@article{HickeySridharWestermannetal.2012, author = {Hickey, Scott F. and Sridhar, Malathy and Westermann, Alexander J. and Qin, Qian and Vijayendra, Pooja and Liou, Geoffrey and Hammond, Ming C.}, title = {Transgene regulation in plants by alternative splicing of a suicide exon}, series = {Nucleic Acids Research}, volume = {40}, journal = {Nucleic Acids Research}, number = {10}, doi = {10.1093/nar/gks032}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-134724}, pages = {4701-4710}, year = {2012}, abstract = {Compared to transcriptional activation, other mechanisms of gene regulation have not been widely exploited for the control of transgenes. One barrier to the general use and application of alternative splicing is that splicing-regulated transgenes have not been shown to be reliably and simply designed. Here, we demonstrate that a cassette bearing a suicide exon can be inserted into a variety of open reading frames (ORFs), generating transgenes whose expression is activated by exon skipping in response to a specific protein inducer. The surprisingly minimal sequence requirements for the maintenance of splicing fidelity and regulation indicate that this splicing cassette can be used to regulate any ORF containing one of the amino acids Glu, Gln or Lys. Furthermore, a single copy of the splicing cassette was optimized by rational design to confer robust gene activation with no background expression in plants. Thus, conditional splicing has the potential to be generally useful for transgene regulation.}, language = {en} } @article{PernitzschSharma2012, author = {Pernitzsch, Sandy R. and Sharma, Cynthia M.}, title = {Transcriptome Complexity and Riboregulation in the Human Pathogen Helicobacter pylori}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-75096}, year = {2012}, subject = {Medizin}, language = {en} } @article{FoersterBeisserGrohmeetal.2012, author = {F{\"o}rster, Frank and Beisser, Daniela and Grohme, Markus A. and Liang, Chunguang and Mali, Brahim and Siegl, Alexander Matthias and Engelmann, Julia C. and Shkumatov, Alexander V. and Schokraie, Elham and M{\"u}ller, Tobias and Schn{\"o}lzer, Martina and Schill, Ralph O. and Frohme, Marcus and Dandekar, Thomas}, title = {Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations}, series = {Bioinformatics and biology insights}, volume = {6}, journal = {Bioinformatics and biology insights}, doi = {10.4137/BBI.S9150}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-123089}, pages = {69-96}, year = {2012}, abstract = {Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade \(Milnesium\) \(tardigradum\) were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from \(Hypsibius\) \(dujardini\), revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for \(M.\) \(tardigradum\) are different from typical motifs known from higher animals. \(M.\) \(tardigradum\) and \(H.\) \(dujardini\) protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of \(M.\) \(tardigradum\). These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and \(M.\) \(tardigradum\) in particular so highly stress resistant.}, language = {en} } @phdthesis{Aminake2012, author = {Aminake, Makoah Nigel}, title = {Towards malaria combination therapy: Characterization of hybrid molecules for HIV/malaria combination therapy and of thiostrepton as a proteasome-targeting antibiotic with a dual mode of action}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-71841}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2012}, abstract = {Malaria and HIV are among the most important global health problems of our time and together are responsible for approximately 3 million deaths annually. These two diseases overlap in many regions of the world including sub-Saharan Africa, Southeast Asia and South America, leading to a higher risk of co-infection. In this study, we generated and characterized hybrid molecules to target P. falciparum and HIV simultaneously for a potential HIV/malaria combination therapy. Hybrid molecules were synthesized by covalent fusion between azidothymidine (AZT) and dihydroartemisinin (DHA), tetraoxane or chloroquine (CQ); and a small library was generated and tested for antiviral and antimalarial activity. Our data suggest that dihyate is the most potent molecule in vitro, with antiplasmodial activity comparable to that of DHA (IC50 = 26 nM, SI > 3000), a moderate activity against HIV (IC50 = 2.9 µM; SI > 35) and safe to HeLa cells at concentrations used in the assay (CC50 > 100 µM). Pharmacokinetic studies further revealed that dihyate is metabolically unstable and is cleaved following an O-dealkylation once in contact with cytochrome P450 enzymes. The later further explains the uneffectiveness of dihyate against the CQ-sensitive P. berghei N strain in mice when administered by oral route at 20 mg/kg. Here, we report on a first approach to develop antimalarial/anti-HIV hybrid molecules and future optimization efforts will aim at producing second generation hybrid molecules to improve activity against HIV as well as compound bioavailability. With the emergence of resistant parasites against all the counterpart drugs of artemisinin derivatives used in artemisinin based combination therapies (ACTs), the introduction of antibiotics in the treatment of malaria has renewed interest on the identification of antibiotics with potent antimalarial properties. In this study we also investigated the antiplasmodial potential of thiostrepton and derivatives, synthesized using combinations of tail truncation, oxidation, and addition of lipophilic thiols to the terminal dehydroamino acid. We showed that derivatives SS231 and SS234 exhibit a better antiplasmodial activity (IC50 = 1 µM SI > 59 and SI > 77 respectively) than thiostrepton (IC50 = 8.95 µM, SI = 1.7). The antiplasmodial activity of these derivatives was observed at concentrations which are not hemolytic and non-toxic to human cell lines. Thiostrepton and derivatives appeared to exhibit transmission blocking properties when administered at their IC50 or IC90 concentrations and our data also showed that they attenuate proteasome activity of Plasmodium, which resulted in an accumulation of ubiquitinated proteins after incubation with their IC80 concentrations. Our results indicate that the parasite's proteasome could be an attractive target for therapeutic intervention. In this regard, thiostrepton derivatives are promising candidates by dually acting on two independent targets, the proteasome and the apicoplast, with the capacity to eliminate both intraerythrocytic asexual and transmission stages of the parasite. To further support our findings, we evaluated the activity of a new class of antimalarial and proteasome inhibitors namely peptidyl sulfonyl fluorides on gametocyte maturation and analogues AJ34 and AJ38 were able to completely suppress gametocytogenesis at IC50 concentrations (0.23 µM and 0.17 µM respectively) suggesting a strong transmission blocking potential. The proteasome, a major proteolytic complex, responsible for the degradation and re-cycling of non-functional proteins has been studied only indirectly in P. falciparum. In addition, an apparent proteasome-like protein with similarity to bacterial ClpQ/hslV threonine-peptidases was predicted in the parasite. Antibodies were generated against the proteasome subunits alpha type 5 (α5-SU), beta type 5 (β5-SU) and pfhslV in mice and we showed that the proteasome is expressed in both sexual and asexual blood stages of P. falciparum, where they localize in the nucleus and in the cytoplasm. However, expression of PfhslV was only observed in trophozoites and shizonts. The trafficking of the studied proteasome subunits was further investigated by generating parasites expressing GFP tagged proteins. The expression of α5-SU-GFP in transgenic parasite appeared to localize abundantly in the cytoplasm of all blood stages, and no additional information was obtained from this parasite line. In conclusion, our data highlight two new tools towards combination therapy. Hybrid molecules represent promising tools for the cure of co-infected individuals, while very potent antibiotics with a wide scope of activities could be useful in ACTs by eliminating resistant parasites and limiting transmission of both, resistances and disease.}, subject = {Malaria}, language = {en} } @phdthesis{Mueller2012, author = {M{\"u}ller, Andreas}, title = {Towards functional oxide heterostructures}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-72478}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2012}, abstract = {Oxide heterostructures attract a lot of attention as they display a vast range of physical phenomena like conductivity, magnetism, or even superconductivity. In most cases, these effects are caused by electron correlations and are therefore interesting for studying fundamental physics, but also in view of future applications. This thesis deals with the growth and characterization of several prototypical oxide heterostructures. Fe3O4 is highly ranked as a possible spin electrode in the field of spintronics. A suitable semiconductor for spin injection in combination with Fe3O4 is ZnO due to its oxide character and a sufficiently long spin coherence length. Fe3O4 has been grown successfully on ZnO using pulsed laser deposition and molecular beam epitaxy by choosing the oxygen partial pressure adequately. Here, a pressure variation during growth reduces an FeO-like interface layer. Fe3O4 films grow in an island-like growth mode and are structurally nearly fully relaxed, exhibiting the same lattice constants as the bulk materials. Despite the presence of a slight oxygen off-stoichiometry, indications of the Verwey transition hint at high-quality film properties. The overall magnetization of the films is reduced compared to bulk Fe3O4 and a slow magnetization behavior is observed, most probably due to defects like anti-phase boundaries originating from the initial island growth. LaAlO3/SrTiO3 heterostructures exhibit a conducting interface above a critical film thickness, which is most likely explained by an electronic reconstruction. In the corresponding model, the potential built-up owing to the polar LaAlO3 overlayer is compensated by a charge transfer from the film surface to the interface. The properties of these heterostructures strongly depend on the growth parameters. It is shown for the first time, that it is mainly the total pressure which determines the macroscopic sample properties, while it is the oxygen partial pressure which controls the amount of charge carriers near the interface. Oxygen-vacancy-mediated conductivity is found for too low oxygen pressures. A too high total pressure, however, destroys interface conductivity, most probably due to a change of the growth kinetics. Post-oxidation leads to a metastable state removing the arbitrariness in controlling the electronic interface properties by the oxygen pressure during growth. LaVO3/SrTiO3 heterostructures exhibit similar behavior compared to LaAlO3/SrTiO3 when it comes to a thickness-dependent metal-insulator transition. But in contrast to LaAlO3, LaVO3 is a Mott insulator exhibiting strong electron correlations. Films have been grown by pulsed laser deposition. Layer-by-layer growth and a phase-pure pervoskite lattice structure is observed, indicating good structural quality of the film and the interface. An electron-rich layer is found near the interface on the LaVO3 side for conducting LaVO3/SrTiO3. This could be explained by an electronic reconstruction within the film. The electrostatic doping results in a band-filling-controlled metal-insulator transition without suffering from chemical impurities, which is unavoidable in conventional doping experiments.}, subject = {Oxide}, language = {en} } @unpublished{Nassourou2012, author = {Nassourou, Mohamadou}, title = {Towards a Knowledge-Based Learning System for The Quranic Text}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-70003}, year = {2012}, abstract = {In this research, an attempt to create a knowledge-based learning system for the Quranic text has been performed. The knowledge base is made up of the Quranic text along with detailed information about each chapter and verse, and some rules. The system offers the possibility to study the Quran through web-based interfaces, implementing novel visualization techniques for browsing, querying, consulting, and testing the acquired knowledge. Additionally the system possesses knowledge acquisition facilities for maintaining the knowledge base.}, subject = {Wissensbanksystem}, language = {en} } @article{HerbortButz2012, author = {Herbort, Oliver and Butz, Martin V.}, title = {Too good to be true? Ideomotor theory from a computational perspective}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-76383}, year = {2012}, abstract = {In recent years, Ideomotor Theory has regained widespread attention and sparked the development of a number of theories on goal-directed behavior and learning. However, there are two issues with previous studies' use of Ideomotor Theory. Although Ideomotor Theory is seen as very general, it is often studied in settings that are considerably more simplistic than most natural situations. Moreover, Ideomotor Theory's claim that effect anticipations directly trigger actions and that action-effect learning is based on the formation of direct action-effect associations is hard to address empirically. We address these points from a computational perspective. A simple computational model of Ideomotor Theory was tested in tasks with different degrees of complexity.The model evaluation showed that Ideomotor Theory is a computationally feasible approach for understanding efficient action-effect learning for goal-directed behavior if the following preconditions are met: (1) The range of potential actions and effects has to be restricted. (2) Effects have to follow actions within a short time window. (3) Actions have to be simple and may not require sequencing. The first two preconditions also limit human performance and thus support Ideomotor Theory. The last precondition can be circumvented by extending the model with more complex, indirect action generation processes. In conclusion, we suggest that IdeomotorTheory offers a comprehensive framework to understand action-effect learning. However, we also suggest that additional processes may mediate the conversion of effect anticipations into actions in many situations.}, subject = {Psychologie}, language = {en} } @phdthesis{Mauder2012, author = {Mauder, Markus}, title = {Time-Optimal Control of the Bi-Steerable Robot: A Case Study in Optimal Control of Nonholonomic Systems}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-75036}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2012}, abstract = {In this thesis, time-optimal control of the bi-steerable robot is addressed. The bi-steerable robot, a vehicle with two independently steerable axles, is a complex nonholonomic system with applications in many areas of land-based robotics. Motion planning and optimal control are challenging tasks for this system, since standard control schemes do not apply. The model of the bi-steerable robot considered here is a reduced kinematic model with the driving velocity and the steering angles of the front and rear axle as inputs. The steering angles of the two axles can be set independently from each other. The reduced kinematic model is a control system with affine and non-affine inputs, as the driving velocity enters the system linearly, whereas the steering angles enter nonlinearly. In this work, a new approach to solve the time-optimal control problem for the bi-steerable robot is presented. In contrast to most standard methods for time-optimal control, our approach does not exclusively rely on discretization and purely numerical methods. Instead, the Pontryagin Maximum Principle is used to characterize candidates for time-optimal solutions. The resultant boundary value problem is solved by optimization to obtain solutions to the path planning problem over a given time horizon. The time horizon is decreased and the path planning is iterated to approximate a time-optimal solution. An optimality condition is introduced which depends on the number of cusps, i.e., reversals of the driving direction of the robot. This optimality condition allows to single out non-optimal solutions with too many cusps. In general, our approach only gives approximations of time-optimal solutions, since only normal regular extremals are considered as solutions to the path planning problem, and the path planning is terminated when an extremal with minimal number of cusps is found. However, for most desired configurations, normal regular extremals with the minimal number of cusps provide time-optimal solutions for the bi-steerable robot. The convergence of the approach is analyzed and its probabilistic completeness is shown. Moreover, simulation results on time-optimal solutions for the bi-steerable robot are presented.}, subject = {Mobiler Roboter}, language = {en} } @article{OPUS4-12812, title = {Time-dependent angular analysis of the decay B\(^0_s\)→J/ψϕ and extraction of ΔΓ\(_s\) and the CP-violating weak phase ϕ\(_s\) by ATLAS}, series = {Journal of High Energy Physics}, volume = {12}, journal = {Journal of High Energy Physics}, number = {072}, organization = {ATLAS Collaboration}, doi = {10.1007/JHEP12(2012)072}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-128125}, year = {2012}, abstract = {A measurement of B\(^0_s\)→J/ψϕ decay parameters, including the CP -violating weak phase ϕ\(_s\) and the decay width difference ΔΓ\(_s\) is reported, using 4.9 fb\(^{-1}\) of integrated luminosity collected in 2011 by the ATLAS detector from LHC pp collisions at a centre-of-mass energy √s=7 TeV. The mean decay width Γ\(_s\) and the transversity amplitudes |A\(_0\)(0)|\(^2\) and |A\(_∥\)(0)|\(^2\) are also measured. The values reported for these parameters are: ϕ\(_s\)=0.22±0.41 (stat.)±0.10 (syst.) rad ΔΓ\(_s\)=0.053±0.021 (stat.)±0.010 (syst.)ps\(^{-1}\) Γ\(_s\)=0.677±0.007 (stat.)±0.004 (syst.) ps\(^{-1}\) |A\(_0\)(0)|\(^2\)=0.528±0.006 (stat.)±0.009 (syst.) |A\(_∥\)(0)|\(^2\)=0.220±0.008 (stat.)±0.007 (syst.) where the values quoted for ϕ\(_s\) and ΔΓ\(_s\) correspond to the solution compatible with the external measurements to which the strong phase δ\(_⊥\) is constrained and where ΔΓ\(_s\) is constrained to be positive. The fraction of S-wave KK or f\(_0\) contamination through the decays B\(^0_s\)→J/ψK\(^+\)K\(^-\)(f\(_0\)) is measured as well and is found to be consistent with zero. Results for ϕ\(_s\) and ΔΓ\(_s\) are also presented as 68\%, 90\% and 95\% likelihood contours, which show agreement with Standard Model expectations.}, language = {en} } @unpublished{Reiss2012, author = {Reiss, Harald}, title = {Time scales and existence of time holes in non-transparent media}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-73554}, year = {2012}, abstract = {The analysis presented in this paper applies to experimental situations where observers or objects to be studied, all at stationary positions, are located in environments the optical thickness of which is strongly different. Non-transparent media comprise thin metallic films, packed or fluidised beds, superconductors, the Earth's crust, and even dark clouds and other cosmological objects. The analysis applies mapping functions that correlate physical events, e, in non-transparent media, with their images, f(e), tentatively located on standard physical time scale. The analysis demonstrates, however, that physical time, in its rigorous sense, does not exist under non-transparency conditions. A proof of this conclusion is attempted in three steps: i) the theorem "there is no time without space and events" is accepted, (ii) images f[e(s,t)] do not constitute a dense, uncountably infinite set, and (iii) sets of images that are not uncountably infinite do not create physical time but only time-like sequences. As a consequence, mapping f[e(s,t)] in non-transparent space does not create physical analogues to the mathematical structure of the ordered, dense half-set R+ of real numbers, and reverse mapping, f-1f[e(s,t)], the mathematical inverse problem, would not allow unique identification and reconstruction of original events from their images. In these cases, causality as well as invariance of physical processes under time reversal, might be violated. An interesting problem is whether temporal cloaking (a time hole) in a transparent medium, as very recently reported in the literature, can be explained by the present analysis. Existence of time holes could perhaps be possible, not in transparent but in non-transparent media, as follows from the sequence of images, f[e(s,t)], that is not uncountably infinite, in contrast to R+. Impacts are expected for understanding physical diffusion-like, radiative transfer processes and stability models to protect superconductors against quenchs. There might be impacts also in relativity, quantum mechanics, nuclear decay, or in systems close to their phase transitions. The analysis is not restricted to objects of laboratory dimensions.}, subject = {Zeitrichtung}, language = {en} }