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The integrity of our genome is continuously endangered by DNA damaging factors. Several cellular mechanisms have evolved to recognize and remove different types of DNA lesions. Despite the wealth of information on the three-dimensional structure and the catalytic mechanism of DNA repair enzymes, the essential process of target site search and identification remains more elusive. How can a small number of repair proteins find and detect the rare sites of damage rapidly and efficiently over an excess of millions of undamaged bases?
To address this pivotal question in DNA repair, I focused on the central players from the two DNA damage excision repair pathways in my studies: nucleotide excision repair (NER) and base excision repair (BER). As examples for completely different approaches of damage search, recognition and verification, I compared the NER protein Xeroderma pigmentosum group D (XPD) with the BER proteins human thymine DNA glycosylase (hTDG) and human 8-oxoguanine glycosylase (hOgg1).
In particular, the single molecule approach of atomic force microscopy (AFM) imaging and complementary biochemical and biophysical techniques were applied. I established a simple, optimized preparation approach, which yields homogeneous and pure samples of long (several hundreds to thousands of base pairs) DNA substrates suitable for the AFM studies with DNA repair proteins. Via this sample preparation, a single target site of interest can be introduced into DNA at a known position, which allows separate analysis of specific protein-DNA complexes bound to the lesion site and nonspecific complexes bound to non-damaged DNA.
The first part of the thesis investigates the XPD protein involved in eukaryotic NER. In general, the NER mechanism removes helix-distorting lesions – carcinogenic UV light induced photoproducts, such as cyclobutane pyrimidine dimers (CPDs) as well as bulky DNA adducts. The 5’-3’ helicase XPD has been proposed to be one of the key players in DNA damage verification in eukaryotic NER, which is still a matter of hot debate. In the studies, I focused on XPD from the archaeal species Thermoplasma acidophilum (taXPD), which shares a relatively high sequence homology with the sequence of the human protein and may serve as a good model for its eukaryotic counterpart. Based on AFM experiments and accompanying DNA binding affinity measurements with the biosensor technology Biolayer Interferometry (BLI), a clear role of XPD in damage verification was deciphered. Specifically, the data suggested that the ATP-dependent 5’-3’ helicase activity of XPD was blocked by the presence of damage leading to stalled XPD-DNA damage verification complexes at the lesion sites.
Successful damage verification led to ATP-dependent conformational changes visible by a significant transition in DNA bend angles from ~ 50° to ~ 65° at the site of the bound protein. Remarkably, this DNA bend angle shift was observed both in the presence of ATP and ATPγs (non-hydrolyzable ATP analog) indicating that ATP-binding instead of ATP hydrolysis was sufficient to induce repair competent conformational changes of XPD. Most importantly, detailed protein binding position and DNA bend angle analyses revealed for the first time that XPD preferably recognizes a bulky fluorescein lesion on the translocated strand, whereas a CPD lesion is preferentially detected on the opposite, non-translocated strand. Despite the different recognition strategies for both types of damages, they share a common verification complex conformation, which may serve as a signal for the recruitment of further NER factors.
In the second part of the thesis, AFM imaging and a 2-Aminopurine fluorescence-based base-flipping assay were combined to investigate damage search and recognition by DNA glycosylases in BER. Exemplarily, I chose to study hTDG as a representative of the vast glycosylase family. hTDG excises thymine and uracil from mutagenic G:T and G:U mispairs contributing to cancer and genetic disease. The AFM data suggested that hTDG uses the intrinsic flexibility of G:T and G:U wobble pairs for initial damage sensing, while scanning DNA as a search complex (SC, slightly bent DNA). Remarkably, hTDG has been indicated to continuously switch between the search and interrogation conformation (IC, stronger bent DNA) during damage search. In the IC, target bases are interrogated by extrahelical base flipping, which is facilitated by protein-induced DNA bending and enhanced DNA flexibility at mismatches. AFM and fluorescence analyses revealed that the flipped base is stabilized via hTDG’s arginine finger. Correct target bases are perfectly stabilized within the enzyme’s catalytic pocket resulting in prolonged residence time and enhanced excision probability. To test for the generalizability of the proposed hTDG damage search model to BER glycosylases, identical studies were performed with a second glycosylase, hOgg1. The data on hOgg1, which removes structurally more stable 8-oxoguanine lesions, supported the hypothesis developed for lesion recognition by hTDG as a common strategy employed by BER glycosylases
Similarity between odours is notoriously difficult to measure. Widely used behavioural approaches in insect olfaction research are cross-adaptation, masking, as well as associative tasks based on olfactory learning and the subsequent testing for how specific the established memory is. A concern with such memory-based approaches is that the learning process required to establish an odour memory may alter the way the odour is processed, such that measures of perception taken at the test are distorted. The present study was therefore designed to see whether behavioural judgements of perceptual distance are different for two different memory-based tasks, namely generalization and discrimination. We used odour-reward learning in larval Drosophila as a study case. In order to challenge the larvae's olfactory system, we chose to work with binary mixtures and their elements (1-octanol, n-amyl acetate, 3-octanol, benzaldehyde and hexyl acetate). We determined the perceptual distance between each mixture and its elements, first in a generalization task, and then in a discrimination task. It turns out that scores of perceptual distance are correlated between both tasks. A re-analysis of published studies looking at element-to-element perceptual distances in larval reward learning and in adult punishment learning confirms this result. We therefore suggest that across a given set of olfactory stimuli, associative training does not grossly alter the pattern of perceptual distances.
[Purpose] A wide variety of accelerometer tools are used to estimate human movement, but there are no adequate data relating to gait symmetry parameters in the context of knee osteoarthritis. This study's purpose was to evaluate a 3D-kinematic system using body-mounted sensors (gyroscopes and accelerometers) on the trunk and limbs. This is the first study to use spectral analysis for data post processing. [Subjects] Twelve patients with unilateral knee osteoarthritis (OA) (10 male) and seven age-matched controls (6 male) were studied. [Methods] Measurements with 3-D accelerometers and gyroscopes were compared to video analysis with marker positions tracked by a six-camera optoelectronic system (VICON 460, Oxford Metrics). Data were recorded using the 3D-kinematic system. [Results] The results of both gait analysis systems were significantly correlated. Five parameters were significantly different between the knee OA and control groups. To overcome time spent in expensive post-processing routines, spectral analysis was performed for fast differentiation between normal gait and pathological gait signals using the 3D-kinematic system. [Conclusions] The 3D-kinematic system is objective, inexpensive, accurate and portable, and allows long-term recordings in clinical, sport as well as ergonomic or functional capacity evaluation (FCE) settings. For fast post-processing, spectral analysis of the recorded data is recommended.
Altering gene expression by aminocoumarins: the role of DNA supercoiling in Staphylococcus aureus
(2014)
BACKGROUND:
It has been shown previously that aminocoumarin antibiotics such as novobiocin lead to immediate downregulation of recA expression and thereby inhibit the SOS response, mutation frequency and recombination capacity in Staphylococcus aureus. Aminocoumarins function by inhibiting the ATPase activity of DNA gyrase subunit B with a severe impact on DNA supercoiling.
RESULTS:
Here, we have analysed the global impact of the DNA relaxing agent novobiocin on gene expression in S. aureus. Using a novobiocin-resistant mutant, it became evident that the change in recA expression is due to gyrase inhibition. Microarray analysis and northern blot hybridisation revealed that the expression levels of a distinct set of genes were increased (e.g., recF-gyrB-gyrA, the rib operon and the ure operon) or decreased (e.g., arlRS, recA, lukA, hlgC and fnbA) by novobiocin. The two-component ArlRS system was previously found to decrease the level of supercoiling in S. aureus. Thus, downregulation of arlRS might partially compensate for the relaxing effect of novobiocin. Global analysis and gene mapping of supercoiling-sensitive genes did not provide any indication that they are clustered in the genome. Promoter fusion assays confirmed that the responsiveness of a given gene is intrinsic to the promoter region but independent of the chromosomal location.
CONCLUSIONS:
The results indicate that the molecular properties of a given promoter, rather than the chromosomal topology, dictate the responsiveness to changes in supercoiling in the pathogen Staphylococcus aureus.
This review addresses the current status of drug therapy for the management of fibromyalgia syndrome (FMS) and is based on interdisciplinary FMS management guidelines, meta-analyses of drug trial data, and observational studies. In the absence of a single gold-standard medication, patients are treated with a variety of drugs from different categories, often with limited evidence. Drug therapy is not mandatory for the management of FMS. Pregabalin, duloxetine, milnacipran, and amitriptyline are the current first-line prescribed agents but have had a mostly modest effect. With only a minority of patients expected to experience substantial benefit, most will discontinue therapy because of either a lack of efficacy or tolerability problems. Many drug treatments have undergone limited study and have had negative results. It is unlikely that these failed pilot trials will undergo future study. However, medications, though imperfect, will continue to be a component of treatment strategy for these patients. Both the potential for medication therapy to relieve symptoms and the potential to cause harm should be carefully considered in their administration.
The impact of imatinib dose on response rates and survival in older patients with chronic myeloid leukemia in chronic phase has not been studied well. We analyzed data from the German CML-Study IV, a randomized five-arm treatment optimization study in newly diagnosed BCR-ABL-positive chronic myeloid leukemia in chronic phase. Patients randomized to imatinib 400 mg/day (IM400) or imatinib 800 mg/day (IM800) and stratified according to age (≥65 years vs. <65 years) were compared regarding dose, response, adverse events, rates of progression, and survival. The full 800 mg dose was given after a 6-week run-in period with imatinib 400 mg/day. The dose could then be reduced according to tolerability. A total of 828 patients were randomized to IM400 or IM800. Seven hundred eighty-four patients were evaluable (IM400, 382; IM800, 402). One hundred ten patients (29 %) on IM400 and 83 (21 %) on IM800 were ≥65 years. The median dose per day was lower for patients ≥65 years on IM800, with the highest median dose in the first year (466 mg/day for patients ≥65 years vs. 630 mg/day for patients <65 years). Older patients on IM800 achieved major molecular remission and deep molecular remission as fast as younger patients, in contrast to standard dose imatinib with which older patients achieved remissions much later than younger patients. Grades 3 and 4 adverse events were similar in both age groups. Five-year relative survival for older patients was comparable to that of younger patients. We suggest that the optimal dose for older patients is higher than 400 mg/day. ClinicalTrials.gov identifier: NCT00055874
There are no European recommendations on issues specifically related to lung transplantation (LTX) in cystic fibrosis (CF). The main goal of this paper is to provide CF care team members with clinically relevant CF-specific information on all aspects of LTX, highlighting areas of consensus and controversy throughout Europe. Bilateral lung transplantation has been shown to be an important therapeutic option for end-stage CF pulmonary disease. Transplant function and patient survival after transplantation are better than in most other indications for this procedure. Attention though has to be paid to pretransplant morbidity, time for referral, evaluation, indication, and contraindication in children and in adults. This review makes extensive use of specific evidence in the field of lung transplantation in CF patients and addresses all issues of practical importance. The requirements of pre-, peri-, and postoperative management are discussed in detail including bridging to transplant and postoperative complications, immune suppression, chronic allograft dysfunction, infection, and malignancies being the most important. Among the contributors to this guiding information are 19 members of the ECORN-CF project and other experts. The document is endorsed by the European Cystic Fibrosis Society and sponsored by the Christiane Herzog Foundation.
Planar microcavities with distributed Bragg reflectors (DBRs) host, besides confined optical modes, also mechanical resonances due to stop bands in the phonon dispersion relation of the DBRs. These resonances have frequencies in the 10- to 100-GHz range, depending on the resonator's optical wavelength, with quality factors exceeding 1,000. The interaction of photons and phonons in such optomechanical systems can be drastically enhanced, opening a new route towards the manipulation of light. Here we implemented active semiconducting layers into the microcavity to obtain a vertical-cavity surface-emitting laser (VCSEL). Thereby, three resonant excitations--photons, phonons and electrons--can interact strongly with each other providing modulation of the VCSEL laser emission: a picosecond strain pulse injected into the VCSEL excites long-living mechanical resonances therein. As a result, modulation of the lasing intensity at frequencies up to 40 GHz is observed. From these findings, prospective applications of active optomechanical resonators integrated into nanophotonic circuits may emerge.
Unlike induced \(Foxp3^+\) regulatory T cells (\(Foxp3^+\) \(iT_{reg}\)) that have been shown to play an essential role in the development of protective immunity to the ubiquitous mold Aspergillus fumigatus, type-(1)-regulatory T cells (Tr1) cells have, thus far, not been implicated in this process. Here, we evaluated the role of Tr1 cells specific for an epitope derived from the cell wall glucanase Crf-1 of A. fumigatus (Crf-1/p41) in antifungal immunity. We identified Crf-1/p41-specific latent-associated \(peptide^+\) Tr1 cells in healthy humans and mice after vaccination with Crf-1/p41+zymosan. These cells produced high amounts of interleukin (IL)-10 and suppressed the expansion of antigen-specific T cells in vitro and in vivo. In mice, in vivo differentiation of Tr1 cells was dependent on the presence of the aryl hydrocarbon receptor, c-Maf and IL-27. Moreover, in comparison to Tr1 cells, \(Foxp3^+\) \(iT_{reg}\) that recognize the same epitope were induced in an interferon gamma-type inflammatory environment and more potently suppressed innate immune cell activities. Overall, our data show that Tr1 cells are involved in the maintenance of antifungal immune homeostasis, and most likely play a distinct, yet complementary, role compared with \(Foxp3^+\) \(iT_{reg}\).
The embryonic vertebrate heart tube develops an atrioventricular canal that divides the atrial and ventricular chambers, forms atrioventricular conduction tissue and organizes valve development. Here we assess the transcriptional mechanism underlying this localized differentiation process. We show that atrioventricular canal-specific enhancers are GATA-binding site-dependent and act as switches that repress gene activity in the chambers. We find that atrioventricular canal-specific gene loci are enriched in H3K27ac, a marker of active enhancers, in atrioventricular canal tissue and depleted in H3K27ac in chamber tissue. In the atrioventricular canal, Gata4 activates the enhancers in synergy with Bmp2/Smad signalling, leading to H3K27 acetylation. In contrast, in chambers, Gata4 cooperates with pan-cardiac Hdac1 and Hdac2 and chamber-specific Hey1 and Hey2, leading to H3K27 deacetylation and repression. We conclude that atrioventricular canal-specific enhancers are platforms integrating cardiac transcription factors, broadly active histone modification enzymes and localized co-factors to drive atrioventricular canal-specific gene activity.