in bilateral frontal brain activation when it comes to the drive and preparedness for action in patients. Finally, with the limitation of the capability model, additional variance in the different findings about frontal asymmetry can be explained by taking the intensity of a state manipulation into account.
Polymorphonuclear neutrophils (PMNs) are phagocytic cells of the innate immune system that efficiently kill bacteria. However, they also have regulatory effects on other immune cells and contribute to immunosuppression in cancer, which worsens the outcome. In particular, this has been demonstrated for a subset of granulocytic cells called myeloid- derived suppressor cells (MDSCs), but its distinction from PMNs is controversial. Most authors have explored the suppressive effects of MDSCs on T cells, but recent data suggest that NK cells are also affected. NK cells are crucial for the combat of tumor cells, in particular leukemic cells. There is hardly data available on the interaction between NK cells and suppressive granulocytic cells. Therefore, the aim of this thesis was to explore the effects of MDSCs and PMNs on the NK cell function against the leukemia cell line K562.
In co-culture experiments, I demonstrate that granulocytic MDSCs and PMNs had similar effects on NK cell function and homeostasis. On the one hand, they positively influenced the survival and maturation of NK cells. On the other, they inhibited the activation, cytotoxicity and cytokine production of NK cells, both IFNγ and TNFα, in response to K562 target cells. Furthermore, I show a down-regulation of the activating receptor NKp30 on NK cells in the presence of MDSCs or PMNs, which may form part of the underlying suppressive mechanisms.
However, there is also evidence for the involvement of other molecules. Further investigations are needed to confirm a relevant suppression of NK cells by granulocytic cells in cancer patients, and to identify therapeutic targets. The recognition that regular PMNs have similar effects on NK cells as MDSCs could simplify future experiments, since MDSCs are heterogeneous and laborious to isolate and identify.
NKcells and granulocytes are among the first immune cells to reconstitute after hematopoietic stem cell transplantation, and NK cells may be particularly exposed to suppressive effects of granulocytes this scenario. Modulating these suppressive effects of granulocytes on NK cells therapeutically may yield a better NK cell function and an improved cancer prognosis.

The main function of the small intestine is the absorption of essential nutrients, water and vitamins. Moreover, it constitutes a barrier protecting us from toxic xenobiotics and pathogens. For a better understanding of these processes, the development of intestinal in vitro models is of great interest to the study of pharmacological and pathological issues such as transport mechanisms and barrier function. Depending on the scientific questions, models of different complexity can be applied.
In vitro Transwell® systems based on a porous PET-membrane enable the standardized study of transport mechanisms across the intestinal barrier as well as the investigation of the influence of target substances on barrier integrity. However, this artificial setup reflects only limited aspects of the physiology of the native small intestine and can pose an additional physical barrier. Hence, the applications of this model for tissue engineering are limited.
Previously, tissue models based on a biological decellularized scaffold derived from porcine gut tissue were demonstrated to be a good alternative to the commonly used Transwell® system. This study showed that preserved biological extracellular matrix components like collagen and elastin provide a natural environment for the epithelial cells, promoting cell adhesion and growth. Intestinal epithelial cells such as Caco-2 cultured on such a scaffold showed a confluent, tight monolayer on the apical surface. Additionally, myofibroblasts were able to migrate into the scaffold supporting intestinal barrier formation.
In this thesis, dendritic cells were additionally introduced to this model mimicking an important component of the immune system. This co-culture model was then successfully proven to be suitable for the screening of particle formulations developed as delivery system for cancer antigens in peroral vaccination studies. In particular, nanoparticles based on PLGA, PEG-PAGE-PLGA, Mannose-PEG-PAGE-PLGA and Chitosan were tested. Uptake studies revealed only slight differences in the transcellular transport rate among the different particles. Dendritic cells were shown to phagocytose the particles after they have passed the intestinal barrier. The particles demonstrated to be an effective carrier system to transport peptides across the intestinal barrier and therefore present a useful tool for the development of novel drugs.
Furthermore, to mimic the complex structure and physiology of the gut including the presence of multiple different cell types, the Caco-2 cell line was replaced by primary intestinal cells to set up a de novo tissue model. To that end, intestinal crypts including undifferentiated stem cells and progenitor cells were isolated from human small intestinal tissue samples (jejunum) and expanded in vitro in organoid cultures. Cells were cultured on the decellularized porcine gut matrix in co-culture with intestinal myofibroblasts. These novel tissue models were maintained under either static or dynamic conditions.
Primary intestinal epithelial cells formed a confluent monolayer including the major differentiated cell types positive for mucin (goblet cells), villin (enterocytes), chromogranin A (enteroendocrine cells) and lysozyme (paneth cells). Electron microscopy images depicted essential functional units of an intact epithelium, such as microvilli and tight junctions. FITC-dextran permeability and TEER measurements were used to assess tightness of the cell layer. Models showed characteristic transport activity for several reference substances. Mechanical stimulation of the cells by a dynamic culture system had a great impact on barrier integrity and transporter activity resulting in a tighter barrier and a higher efflux transporter activity.
In Summary, the use of primary human intestinal cells combined with a biological decellularized scaffold offers a new and promising way to setup more physiological intestinal in vitro models. Maintenance of primary intestinal stem cells with their proliferation and differentiation potential together with adjusted culture protocols might help further improve the models. In particular, dynamic culture systems and co culture models proofed to be a first crucial steps towards a more physiological model. Such tissue models might be useful to improve the predictive power of in vitro models and in vitro in vivo correlation (IVIVC) studies. Moreover, these tissue models will be useful tools in preclinical studies to test pharmaceutical substances, probiotic active organisms, human pathogenic germs and could even be used to build up patient-specific tissue model for personalized medicine.
Human Vγ9Vδ2 T cells are the main γδ T cell subset in the circulation, accounting for up to 5% of the total peripheral blood lymphocyte population. They have been suggested to be important in response to tumors and infections. Their immune mechanisms encompass cell killing via cytotoxicity and secretion of pro-inflammatory cytokines such as IFNγ and tumor necrosis factor (TNF). The main stimulators of Vγ9Vδ2 T cells are isopentenyl pyrophosphate (IPP) and (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), denominated phosphoantigens (PAg).
A major advance in the understanding of PAg detection and Vγ9Vδ2 T cell activation has been the identification of the butyrophlin 3A (BTN3A) proteins as key mediators in these processes. In humans, three isoforms constitute the BTN3A family: BTN3A1, BTN3A2, and BTN3A3; and their genes are localized on the short arm of chromosome 6. The role of BTN3A1 has been highlighted by BTN3A-specific monoclonal antibody 20.1 (mAb 20.1), which has an agonist effect and causes proliferation, expansion, and activation of primary human Vγ9Vδ2 T cells. On the other hand, BTN3A-specific monoclonal antibody 103.2 (mAb 103.2) is antagonistic, inhibiting the Vγ9Vδ2 T cell response. The actual mechanism underlying both PAg- and mAb 20.1-mediated activation is not completely elucidated, but the importance of BTN3A1 is clear.
The main objective of this dissertation was to characterize the role of BTN3A1 in the PAg-dependent and PAg-independent Vγ9Vδ2 T cell activation and to evaluate its contribution in the response to influeza A virus infected cells. This research work demonstrated, by using Vγ9Vδ2 TCR MOP-transduced murine cells (reporter cells), that human chromosome 6 (Chr6) is mandatory for PAg-induced stimulation, but not for stimulation with mAb 20.1. The reporter cells responded to mAb 20.1 in cultures with BTN3A1-transduced Chinese hamster ovary cells (CHO BTN3A1) as antigen presenting cells. Nevertheless, for PAg-dependent activation the presence of Chr6 in CHO BTN3A1 was mandatory.
Although reporter cells expressing clonotypically different Vγ9Vδ2 TCRs showed similar PAg response, they clearly differed in the mAb 20.1 response. The reporter cell line transduced with Vγ9Vδ2 TCR D1C55 demonstrated essentially no response to mAb 20.1 compared to Vγ9Vδ2 TCR MOP cells. These findings were further supported by experiments performed with human PBMCs-derived Vγ9Vδ2 T cell clones. The results indicate heterogeneity in the PAg- and 20.1-dependent responses, in terms of CD25 and CD69 expression, among three different Vγ9Vδ2 T cells clones.
Co-cultures of reporter cells with Raji RT1BI and PAg plus mAb 20.1 or single chain antibody 20.1 (sc 20.1) revealed no additive or synergistic activating effects. In contrast, mAb 20.1 or sc 20.1 inhibited the PAg-mediated activation of the reporter cells.
The comparison of the relative contribution of the isoforms BTN3A2 and BTN3A3, in the activation of Vγ9Vδ2 T cells, was undertaken by overexpression of these isoforms in CHO cells. The results showed that BTN3A2 contributes to both PAg- and mAb-induced Vγ9Vδ2 T cell activation. On the contrary, BTN3A3 does not support PAg-mediated γδ T cell response.
Additionally, mutations in the proposed PAg- and mAb 20.1-binding sites of the extracellular BTN3A1 domain were generated by means of site-directed mutagenesis. These mutations revoked the mAb 20.1-induced Vγ9Vδ2 T cell activation, but not that induced by PAg.
Finally, co-cultures of Vγ9Vδ2 TCR MOP-transduced murine reporter cells with influenza A/PR/8/34-infected cells, or infection of PBMCs with this virus strain indicated that BTN3A1 might be dispensable for the Vγ9Vδ2 T cell response against influenza A.
The data of this research work points out that: i) in addition to BTN3A1, other Chr6-encoded genes are necessary for Vγ9Vδ2 T cell activation with PAg; ii) clonotypical (CDR3) differences influence the PAg- and mAb 20.1-mediated Vγ9Vδ2 T cell activation; iii) the PAg- and mAb 20.1-induced responses are not synergistic and interfere with each other; iv) BTN3A2 and BTN3A3 isoforms differ in the ability to support PAg- or mAb 20.1-dependent Vγ9Vδ2 T cell activation; v) the importance of the intracellular B30.2 domain of BTN3A1, in the Vγ9Vδ2 T cell activation, might be higher than that of the extracellular domain; and vi) in spite of the importance of BTN3A1 in the activation of Vγ9Vδ2 T cells, it is possible that many molecules with redundant functions are involved in the elimination of influenza virus infection by these cells.
In summary, it is possible to hypothesize a model in which BTN3A1 detects prenyl pyrophosphates in the cytoplasm via its B30.2 domain and in association with another protein(s). The binding of PAg to this domain induces a multimerization of BTN3A1 or a conformational change of its extracellular domain (mimicked by mAb 20.1). These modifications might be recognized by the Vγ9Vδ2 TCR or by an associated T cell protein. In the case that the TCR directly recognizes BTN3A1, the intensity of the response will depend on the Vγ9Vδ2 TCR clonotype. Future research will allow to gain a better understanding of BTN3A1, its interaction with other proteins, its actual role in the activation of Vγ9Vδ2 T cells, and its importance in specific models of cancer or infection. This knowledge will be necessary to transform these cells into effective tools in the clinic.
Motoneuron diseases form a heterogeneous group of pathologies characterized by the progressive degeneration of motoneurons. More and more genetic factors associated with motoneuron diseases encode proteins that have a function in RNA metabolism, suggesting that disturbed RNA metabolism could be a common underlying problem in several, perhaps all, forms of motoneuron diseases. Recent results suggest that SMN interacts with hnRNP R and TDP-43 in neuronal processes, which are not part of the classical SMN complex. This point to an additional function of SMN, which could contribute to the high vulnerability of spinal motoneurons in spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS). The current study elucidates functional links between SMN, the causative factor of SMA (spinal muscular atrophy), hnRNP R, and TDP-43, a genetic factor in ALS (amyotrophic lateral sclerosis). In order to characterize the functional interaction of SMN with hnRNP R and TDP-43, we produced recombinant proteins and investigated their interaction by co-immunoprecipitation. These proteins bind directly to each other, indicating that no other co-factors are needed for this interaction. SMN potentiates the ability of hnRNP R and TDP-43 to bind to ß-actin mRNA. Depletion of SMN alters the subcellular distribution of hnRNP R in motoneurons both in SMN-knockdown motoneurons and SMA mutant mouse (delta7 SMA). These data point to functions of SMN beyond snRNP assembly which could be crucial for recruitment and transport of RNA particles into axons and axon terminals, a mechanism which may contribute to SMA pathogenesis and ALS.
ALS and FTLD (frontotemporal lobar degeneration) are linked by several lines of evidence with respect to clinical and pathological characteristics. Both sporadic and familial forms are a feature of the ALS-FTLD spectrum, with numerous genes having been associated with these pathological conditions. Both diseases are characterized by the pathological cellular aggregation of proteins. Interestingly, some of these proteins such as TDP-43 and FUS have also common relations not only with ALS-FTLD but also with SMA. Intronic hexanucleotide expansions in C9ORF72 are common in ALS and FTLD but it is unknown whether loss of function, toxicity by the expanded RNA or dipeptides from non ATG-initiated translation is responsible for the pathophysiology. This study tries to characterize the cellular function of C9ORF72 protein. To address this, lentiviral based knockdown and overexpression of C9ORF72 was used in isolated mouse motoneurons. The results clearly show that survival of these motoneurons was not affected by altered C9ORF72 levels, whereas adverse effects on axon growth and growth cone size became apparent after C9ORF72 suppression. Determining the protein interactome revealed several proteins in complexes with C9ORF72. Interestingly, C9ORF72 is present in a complex with cofilin and other actin binding proteins that modulate actin dynamics. These interactions were confirmed both by co-precipitation analyses and in particular by functional studies showing altered actin dynamics in motoneurons with reduced levels of C9ORF72. Importantly, the phosphorylation of cofilin is enhanced in C9ORF72 depleted motoneurons and patient derived lymphoblastoid cells with reduced C9ORF72 levels. These findings indicate that C9ORF72 regulates axonal actin dynamics and the loss of this function could contribute to disease pathomechanisms in ALS and FTLD.
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.
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.
Gambling is a popular activity in Germany, with 40% of a representative sample reporting having gambled at least once in the past year (Bundeszentrale für gesundheitliche Aufklärung, 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.
Adjuvants are compounds added to an agrochemical spray formulation to improve or modify the action of an active ingredient (AI) or the physico-chemical characteristics of the spray liquid. Adjuvants can have more than only one distinct mode of action (MoA) during the foliar spray application process and they are generally known to be the best tools to improve agrochemical formulations. The main objective for this work was to elucidate the basic MoA of adjuvants by uncoupling different aspects of the spray application. Laboratory experiments, beginning from retention and spreading characteristics, followed by humectant effects concerning the spray deposit on the leaf surface and ultimately the cuticular penetration of an AI, were figured out to evaluate overall in vivo effects of adjuvants which were also obtained in a greenhouse spray test. For this comprehensive study, the surfactant classes of non-ionic sorbitan esters (Span), polysorbates (Tween) and oleyl alcohol polyglycol ether (Genapol O) were generally considered because of their common promoting potential in agrochemical formulations and their structural diversity.
The reduction of interfacial tension is one of the most crucial physico-chemical properties of surfactants. The dynamic surface tension (DST) was monitored to characterise the surface tension lowering behaviour which is known to influence the droplet formation and retention characteristics. The DST is a function of time and the critical time frame of droplet impact might be at about 100 ms. None of the selected surfactants were found to lower the surface tension sufficiently during this short timeframe (chapter I). At ca. 100 ms, Tween 20 resulted in the lowest DST value. When surfactant monomers are fully saturated at the droplet-air-interface, an equilibrium surface tension (STeq) value can be determined which may be used to predict spreading or run-off effects. The majority of selected surfactants resulted in a narrow distribution of STeq values, ranging between 30 and 45 mN m- 1. Nevertheless, all surfactants were able to decrease the surface tension considerably compared to pure water (72 mN m- 1). The influence of different surfactants on the wetting process was evaluated by studying time-dependent static contact angles on different surfaces and the droplet spread area on Triticum aestivum leaves after water evaporation. The spreading potential was observed to be better for Spans than for Tweens. Especially Span 20 showed maximum spreading results. To transfer laboratory findings to spray application, related to field conditions, retention and leaf coverage was measured quantitatively on wheat leaves by using a variable track sprayer. Since the retention process involves short time dynamics, it is well-known that the spray retention on a plant surface is not correlated to STeq but to DST values. The relationship between DST at ca. 100 ms and results from the track sprayer showed increasing retention results with decreasing DST, whereas at DST values below ca. 60 mN m- 1 no further retention improvement could be observed.
Under field conditions, water evaporates from the droplet within a few seconds to minutes after droplet deposition on the leaf surface. Since precipitation of the AI must essentially being avoided by holding the AI in solution, so-called humectants are used as tank-mix adjuvants. The ability of pure surfactants to absorb water from the surrounding atmosphere was investigated comprehensively by analysing water sorption isotherms (chapter II). These isotherms showed an exponential shape with a steep water sorption increase starting at 60% to 70% RH. Water sorption was low for Spans and much more distinct for the polyethoxylated surfactants (Tweens and Genapol O series). The relationship between the water sorption behaviour and the molecular structure of surfactants was considered as the so-called humectant activity. With an increasing ethylene oxide (EO) content, the humectant activity increased concerning the particular class of Genapol O. However, it could be shown that the moisture absorption across all classes of selected surfactants correlates rather better with their hydrophilic-lipophilic balance values with the EO content.
All aboveground organs of plants are covered by the cuticular membrane which is therefore the first rate limiting barrier for AI uptake. In vitro penetration experiments through an astomatous model cuticle were performed to study the effects of adjuvants on the penetration of the lipophilic herbicide Pinoxaden (PXD) (chapter III). In order to understand the influence of different adjuvant MoA like humectancy, experiments were performed under three different humidity levels. No explicit relationship could be found between humidity levels and the PXD penetration which might be explained by the fact that humidity effects would rather affect hydrophilic AIs than lipophilic ones. Especially for Tween 20, it became obvious that a complex balance between multiple MoA like spreading, humectancy and plasticising effects have to be considered.
Greenhouse trials, focussing the adjuvant impact on in vivo action of PXD, were evaluated on five different grass-weed species (chapter III). Since agrochemical spray application and its following action on living plants also includes translocation processes in planta and species dependent physiological effects, this investigation may help to simulate the situation on the field. Even though the absolute weed damage was different, depending both on plant species and also on PXD rates, adjuvant effects in greenhouse experiments displayed the same ranking as in cuticular penetration studies: Tween 20 > Tween 80 > Span 20 ≥ Span 80.
Thus, the present work shows for the first time that findings obtained in laboratory experiments can be successfully transferred to spray application studies on living plants concerning adjuvant MoA. A comparative analysis, using radar charts, could demonstrate systematic derivations from structural similarities of adjuvants to their MoA (summarising discussion and outlook). Exemplarily, Tween 20 and Tween 80 cover a wide range of selected variables by having no outstanding MoA improving one distinct process during foliar application, compared to non-ethoxylated Span 20 and Span 80 which primarily revealed a surface active action. Most adjuvants used in this study represent polydisperse mixtures bearing a complex distribution of EO and aliphatic chains. From this study it seems alike that adjuvants having a wide EO distribution offer broader potential than adjuvants with a small EO distribution. It might be a speculation that due to this broad distribution of single molecules, all bearing their individual specific physico-chemical nature, a wide range of properties concerning their MoA is covered.
Amyotrophic lateral sclerosis and spinal muscular atrophy are the two most common motoneuron diseases. Both are characterized by destabilization of axon terminals, axon degeneration and alterations in neuronal cytoskeleton. Accumulation of neurofilaments has been observed in several neurodegenerative diseases but the mechanisms how elevated neurofilament levels destabilize axons are unknown so far. Here, I show that increased neurofilament expression in motor nerves of pmn mutant mice causes disturbed microtubule dynamics. Depletion of neurofilament by Nefl knockout increases the number and regrowth of microtubules in pmn mutant motoneurons and restores axon elongation. This effect is mediated by interaction of neurofilament with the stathmin complex. Depletion of neurofilament increases stathmin-Stat3 interaction and stabilizes the microtubules. Consequently, the axonal maintenance is improved and the pmn mutant mice survive longer. We propose that this mechanism could also be relevant for other neurodegenerative diseases in which neurofilament accumulation is a prominent feature.
Next, using Smn-/-;SMN2 mouse as a model, the molecular mechanism behind synapse loss in SMA is studied. SMA is characterized by degeneration of lower α-motoneurons in spinal cord; however, how reduction of ubiquitously expressed SMN leads to MN-specific degeneration remains unclear. SMN is involved in pre-mRNA splicing (Pellizzoni, Kataoka et al. 1998) and its deficiency in SMA affects the splicing machinery. Neuromuscular junction denervation precedes neurodegeneration in SMA. However, there is no evidence of a link between aberrant splicing of transcripts downstream of Smn and reduced presynaptic axon excitability observed in SMA. In this study, we observed that expression and splicing of Nrxn2, that encodes a presynaptic protein is affected in the SMA mouse and that Nrxn2 could be a candidate that relates aberrant splicing to synaptic motoneuron defects in SMA.
Several cohort studies showed that obesity increases the risk of chronic disease such as T2DM, hypertension and non-alcoholic fatty liver disease and various types of cancer. Different factors were described that might be involving in these diseases in obesity. Some of these suggested factors were chronic infection, elevated free fatty acids, increased ROS formation, mitochondrial dysfunction and raised NAPDH oxidase activity. Obesity is a multifactorial disease and it is very hard to distinguish between all of these factors. In this study, we wanted to focus on the association between obesity, oxidative stress and genomic damage in kidney, liver and colon, which are the most relevant organs for cancer risk according to the cohort studies. Our findings indicated elevated oxidative stress in kidney, liver and colon together with elevated lipid, RNA and DNA oxidation in the whole body. Additionally, we were able to show increased DNA damage in kidney, liver and colon.
Since obesity has become an epidemic all over the world, possible therapeutic applications such as life style changes (diet and sport), pharmacological supplements and various type of surgeries are increasing. As a second question, we focused on the effect of weight loss, which is supplied either by Roux-en-Y gastric bypass surgery or by caloric restriction designed in a way to provide the same extent of weight loss, on oxidative stress and genomic damage. Our results indicated that weight loss either by gastric bypass surgery or by caloric restriction led to reduced oxidative stress and genomic damage in kidney, liver and colon. We could not find any difference between the weight loss methods, except the DNA oxidation and repair marker urinary 8-oxodG, which was still elevated after RYGB, but not after caloric restriction.
It is known that hyperinsulinemia and in the long term T2DM are among the biggest concerns in obese individuals. Since we know the mutagenic potential of elevated insulin levels from previous data in our working group, the correlation between the highly mutagenic DNA DBSs marker, γ-H2AX and the plasma insulin level was tested and the findings indicated a positive correlation. In order to demonstrate the association between insulin-related oxidative stress and genomic damage, we used in vitro and in vivo models with Pten deficiency. In this part of study, the work was focused on liver.
Pten is a known negative regulator of the PI3K/Akt pathway, which is responsible for the elevated NADPH oxidase activity and mitochondrial dysfunction through elevated insulin levels. Pten inhibition or deficiency were used to sensitize the system to insulin. Non-transformed immortalized human hepatocytes were used to show the mutagenic potential of elevated insulin and these in vitro data revealed once more the link between insulin signaling, elevated oxidative stress and genomic damage. Since the metabolic function of the liver is not only due to the extent of the hepatic insulin response but is also affected by systemic interactions, a whole-body Pten haplodeficient mouse model with an additional Pten+/-/Akt2-/- group was utilized for in vivo investigation of insulin-mediated toxicity. Our findings in this model suggested that Pten deficiency alone can cause an increase in oxidative stress. HFD alone was sufficient to increase the expression of HO-1 and genomic damage significantly. Moreover, the combination (whole-body Pten haplodeficient mice fed with HFD) showed significantly elevated oxidative stress and genomic damage in mouse liver. However, Akt2 knockout could only reduce the oxidative stress and DNA damage in high fat diet fed mice significantly.
All these findings demonstrated that obesity can induce oxidative stress and genomic damage. Elevated insulin levels are associated with obesity-mediated oxidative stress and genomic damage. However, the underlying mechanisms are surely multifaceted and complicated. For example, Pten as oncogene might also induce other mechanisms besides the elevation of the PI3K/Akt pathway activity.
In conclusion, it is clear that oxidative stress and DNA damage are linked to obesity and that weight loss can reduce these two factors. Since DNA-damage is associated with an elevated cancer risk, it might be logical to use an antioxidant therapy in obese individuals to reduce the side effects and oxidative stress dependent mutagenicity and cancer risk in these individuals. However, much more research will be needed to support this idea experimentally.
The rotation of the earth around its own axis determines periodically changing environmental conditions, like alterations in light and temperature. For the purpose of adapting all organisms’ behavior, physiology and metabolism to recurring changes, endogenous clocks have evolved, which allow the organisms to anticipate environmental changes. In chronobiology, the scientific field dealing with the investigation of the underlying mechanisms of the endogenous clock, the fruit fly Drosophila melanogaster serves as a beneficial model organism. The fruit fly’s circadian clock exhibits a rather simple anatomical organization, but nevertheless constitutes homologies to the mammalian system. Thus also in this PhD-thesis the fruit fly was used to decipher general features of the circadian clock’s interneuronal communication.
Drosophila melanogaster’s circadian clock consists of about 150 clock neurons, which are located in the central nervous system of the fly. These clock neurons can be subdivided regarding to their anatomical position in the brain into the dorsal neurons (DN1s, DN2s, DN3s), as well as into the lateral neurons (LPNs, LNds, s-LNvs, l-LNvs). Functionally these clock neuron clusters can be classified as Morning- and Evening oscillators (M- and E- oscillators), driving different parts of the fly’s locomotor activity in light-dark conditions (LD). The Morning-oscillators are represented by the s-LNvs and are known to be the main pacemakers, driving the pace of the clock in constant conditions (constant darkness; DD). The group of Evening-oscillators consists of the LNds, the DN1s and the 5th s-LNv and is important for the proper timing of the evening activity in LD. All of these clock neurons are not functionally independent, but form complex neuronal connections, which are highly plastic in their response to different environmental stimuli (Zeitgebers), like light or temperature.
Even though a lot is known about the function and the importance of some clock neuron clusters, the exact interplay between the neurons is not fully known yet. To investigate the mechanisms, which are involved in communication processes among different clock neurons, we depolarized specific clock cells in a temporally and cell-type restricted manner using dTrpA1, a thermosensitive cation channel, which allows the depolarization of neurons by application of temperature pulses (TP) above 29°C to the intact and freely moving fly. Using different clock specific GAL4-driver lines and applying TPs at different time points within the circadian cycle in DD enabled us with the help of phase shift experiments to draw conclusions on the properties of the endogenous clock. The obtained phase shifts in locomotor behavior elicited by specific clock neuronal activation were plotted as phase response curves (PRCs).
The depolarization of all clock neurons shifted the phase of activity the strongest, especially in the delay zone of the PRC. The exclusive depolarization of the M oscillators together with the l-LNvs (PDF+ neurons: s-LNvs & l-LNvs) caused shifts in the delay and in the advance zone as well, however the advances were severely enhanced in their temporal occurrence ranging into the subjective day. We concluded that light might have inhibitory effects on the PDF+ cells in that particular part of the PRC, as typical light PRCs do not exhibit that kind of distinctive advances. By completely excluding light in the PRC-experiments of this PhD-thesis, this photic inhibitory input to the PDF+ neurons is missing, probably causing the broadened advance zone. These findings suggest the existence of an inhibitory light-input pathway to the PDF+ cells from the photoreceptive organs (Hofbauer-Buchner eyelet, photoreceptor cells of compound eyes, ocelli) or from other clock neurons, which might inhibit phase advances during the subjective day.
To get an impression of the molecular state of the clock in the delay and advance zone, staining experiments against Period (PER), one of the most important core clock components, and against the neuropeptide Pigment Dispersing Factor (PDF) were performed. The cycling of PER levels mirrored the behavioral phase shifts in experimental flies, whereas the controls were widely unaffected. As just those neurons, which had been depolarized, exhibited immediate shifted PER oscillations, this effect has to be rapidly regulated in a cell-autonomous manner.
However, the molecular link between clock neuron depolarization and shifts in the molecular clock’s cycling is still missing. This issue was addressed by CREB (cAMP responsive element binding protein) quantification in the large ventrolateral neurons (l-LNvs), as these neurons responded unexpectedly and strongest to the artificial depolarization exhibiting a huge increase in PER levels. It had been previously suggested that CREB is involved in circadian rhythms by binding to regulatory sequences of the period gene (Belvin et al., 1999), thus activating its transcription. We were able to show, that CREB levels in the l-LNvs are under circadian regulation, as they exhibit higher CREB levels at the end of the subjective night relative to the end of the subjective day. That effect was further reinforced by artificial depolarization, independently of the time point of depolarization. Furthermore the data indicate that rises in CREB levels are coinciding with the time point of increases of PER levels in the l-LNvs, suggesting CREB being the molecular link between the neuronal electrical state and the molecular clock.
Taking together, the results indicate that a temporal depolarization using dTrpA1 is able to significantly phase shift the clock on the behavioral and protein level. An artificial depolarization at the beginning of the subjective night caused phase delays, whereas a depolarization at the end of the subjective night resulted in advances. The activation of all clock neurons caused a PRC that roughly resembled a light-PRC. However, the depolarization of the PDF+ neurons led to a PRC exhibiting a shape that did not resemble that of a light-mediated PRC, indicating the complex processing ability of excitatory and inhibitory input by the circadian clock. Even though this experimental approach is highly artificial, just the exclusion of light-inputs enabled us to draw novel conclusions on the network communication and its light input pathways.
The protozoan parasite Trypanosoma brucei is the causal agent of sleeping sickness and besides its epidemiological importance it has been used as model organism for the study of many aspects of cellular and molecular biology especially the post-transcriptional control of gene expression.
Several studies in the last 30 years have shown the importance of mRNA processing and stability for gene regulation. In T. brucei genes are unusually arranged in polycistronic transcription units (PTUs) and a coupled process of trans-splicing and polyadenylation produces the mature mRNAs. Both processes, mRNA processing and stability, cannot completely explain the control of gene expression in the different life cycle stages analyzed in T. brucei so far.
In recent years, the relevance of expression regulation at the level of translation has become evident in other eukaryotes. Therefore, in the first part of my thesis I studied the impact of translational regulation by means of a genome-wide ribosome profiling approach. My data suggest that translational efficiencies vary between life cycle stages of the parasite as well as between genes within one life cycle stage. Furthermore, using ribosome profiling I was able to identify many new putative un-annotated coding sequences and to evaluate the coding potential of upstream open reading frames (uORF). Comparing my results with previously published proteomic and RNA interference (RNAi) target sequencing (RIT-seq) datasets allowed me to validate some of the new coding sequences and to evaluate their relevance for the fitness of the parasite.
In the second part of my thesis I used the transcriptomic and translatomic profiles obtained from the ribosome profiling analysis for the identification of putative non-coding RNAs (ncRNAs). These results led to the analysis of the coding potential in the regions upstream and downstream of the expressed variant surface glycoprotein (VSG), which is outlined in the third part of the results section. The region upstream of the VSG, the co-transposed region (CTR), has been implicated in an increase of the in situ switching rate upon its deletion. The ribosome profiling results indicated moderate transcription but not translation in this region. These results raised the possibility that the CTR may be transcribed into ncRNA. Therefore, in the third part of my thesis, I performed a primary characterization of the CTR-derived transcripts based on northern blotting and RACE. The results suggested the presence of a unique transcript species of about 1,200 nucleotides (nt) and polyadenylated at the 3’-end of the sequence.
The deletion of the CTR sequence promoting and increase of the in situ switching rates was performed around 20 years ago by means of inserting reporter genes. With the recent development of endonuclease-based tools for genome editing, it is now possible to delete sequences in a marker-free way. In the fourth part of my thesis, I show the results on the implementation of the highly efficient genome-editing CRISPR-Cas9 system in T. brucei using episomes. As a proof of principle, I inserted the sequence coding for the enhanced green fluorescent protein (eGFP) at the end of the SCD6 coding sequence (CDS). Fluorescent cells were observed as early as two days after transfection. Therefore, after the successful set up of the CRISPR-Cas9 system it will be possible to modify genomic regions with more relevance for the biology of the parasite, such as the substitution of codons present in gene tandem arrays.
The implementation of ribosome profiling in T. brucei opens the opportunity for the study of translational regulation in a genome-wide scale, the re-annotation of the currently available genome, the search for new putative coding sequences, the detection of putative ncRNAs, the evaluation of the coding potential in uORFs and the role of unstranslated regions (UTRs) in the regulation of translation. In turn, the implementation of the CRISPR-Cas9 system offers the possibility to manipulate the genome of the parasite at a nucleotide resolution and without the need of including resistant makers. The CRISPR-Cas9 system is a powerful tool for editing ncRNAs, UTRs, multicopy gene families and CDSs keeping their endogenous UTRs. Moreover, the system can be used for the modification of both alleles after just one round of transfection and of codons coding for amino acids carrying post-translational modifications (PTMs) among other possibilities.
Cuticles cover all above-ground primary plant organs and are lipoid in nature consisting of a cutin matrix with cuticular waxes embedded within or deposited on its surface. The foremost function of the plant cuticle is the limitation of transpirational water loss into the surrounding atmosphere. Transpiration of water vapour from plants differs between stomatal and cuticular transpiration. Stomatal closure minimises the stomatal water loss and the remaining, much lower water transpiration occurs through the plant cuticle.
Temperature influence on the transpiration barrier properties of intact leaves is not yet known, despite the importance of the cuticular transpiration especially under drought and heat conditions. The present study focuses on the temperature-dependent minimum water permeability of whole leaves, in comparison to the temperature effect on the cuticular permeance of isolated, astomatous cuticles (Chapter I - III).
The minimum water permeability was determined gravimetrically from leaf drying curves and represents the cuticular water permeability of intact, stomatous leaves under conditions of complete stomatal closure. The temperature effect on the transpiration barrier of the desert plant Rhazya stricta and the Mediterranean sclerophyll Nerium oleander exposed a continuous increase of minimum water permeabilities with an increase in temperature. In contrast to other published studies, no abrupt and steep increase of the water permeability at high temperatures was detected. This steep increase indicates structural changes of the barrier properties of isolated cuticular membranes with a drastic decrease of efficiency. A stabilising impact of the cell wall on the plant cuticle of intact leaves was proposed. This steadying effect was confirmed with different experimental approaches measuring the cuticular water permeability of Prunus laurocerasus intact leaves.
Physiological analysis of water transport on isolated, astomatous leaf cuticles indicated a drastic decline of the barrier properties at elevated temperatures for Prunus laurocerasus but not for Nerium oleander. Cuticular components were quantitatively and qualitatively analysed by gas chromatography with a flame ionisation detector and a mass spectrometric detector, respectively. A high accumulation of pentacyclic triterpenoids as cuticular wax components in relation to the cutin monomer coverage was detected for Nerium oleander and for Rhazya stricta leaves, too. Accordingly, reinforcing of the cutin matrix by triterpenoids was proposed to improve the mechanical strength and to reduce the extensibility of plant cuticles. Thus, structural changes of the cuticular barrier properties were potentially suppressed at elevated temperatures.
The function of the cuticular wax amount and/or wax composition and its relation with the cuticular water permeability remains to be elucidated. In the second part of this work the cuticular wax quantity and quality as well as its impact on the transpiration barrier properties was analysed in order to deduce a potential relation between chemistry and function of plant cuticles (Chapter IV - V).
Chemical analyses of the cuticular wax components of a wide range of plant species, including one tropical (Vanilla planifolia), temperate (Juglans regia, Plantago lanceolata), Mediterranean (Nerium oleander, Olea europaea) and one desert (Rhazya stricta) plant species, were conducted. The cuticular wax compositions of nine characteristic plant species from xeric limestone sites naturally located in Franconia (Southern Germany) were determined for the first time. The corresponding minimum or cuticular water permeabilities of both stomatous and astomatous leaf surfaces were measured to detect a potential relationship between the cuticular wax amount, wax composition and the cuticular barrier properties.
It was demonstrated that abundant cuticular wax amounts did not constitute more efficient transpiration barriers. However, 55% of the cuticular barrier function can be attributed to the very-long-chain aliphatic wax coverages. These new findings provide evidence that the acyclic wax constituents play a pivotal role establishing efficient transpiration barriers. Additionally, these findings strengthen the hypothesis that cyclic components, such as pentacyclic triterpenoids, do not hinder the water diffusion through plant cuticles as effectively as acyclic constituents. For the first time a relationship between the cuticular wax composition and the transpiration barrier properties of a wide range of plant species proved insights into the potential relation between chemistry and function of plant cuticles.