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The U-turn is a classical three-dimensional RNA folding motif first identified in the anticodon and T-loops of tRNAs. It also occurs frequently as a building block in other functional RNA structures in many different sequence and structural contexts. U-turns induce sharp changes in the direction of the RNA backbone and often conform to the 3-nt consensus sequence 5'-UNR-3' (N = any nucleotide, R = purine). The canonical U-turn motif is stabilized by a hydrogen bond between the N3 imino group of the U residue and the 3' phosphate group of the R residue as well as a hydrogen bond between the 2'-hydroxyl group of the uridine and the N7 nitrogen of the R residue. Here, we demonstrate that a protonated cytidine can functionally and structurally replace the uridine at the first position of the canonical U-turn motif in the apical loop of the neomycin riboswitch. Using NMR spectroscopy, we directly show that the N3 imino group of the protonated cytidine forms a hydrogen bond with the backbone phosphate 3' from the third nucleotide of the U-turn analogously to the imino group of the uridine in the canonical motif. In addition, we compare the stability of the hydrogen bonds in the mutant U-turn motif to the wild type and describe the NMR signature of the C+-phosphate interaction. Our results have implications for the prediction of RNA structural motifs and suggest simple approaches for the experimental identification of hydrogen bonds between protonated C-imino groups and the phosphate backbone.
A consistent muscle activation strategy underlies crawling and swimming in Caenorhabditis elegans
(2014)
Although undulatory swimming is observed in many organisms, the neuromuscular basis for undulatory movement patterns is not well understood. To better understand the basis for the generation of these movement patterns, we studied muscle activity in the nematode Caenorhabditis elegans. Caenorhabditis elegans exhibits a range of locomotion patterns: in low viscosity fluids the undulation has a wavelength longer than the body and propagates rapidly, while in high viscosity fluids or on agar media the undulatory waves are shorter and slower. Theoretical treatment of observed behaviour has suggested a large change in force–posture relationships at different viscosities, but analysis of bend propagation suggests that short-range proprioceptive feedback is used to control and generate body bends. How muscles could be activated in a way consistent with both these results is unclear. We therefore combined automated worm tracking with calcium imaging to determine muscle activation strategy in a variety of external substrates. Remarkably, we observed that across locomotion patterns spanning a threefold change in wavelength, peak muscle activation occurs approximately 45° (1/8th of a cycle) ahead of peak midline curvature. Although the location of peak force is predicted to vary widely, the activation pattern is consistent with required force in a model incorporating putative length- and velocity-dependence of muscle strength. Furthermore, a linear combination of local curvature and velocity can match the pattern of activation. This suggests that proprioception can enable the worm to swim effectively while working within the limitations of muscle biomechanics and neural control.
D2.1. provides further elaboration of the original research design and informs about ideas for the final Volume II of bEUcitizen. It is closely connected to task 1 of work package 2: specifying various concrete tasks for the different work packages and formulating overarching questions suitable to provide substantive cohesion and integration of the overall project. The elaboration of 10 crosscutting topics (to become chapters in the “horizontal” book, D2.3.) is a first step towards this goal. Discussing these cross-cutting topics is supposed to feed, infuse and inspire the work done in the different work packages and to build cross-cutting connections between them. Themes 1-10 merge into a valuable overview of the multi-faceted research on (EU) citizenship. They access the main issues of EU-citizenship and citizenship in general from different angles and different disciplines. Taken together these contributions help to identify barriers towards EU citizenship and ways to overcome them. Each Theme formulates questions how it might feed and be fed by further information and findings in the other work packages.
D2.1. is mainly meant for internal use. Its functions are firstly to inform about preliminary ideas, eventual contributions to planned final results and secondly to make out some more of less specific guiding questions that connect the work done by the single researchers in every different work package to the project as a whole. This task implies a normative yardstick, a clear picture of what would be a "good" EU citizenship practice. Elaborating on such a normative yardstick is a meta-topic that cuts across the range of cross-cutting topics presented in this working paper.
This article focuses on the opportunities and challenges of implementing an extensive reading project in an English as a foreign language classroom in Germany. Studies such as PISA have shown that comparatively poor German and foreign language reading skills are still a prevalent issue in German society today. Consequently, the question of how these poor results can be improved is of utmost importance. Reading motivation is often described as the ‘driving force of reading’. Research has shown that if reading motivation and reading for pleasure are supported, interest in reading in a foreign language can be created, which may in turn have a positive impact on the other influential factors in reading and related skills. Dörnyei’s framework of L2 motivation sums up the current thinking on reading motivation. With its constituents ‘language’, ‘learner’, and ‘learning situation’, it shows the aspects to be taken into consideration when it comes to the improvement of motivation. Within this theoretical framework, an ER project was conducted at a grammar school (Gymnasium) in Frankfurt/Main, Germany. On the basis of the gathered data, gained from questionnaires, worksheets and the transcript of a focus group discussion, six main categories could be identified. They point to the development of a positive attitude towards reading among the students and the potential of graphic novels as a motivating factor. It was also confirmed that a successful application of reading strategies led to increased motivation. Generally, the project showed that reading is still an issue amongst many teenagers and that an ER project can affect learners, their motivation and related language skills in a positive way.
Aim: The cytokine receptor tumor necrosis factor receptor superfamily member 9 (TNFRSF9) is mainly considered to be a co-stimulatory activation marker in hematopoietic cells. Several preclinical models have shown a dramatic beneficial effect of treatment approaches targeting TNFRSF9 with agonistic antibodies. However, preliminary clinical phase I/II studies were stopped after the occurrence of several severe deleterious side effects. In a previous study, it was demonstrated that TNFRSF9 was strongly expressed by reactive astrocytes in primary central nervous system (CNS) tumors, but was largely absent from tumor or inflammatory cells. The aim of the present study was to address the cellular source of TNFRSF9 expression in the setting of human melanoma brain metastasis, a highly immunogenic tumor with a prominent tropism to the CNS.
Methods: Melanoma brain metastasis was analyzed in a cohort of 78 patients by immunohistochemistry for TNFRSF9 and its expression was correlated with clinicopathological parameters including sex, age, survival, tumor size, number of tumor spots, and BRAF V600E expression status.
Results: Tumor necrosis factor receptor superfamily member 9 was frequently expressed independently on both melanoma and endothelial cells. In addition, TNFRSF9 was also present on smooth muscle cells of larger vessels and on a subset of lymphomonocytic tumor infiltrates. No association between TNFRSF9 expression and patient survival or other clinicopathological parameters was seen. Of note, several cases showed a gradual increase in TNFRSF9 expression on tumor cells with increasing distance from blood vessels, an observation that might be linked to hypoxia-driven TNFRSF9 expression in tumor cells.
Conclusion: The findings indicate that the cellular source of TNFRSF9 in melanoma brain metastasis largely exceeds the lymphomonocytic pool, and therefore further careful (re-) assessment of potential TNFRSF9 functions in cell types other than hematopoietic cells is needed. Furthermore, the hypothesis of hypoxia-driven TNFRSF9 expression in brain metastasis melanoma cells requires further functional testing.
Speolepta leptogaster (Winnertz, 1863) is frequently occurring in European subterranean environments. As for most cave animals, studies addressing non-anatomical aspects are sparse. Here we present the first molecular study on S. leptogaster. We investigated the demographic structure (i.e. COI locus) of 69 specimens from 36 underground populations in Hesse (Central German Uplands) to get first insights into the species’ dispersal ability.
In total, 14 haplotypes were revealed. Haplotype diversity was relatively high, whereas nucleotide diversity was low. Furthermore, a significant but low pattern of isolation-by-distance and (a) past population expansion event(s) were detected.
Our genetic results suggest a (good) active dispersal ability for Speolepta leptogaster. The occurrence of several surface records of adult specimens corroborates this hypothesis. We discuss the developmental stages of S. leptogaster in the context of the ecological classification system and regard the species as a eutroglophile. Evidence has been found to distinguish two larval types. A reconstructed life-cycle of the species is provided.
Does the rotten child spoil his companion? : spatial peer effects among children in rural India
(2014)
This paper identifies the effect of neighborhood peer groups on childhood skill acquisition using observational data. We incorporate spatial peer interaction, defined as a child's nearest geographical neighbors, into a production function of child cognitive development in Andhra Pradesh, India. Our peer group definition takes the form of networks, whose structure allows us to identify endogenous peer effects and contextual effects separately. We exploit variation over time to avoid confounding correlated with social effects. Our results suggest that spatial peer and neighborhood effects are strongly positively associated with a child's cognitive skill formation. Further, we explore the effect of peer groups in helping to provide insurance against the negative impact of idiosyncratic shocks to child learning. We find that the data reject full risk-sharing, but cannot rule out the existence of partial risk-sharing on behalf of peers. We show that peer effects are robust to different specifications of peer interactions and investigate the sensitivity of our estimates to potential misspecification of the network structure using Monte Carlo experiments.
Research in the field of Digital Humanities, also known as Humanities Computing, has seen a steady increase over the past years. Situated at the intersection of computing science and the humanities, present efforts focus on making resources such as texts, images, musical pieces and other semiotic artifacts digitally available, searchable and analysable. To this end, computational tools enabling textual search, visual analytics, data mining, statistics and natural language processing are harnessed to support the humanities researcher. The processing of large data sets with appropriate software opens up novel and fruitful approaches to questions in the traditional humanities. This report summarizes the Dagstuhl seminar 14301 on “Computational Humanities - bridging the gap between Computer Science and Digital Humanities”.
1998 ACM Subject Classification I.2.7 Natural Language Processing, J.5 Arts and Humanities
Ultrafast protein dynamics are of great interest for understanding the molecular basis of biochemical function. One method to study structural changes with highest time-resolution starting in the femtosecond regime is 2D-IR spectroscopy. However its application to investigate protein dynamics both with high temporal and spatial resolution is currently limited to few biological systems with intrinsic chromophores. Spectral congestion, the contribution of many similar oscillators to the same signals, makes it difficult to draw conclusions about local structural dynamics in most other proteins.
The aim of this thesis is to extend the application of 2D-IR spectroscopy to a wider range of proteins by introducing unnatural amino acids (UAAs) with azide or nitrile groups as site-specific vibrational probes, which absorb in the free spectral window between 1800 to 3000 cm-1 by using methods from chemical biology.
In a comparative experimental study using FTIR and 2D-IR spectroscopy of single amino acids azidohomoalanine (Aha), a methionine analogue, was identified as preferred label. To demonstrate the application potential of UAAs as site-specific probes, Aha was then incorporated into different positions in a small globular protein. By using both FTIR and ultrafast 2D-IR it was shown, that indeed the local microenvironment as well as conformational fluctuations on picosecond timescale could be monitored with high spatial information. The azide moiety shows a shift of its absorption frequency depending on the polarity of its surrounding. Using this approach, different subensembles for the protein conformations with more polar and less polar environment around the vibrational probe can be distinguished.
A second major application of site-specific labels is the study of vibrational energy transfer processes (VET), predicted to be relevant for allosteric communication in protein domains such as the PDZ domain. VET can be tracked with high spatial resolution using time-resolved IR spectroscopy by exciting a localized vibrational mode and probing separate modes in a two-colour 2D-IR experiment. To extend this kind of experiment to proteins, a specific donor-acceptor pair of two UAAs was introduced. It uses an azulene moiety as donor that can be excited in the visible range but deposits the excess energy by internal conversion into the vibrational modes of the ground state. In small peptides this VET pair was applied successfully, showing a distance-dependent energy transfer induced signal for VET through covalent bonds. These findings bare great promise for the direct observation of vibrational energy flow in proteins in real-time.
Overall this thesis is the basis for extending the usability of 2D-IR spectroscopy to study structural dynamics in a wide range of proteins systems both with high temporal and spatial resolution.
Benjamin's early reception in the United States can be broken into eight phases: 1) a few notices of his work in the 1930s; 2) the appearance of two major works, without translation, in the 'Zeitschrift für Sozialforschung', when it was published in New York and mimeographed in Los Angeles; 3) several reports of his suicide along with the death of other Jewish and left-wing writers who fell victim to Nazi terror; 4) scattered use of his work in the late 1940s and 1950s; 5) a growing realization in the early 1960s that American literary and cultural criticism was missing something of significance by neglecting Benjamin's work; 6) the appearance in the 1960s of competing portraits of Benjamin by four of his surviving friends, including Hannah Arendt, who edited and introduced the first collection of his writings in English; 7) an uncanny repetition of the earlier neglect, as a significant number of Benjamin's texts are published in Great Britain during the 1970s and early 1980s but remain unavailable in the States; 8) the beginning of a sustained critical engagement with Benjamin in the late 1970s.