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Neoplasms of the skin represent the most frequent tumors worldwide; fortunately, most of them are benign or semi-malignant and well treatable. However, the two most aggressive and deadly forms of malignant skin-neoplasms are melanoma and Merkel cell carcinoma (MCC), being responsible for more than 90% of skin-cancer related deaths. The last decade has yielded enormous progress in melanoma therapy with the advent of targeted therapies, like BRAF or MEK inhibitors, and immune-stimulating therapies, using checkpoint antibodies targeting CTLA- 4, PD-1 or PD-L1. Very recent studies suggest that also MCC patients benefit from a treatment with checkpoint antibodies. Nevertheless, in an advanced metastatic stage, a cure for both of these aggressive malignancies is still hard to achieve: while only a subset of patients experience durable benefit from the immune-based therapies, the widely applicable targeted therapies struggle with development of resistances that inevitably occur in most patients, and finally lead to their death. The four articles included in this thesis addressed current questions concerning therapy and carcinogenesis of melanoma and MCC. Moreover, they are discussed in the light of the up-to-date research regarding targeted and immune-based therapies. In article I we demonstrated that besides apoptosis, MAPK pathway inhibition in BRAF-mutated melanoma cells also induces senescence, a permanent cell cycle arrest. These cells may provide a source for relapse, as even permanently arrested cancer cells can contribute to a pro-tumorigenic milieu. To identify molecular factors determining the differential response, we established M14 melanoma cell line derived single cell clones that either undergo cell death or arrest when treated with BRAF/MEK inhibitors. Using these single cell clones, we demonstrated in article IV that downregulation of the pro-apoptotic BH3-only protein BIK via epigenetic silencing is involved in apoptosis deficiency, which can be overcome by HDAC inhibitors. These observations provide a possible explanation for the lack of a complete and durable response to MAPK inhibitor treatment in melanoma patients, and suggest the application of HDAC inhibitors as a complimentary therapy to MAPK pathway inhibition. Concerning MCC, we scrutinized the interactions between the Merkel cell polyomavirus’ (MCV) T antigens (TA) and the tumor suppressors p53 and Rb in article II and III, respectively. In article III, we demonstrated that the cell cycle master regulator Rb is the crucial target of MCV large T (LT), while it - in contrast to other polyomavirus LTs - exhibits much lower affinity to the related proteins p107 and p130. Knockdown of MCV LT led to proliferation arrest in MCC cells, which can be rescued by knockdown of Rb, but not by knockdown of p107 and p130. Contrary to Rb, restriction of p53 in MCC seems to be independent of the MCV TAs, as we demonstrated in article II. In conclusion, the presented thesis has revealed new molecular details, regarding the response of melanoma cells towards an important treatment modality and the mechanisms of viral carcinogenesis in MCC.
It was the scope of this work to gain a deeper understanding of the correlation between Interface energetics of molecular semiconductors in planar organic solar cells and the corresponding optoelectronic characteristics. For this aim, different approaches were followed. At first, a direct variation of donor/acceptor (D/A) interface energetics of bilayer cells was achieved by utilizing systematically modified donor compounds. This change could be correlated to the macroscopic device performance. At second, the impact of interface energetics was illustrated, employing a more extended device architecture. By introducing a thin interlayer between a planar D/A heterojunction, an energetic staircase was established. Exciton dissociation in such devices could be linked to the cascade energy level alignment of the photo-active materials. Finally, two different fullerene molecules C60 and C70 were employed in co-evaporated acceptor phases. The expected discrepancy in their electronic structure was related to the transport properties of the corresponding organic photovoltaic cells (OPVCs). The fullerenes are created simultaneously in common synthesis procedures. Next to the photo-physical relevance, the study was carried-out to judge on the necessity of separating the components from each other by purification which constitutes the cost-determining step in the total production costs.
Host–microbe interactions are the key to understand why and how microbes inhabit specific environments. With the scientific fields of microbial genomics and metagenomics, evolving on an unprecedented scale, one is able to gain insights in these interactions on a molecular and ecological level. The goal of this PhD thesis was to make (meta–)genomic data accessible, integrate it in a comparative manner and to gain comprehensive taxonomic and functional insights into bacterial strains and communities derived from two different environments: the phyllosphere of Arabidopsis thaliana and the mesohyl interior of marine sponges.
This thesis focused first on the de novo assembly of bacterial genomes. A 5–step protocol was developed, each step including a quality control. The examination of different assembly software in a comparative way identified SPAdes as most suitable. The protocol enables the user to chose the best tailored assembly. Contamination issues were solved by an initial filtering of the data and methods normally used for the binning of metagenomic datasets. This step is missed in many published assembly pipelines. The described protocol offers assemblies of high quality ready for downstream analysis.
Subsequently, assemblies generated with the developed protocol were annotated and explored
in terms of their function. In a first study, the genome of a phyllosphere bacterium, Williamsia sp. ARP1, was analyzed, offering many adaptions to the leaf habitat: it can deal with temperature shifts, react to oxygen species, produces mycosporins as protection against UV–light, and is able to uptake photosynthates. Further, its taxonomic position within the Actinomycetales was infered from 16S rRNA and comparative genomics showing the close relation between the genera Williamsia and Gordonia.
In a second study, six sponge–derived actinomycete genomes were investigated for secondary metabolism. By use of state–of–the–art software, these strains exhibited numerous gene clusters, mostly linked to polykethide synthases, non–ribosomal peptide synthesis, terpenes, fatty acids and saccharides. Subsequent predictions on these clusters offered a great variety of possible produced compounds with antibiotic, antifungal or anti–cancer activity. These analysis highlight the potential for the synthesis of natural products and the use of genomic data as screening toolkit.
In a last study, three sponge–derived and one seawater metagenomes were functionally compared. Different signatures regarding the microbial composition and GC–distribution were observed between the two environments. With a focus on bacerial defense systems, the data indicates a pronounced repertoire of sponge associated bacteria for bacterial defense systems, in particular, Clustered Regularly Interspaced Short Palindromic Repeats, restriction modification system, DNA phosphorothioation and phage growth limitation. In addition, characterizing genes for secondary metabolite cluster differed between sponge and seawater microbiomes. Moreover, a variety of Type I polyketide synthases were only found within the sponge microbiomes. With that, metagenomics are shown to be a useful tool for the screening of secondary metabolite genes. Furthermore, enriched defense systems are highlighted as feature of sponge-associated microbes and marks them as a selective trait.
Investigation of Nanostructure-Induced Localized Light Phenomena Using Ultrafast Laser Spectroscopy
(2017)
In recent years, the interaction of light with subwavelength structures, i.e., structures that are smaller than the optical wavelength, became more and more interesting to scientific research, since it provides the opportunity to manipulate light-induced dynamics below the optical diffraction limit. Specifically designed nanomaterials can be utilized to tailor the temporal evolution of electromagnetic fields at the nanoscale. For the investigation of strongly localized processes, it is essential to resolve both their spatial and their temporal behavior. The aim of this thesis was to study and/or control the temporal evolution of three nanostructure-induced localized light phenomena by using ultrafast laser spectroscopy with high spatial resolution.
In Chapter 4, the absorption of near-infrared light in thin-film a-Si:H solar cells was investigated. Using nanotextured instead of smooth interfaces for such devices leads to an increase of absorption from < 20% to more than 50% in the near-infrared regime. Time-resolved experiments with femtosecond laser pulses were performed to clarify the reason for this enhancement. The coherent backscattered radiation from nanotextured solar cell devices was measured as a function of the sample position and evaluated via spectral interferometry. Spatially varying resonance peaks in the recorded spectra indicated the formation of localized photonic modes within the nanotextured absorber layers. In order to identify the modes separately from each other, coherent two-dimensional (2D) nanoscopy was utilized, providing a high spatial resolution < 40 nm. In a nanoscopy measurement on a modified device with an exposed nanotextured a-Si:H absorber layer, hot-spot electron emission was observed and confirmed the presence of localized modes. Fitting the local 2D nanospectra at the hot-spot positions enabled the determination of the resonance frequencies and coherence lifetimes of the modes. The obtained lifetime values varied between 50 fs and 130 fs. Using a thermionic emission model allowed the calculation of the locally absorbed energy density and, with this, an estimation of the localization length of the photonic modes (≈1 μm). The localization could be classified by means of the estimated localization length and additional data evaluation of the backscattered spectra as strong localization ─ the so-called Anderson localization.
Based on the experimental results, it was concluded that the enhanced absorption of near-infrared light in thin-film silicon solar cells with nanotextured interfaces is caused by the formation of strongly localized photonic modes within the disordered absorber layers. The incoming near-infrared light is trapped in these long-living modes until absorption occurs.
In Chapter 5, a novel hybridized plasmonic device was introduced and investigated in both theory and experiment. It consists of two widely separated whispering gallery mode (WGM) nanoantennas located in an elliptical plasmonic cavity. The goal was to realize a periodic long-range energy transfer between the nanoantennas. In finite-difference time-domain (FDTD) simulations, the device was first optimized with respect to strong coupling between the localized antenna modes and the spatially-extended cavity mode. The geometrical parameters of the antennas and the cavity were adjusted separately so that the m="0" antenna mode and the cavity mode were resonant at λ="800 nm" . A high spatial overlap of the modes was achieved by positioning the two antennas in the focal spots of the cavity, leading to a distance between the antenna centers of more than twice the resonant wavelength of the modes. The spectral response of the optimized device revealed an energy splitting of the antenna and the cavity mode into three separated hybridized eigenmodes within an energy range of about 90 meV due to strong coupling. It could be well reproduced by a simple model of three coupled Lorentzian oscillators. In the time domain, an oscillatory energy transfer between both antennas with a period of 86 fs and an energy transfer efficiency of about 7% was observed for single-pulse excitation. For the experiments, devices with cavities and antennas of varying size were fabricated by means of focused-ion-beam (FIB) milling. Time-resolved correlation measurements were performed with high spatial and temporal resolution by using sequences of two femtosecond laser pulses for excitation and photoemission electron microscopy (PEEM) for detection. Local correlation traces at antennas in resonant devices, i.e., devices with enhanced electron emission at both antenna positions, were investigated and reconstructed by means of the coupled-oscillator model. The corresponding spectral response revealed separated peaks, confirming the formation of hybridized eigenmodes due to strong coupling. In a subsequent simulation for single-pulse excitation, one back-and-forth energy transfer between both antennas with an energy transfer efficiency of about 10% was observed.
Based on the theoretical and experimental results, it was demonstrated that in the presented plasmonic device a periodic long-range energy transfer between the two nanoantennas is possible. Furthermore, the coupled-oscillator model enables one to study in depth how specific device properties impact the temporal electric-field dynamics within the device. This can be exploited to further optimize energy transfer efficiency of the device. Future applications are envisioned in ultrafast plasmonic nanocircuitry. Moreover, the presented device can be employed to realize efficient SPP-mediated strong coupling between widely separated quantum emitters.
In Chapter 6, it was investigated in theory how the local optical chirality enhancement in the near field of plasmonic nanostructures can be optimized by tuning the far-field polarization of the incident light. An analytic expression was derived that enables the calculation of the optimal far-field polarizations, i.e., the two far-field polarizations which lead to the highest positive and negative local optical chirality, for any given nanostructure geometry. The two optimal far-field polarizations depend on the local optical response of the respective nanostructure and thus are functions of both the frequency ω and the position r. Their ellipticities differ only in their sign, i.e., in their direction of rotation in the time domain, and the angle between their orientations, i.e., the angle between the principal axes of their ellipses, is ±π/"2" . The handedness of optimal local optical chirality can be switched by switching between the optimal far-field polarizations. In numerical simulations, it was exemplarily shown for two specific nanostructure assemblies that the optimal local optical chirality can significantly exceed the optical chirality values of circularly polarized light in free space ─ the highest possible values in free space. The corresponding optimal far-field polarizations were different from linear and circular and varied with frequency. Using femtosecond polarization pulse shaping provides the opportunity to coherently control local optical chirality over a continuous frequency range. Furthermore, symmetry properties of nanostructures can be exploited to determine which far-field polarization is optimal.
The theoretical findings can have impact on future experimental studies about local optical chirality enhancement. Tuning the far-field polarization of the incident light offers a promising tool to enhance chirally specific interactions of local electromagnetic fields with molecular and other quantum systems in the vicinity of plasmonic nanostructures. The presented approach can be utilized for applications in chiral sensing of adsorbed molecules, time-resolved chirality-sensitive spectroscopy, and chiral quantum control.
In conclusion, each of the localized light phenomena that were investigated in this thesis ─ the enhanced local absorption of near-infrared light due to the formation of localized photonic modes, the periodic long-range energy transfer between two nanoantennas within an elliptical plasmonic cavity, and the optimization of local optical chirality enhancement by tuning the far-field polarization of the incident light ─ can open up new perspectives for a variety of future applications.
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Modern software is often realized as a modular combination of subsystems for, e. g.,
knowledge management, visualization, verification, or the interaction with users. As
a result, software libraries from possibly different programming languages have to
work together. Even more complex the case is if different programming paradigms
have to be combined. This type of diversification of programming languages and
paradigms in just one software application can only be mastered by mechanisms
for a seamless integration of the involved programming languages. However, the
integration of the common logic programming language Prolog and the popular
object-oriented programming language Java is complicated by various interoperability
problems which stem on the one hand from the paradigmatic gap between the
programming languages, and on the other hand, from the diversity of the available
Prolog systems.
The subject of the thesis is the investigation of novel mechanisms for the integration
of logic programming in Prolog and object–oriented programming in Java. We are
particularly interested in an object–oriented, uniform approach which is not specific
to just one Prolog system. Therefore, we have first identified several important
criteria for the seamless integration of Prolog and Java from the object–oriented
perspective. The main contribution of the thesis is a novel integration framework
called the Connector Architecture for Prolog and Java (CAPJa). The framework is
completely implemented in Java and imposes no modifications to the Java Virtual
Machine or Prolog. CAPJa provides a semi–automated mechanism for the integration
of Prolog predicates into Java. For compact, readable, and object–oriented
queries to Prolog, CAPJa exploits lambda expressions with conditional and relational
operators in Java. The communication between Java and Prolog is based
on a fully automated mapping of Java objects to Prolog terms, and vice versa. In
Java, an extensible system of gateways provides connectivity with various Prolog
system and, moreover, makes any connected Prolog system easily interchangeable,
without major adaption in Java.
Upon complexation to CuOTf, a PMe\(_3\)-stabilized bis(9-anthryl) diborene slowly undergoes an intramolecular hydroarylation reaction at room temperature. Subsequent triflation of the B–H bond with CuOTf, followed by a PMe\(_3\) transfer, finally yields a cyclic sp\(^2\)-sp\(^3\) boryl-substituted boronium triflate salt.
Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhea, has the potential to spread in the human host and cause a severe complication called disseminated gonococcal infection (DGI). The expression of the major outer membrane porin PorBIA is a characteristic of most gonococci associated with DGI. PorBIA binds to the scavenger receptor expressed on endothelial cells (SREC-I), which mediates the so-called low phosphate-dependent invasion (LPDI). This uptake mechanism enables N. gonorrhoeae to rapidly invade epithelial and endothelial cells in a phosphate-sensitive manner.
We recently demonstrated that the neutral sphingomyelinase, which catalyses the hydrolysis of sphingomyelin to ceramide and phosphorylcholine, is required for the LPDI of gonococci in non-phagocytic cells. Neutral sphingomyelinase 2 (NSM2) plays a key role in the early PorBIA signaling by recruiting the PI3 kinase to caveolin. The following activation of the PI3 kinase-dependent downstream signaling leads to the engulfment of the bacteria. As a part of this work, I could confirm the involvement of the NSM2. The role of the enzyme was further elucidated by the generation of antibodies directed against NSM2 and the construction of an epithelium-based NSM2 knockout cell line using CRISPR/Cas9. The knockout of the NSM2 strongly inhibits the LPDI. The invasion could be, however, restored by the complementation of the knockout using an NSM2-GFP construct. However, the results could not be reproduced.
In this work, I could show the involvement of further members of the sphingolipid pathway in the PorBIA-mediated invasion. Lipidome analysis revealed an increase of the bioactive molecules ceramide and sphingosine due to gonococcal infection. Both molecules do not only affect the host cell, but seem to influence the bacteria as well: while ceramide seems to be incorporated by the gonococci, sphingosine is toxic for the bacteria. Furthermore, the sphingosine kinase 2 (SPHK2) plays an important role in invasion, since the inhibition and knockdown of the enzyme revealed a negative effect on gonococcal invasion. To elucidate the role of the sphingosine kinases in invasion in more detail, an activity assay was established in this study. Additionally, the impact of the sphingosine-1-phosphate lyase (S1PL) on invasion was investigated. Inhibitor studies and infection experiments conducted with a CRISPR/Cas9 HeLa S1PL knockout cell line revealed a role of the enzyme not only in the PorBIA-mediated invasion, but also in the Opa50/HSPG-mediated gonococcal invasion. The signaling experiments allowed the categorization of the SPHK and S1PL activation in the context of infection. Like the NSM2, both enzymes play a role in the early PorBIA signaling events leading to the uptake of the bacteria. All those findings indicate an important role of sphingolipids in the invasion and survival of N. gonorrhoeae.
In the last part of this work, the role of the NSM2 in the inhibition of apoptosis in neutrophils due to gonococcal infection was investigated. It could be demonstrated that the delayed onset of apoptosis is independent of neisserial porin and Opa proteins. Furthermore, the influence of neisserial peptidoglycan on PMN apoptosis was analysed using mutant strains, but no connection could be determined. Since the NSM2 is the most prominent sphingomyelinase in PMNs, fulfils manifold cell physiological functions and has already been connected to apoptosis, the impact of the enzyme on apoptosis inhibition due to gonococcal infection was investigated using inhibitors, with no positive results.
This dissertation investigates selected causes and effects of worker mobility between firms in three empirical studies for Germany. Chapter 2 investigates the productivity effects of worker inflows to manufacturing establishments, distinguishing inflows by their previous employers’ wage level, as a proxy for productivity. The chapter is motivated by several empirical studies which find that worker inflows from more productive or higher-paying firms increase hiring firms’ productivity. The analyses in chapter 2 are based on a unique linked employer-employee data set. The findings indicate that inflows from higher-paying establishments do not increase hiring establishments’ productivity, but inflows from lower-paying establishments do. Further analyses suggest that this effect is due to a positive selectivity of such inflows from their sending establishments. These findings can be interpreted as evidence of a reallocation process by which the best employees of lower-paying establishments become hired by higher-paying establishments. This process reflects the assortative pattern of worker mobility in Germany documented by Card et al. (2013) for the past decades. The chapter thus contributes to the literature by linking establishment-level productivity analysis to the assortative pattern of inter-firm worker mobility, thereby providing a micro-foundation for the latter.
Chapter 3 focuses on a positive selection of workers moving between firms from another, more specific perspective. The analysis focuses on the importance of regional labor market competition for establishments’ apprentice training and poaching of apprenticeship completers. Previous studies have found that firms provide less training if they are located in regions with strong labor market competition. This finding is usually interpreted as evidence of a higher risk of poaching in these regions. Yet, there is no direct evidence that regional competition is positively correlated with poaching. Building on a recently established approach to ex-post identify poaching of apprenticeship completers, this chapter is the first to directly investigate the correlation between regional labor market competition and poaching. Using German administrative data, it is found that competition indeed increases training establishments’ probability of becoming poaching victims. However, poaching victims do not change their apprenticeship training activity in reaction to poaching. Instead, the findings indicate that the lower training activity in competitive regions can be attributed to lower retention rates, as well as a less adverse selection and lower labor and hiring costs of apprenticeship completers hired from rivals.
Chapter 4 investigates the effects of local broadband internet availability on establishment-level employment growth. The analysis uses data for Germany in the years 2005-2009, when broadband was introduced in rural regions of Western Germany and in large parts of Eastern Germany. Technical frictions in broadband rollout are exploited to obtain exogenous variation in local broadband availability. The results suggest that broadband expansion had a positive effect on employment growth in the Western German service sector and a negative effect in Western German manufacturing, suggesting that broadband expansion has accelerated the reallocation of workers from manufacturing to services. Furthermore, this pattern of results is driven by pronounced positive effects in knowledge- and computer-intensive industries, suggesting that it is the actual use of broadband in the production process that leads to complementary hiring, respectively a slowdown of employment growth, in the respective sectors. For Eastern Germany, no significant employment growth effects are found.
This dissertation is dealing with three mathematical areas, namely polynomial matrices over finite fields, linear systems and coding theory.
Coprimeness properties of polynomial matrices provide criteria for the reachability and observability of interconnected linear systems. Since time-discrete linear systems over finite fields and convolutional codes are basically the same objects, these results could be transfered to criteria for non-catastrophicity of convolutional codes.
We calculate the probability that specially structured polynomial matrices are right prime. In particular, formulas for the number of pairwise coprime polynomials and for the number of mutually left coprime polynomial matrices are calculated. This leads to the probability that a parallel connected linear system is reachable and that a parallel connected convolutional codes is non-catastrophic.
Moreover, the corresponding probabilities are calculated for other networks of linear systems and convolutional codes, such as series connection.
Furthermore, the probabilities that a convolutional codes is MDP and that a clock code is MDS are approximated.
Finally, we consider the probability of finding a solution for a linear network coding problem.
African trypanosomiasis is a disease endemic to sub-Saharan Africa. It affects humans as well as wild and domestic animals. The human form of the disease is known as sleeping sickness and the animal form as nagana, which are usually fatal if left untreated. The cause of African trypanosomiasis is the unicellular parasite Trypanosoma brucei. During its life cycle, Trypanosoma brucei shuttles between a mammalian host and the tsetse fly vector. In the mammalian host the parasite multiplies as bloodstream form (BSF) extracellularly in the bloodstream or the lymphatic system. Survival of BSF parasites relies on immune evasion by antigenic variation of surface proteins because its extracellular lifestyle leads to direct exposure to immune responses. At any given time each BSF cell expresses a single type of variant surface glycoprotein (VSG) on its surface from a large repertoire. The active VSG is transcribed from one of 15 specialized subtelomeric domains, termed bloodstream expression sites (BESs). The remaining 14 BESs are silenced. This monoallelic expression and periodic switching of the expressed VSG enables to escape the immune response and to establish a persistent infection in the mammalian host. During developmental differentiation from BSF to the insect vector-resident procyclic form (PCF), the active BES is transcriptionally silenced to stop VSG transcription. Thus, all 15 BESs are inactive in the PCF cells as surface protein expression is developmentally regulated.
Previous reports have shown that the telomere complex components TbTRF, TbRAP1 and TbTIF2 are involved in VSG transcriptional regulation. However, the precise nature of their contribution remains unclear. In addition, no information is available about the role of telomeres in the initiation and regulation of developmental BES silencing. To gain insights into the regulatory mechanisms of telomeres on VSG transcription and developmental repression it is therefore essential to identify the complete composition of the trypanosome telomere complex.
To this end, we used two complementary biochemical approaches and quantitative label-free interactomics to determine the composition of telomere protein complexes in T. brucei. Firstly, using a telomeric pull-down assay we found 17 potential telomere-binding proteins including the known telomere-binding proteins TbTRF and TbTIF2. Secondly, by performing a co-immunoprecipitation experiment to elucidate TbTRF interactions we co-purified five proteins. All of these five proteins were also enriched with telomeric DNA in the pull-down assay.
To validate these data, I characterized one of the proteins found in both experiments (TelBP1). In BSF cells, TelBP1 co-localizes with TbTRF and interacts with already described telomere-binding proteins such as TbTRF, TbTIF2 and TbRAP1 indicating that TelBP1 is a novel component of the telomere complex in trypanosomes. Interestingly, protein interaction studies in PCF cells suggested a different telomere complex composition compared to BSF cells. In contrast to known members of the telomere complex, TelBP1 is dispensable for cell viability indicating that its function might be uncoupled from the known telomere-binding proteins. Overexpression of TelBP1 had also no effect on cell viability, but led to the discovery of two additional shorter isoforms of TelBP1. However, their source and function remained elusive.
Although TelBP1 is not essential for cell viability, western blot analysis revealed a 4-fold upregulation of TelBP1 in the BSF stage compared to the PCF stage supporting the concept of a dynamic telomere complex composition. We observed that TelBP1 influences the kinetics of transcriptional BES silencing during developmental transition from BSF to PCF. Deletion of TelBP1 caused faster BES silencing compared to wild-type parasites.
Taken together, TelBP1 function illustrates that developmental BES silencing is a fine-tuned process, which involves stage-specific changes in telomere complex formation.