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991.
Felix Spenkuch Gerald Hinze Stefanie Kellner Christoph Kreutz Ronald Micura Thomas Basché Mark Helm 《Nucleic acids research》2014,42(20):12735-12745
The interest in RNA modification enzymes surges due to their involvement in epigenetic phenomena. Here we present a particularly informative approach to investigate the interaction of dye-labeled RNA with modification enzymes. We investigated pseudouridine (Ψ) synthase TruB interacting with an alleged suicide substrate RNA containing 5-fluorouridine (5FU). A longstanding dogma, stipulating formation of a stable covalent complex was challenged by discrepancies between the time scale of complex formation and enzymatic turnover. Instead of classic mutagenesis, we used differentially positioned fluorescent labels to modulate substrate properties in a range of enzymatic conversion between 6% and 99%. Despite this variegation, formation of SDS-stable complexes occurred instantaneously for all 5FU-substrates. Protein binding was investigated by advanced fluorescence spectroscopy allowing unprecedented simultaneous detection of change in fluorescence lifetime, anisotropy decay, as well as emission and excitation maxima. Determination of Kd values showed that introduction of 5FU into the RNA substrate increased protein affinity by 14× at most. Finally, competition experiments demonstrated reversibility of complex formation for 5FU-RNA. Our results lead us to conclude that the hitherto postulated long-term covalent interaction of TruB with 5FU tRNA is based on the interpretation of artifacts. This is likely true for the entire class of pseudouridine synthases. 相似文献
992.
Stefanie Rosa Vardis Ntoukakis Nobuko Ohmido Ali Pendle Rita Abranches Peter Shaw 《The Plant cell》2014,26(12):4821-4833
The mechanism whereby the same genome can give rise to different cell types with different gene expression profiles is a fundamental problem in biology. Chromatin organization and dynamics have been shown to vary with altered gene expression in different cultured animal cell types, but there is little evidence yet from whole organisms linking chromatin dynamics with development. Here, we used both fluorescence recovery after photobleaching and two-photon photoactivation to show that in stem cells from Arabidopsis thaliana roots the mobility of the core histone H2B, as judged by exchange dynamics, is lower than in the surrounding cells of the meristem. However, as cells progress from meristematic to fully differentiated, core histones again become less mobile and more strongly bound to chromatin. We show that these transitions are largely mediated by changes in histone acetylation. We further show that altering histone acetylation levels, either in a mutant or by drug treatment, alters both the histone mobility and markers of development and differentiation. We propose that plant stem cells have relatively inactive chromatin, but they keep the potential to divide and differentiate into more dynamic states, and that these states are at least in part determined by histone acetylation levels. 相似文献
993.
M Grusdat D R McIlwain H C Xu V I Pozdeev J Knievel S Q Crome C Robert-Tissot R J Dress A A Pandyra D E Speiser E Lang S K Maney A R Elford S R Hamilton S Scheu K Pfeffer J Bode H-W Mittrücker M Lohoff M Huber D H?ussinger P S Ohashi T W Mak K S Lang P A Lang 《Cell death and differentiation》2014,21(7):1050-1060
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996.
Nikolaus Fries Stefanie Hellweg 《The International Journal of Life Cycle Assessment》2014,19(3):546-557
Purpose
A major task concerning the greening of freight transportation is to influence the process of choosing an appropriate transport solution for a shipment. This paper presents the results of a detailed environmental benchmark study of freight transport chains recorded during a shipper survey administered in Switzerland in 2008.Materials and methods
For the environmental evaluation, life cycle assessment was applied and enhanced with a new method for integrating damage to human health caused by traffic accidents based on the disability adjusted life year concept.Results and discussion
The results show that in land-based transport, road generally has a lower environmental performance compared to intermodal and rail-only transport. Exceptions exist, e.g. for long pre- and post-haulage distances in intermodal transport or for very low train-load factors. The most relevant environmental interventions to pay attention to are, according to the methods applied, emissions of CO2, NOx and particulates as well as accident damages.Conclusions
Rail transport is often, but not always, environmentally preferable than truck transport. Accident damages to human health should be included in each benchmark study. For practical application, a simplified benchmark methodology is proposed requiring a reduced level of detail for the input data. 相似文献997.
Burkhard Büdel Claudia Colesie T. G. Allan Green Martin Grube Roberto Lázaro Suau Katharina Loewen-Schneider Stefanie Maier Thomas Peer Ana Pintado José Raggio Ulrike Ruprecht Leopoldo G. Sancho Burkhard Schroeter Roman Türk Bettina Weber Mats Wedin Martin Westberg Laura Williams Lingjuan Zheng 《Biodiversity and Conservation》2014,23(7):1639-1658
Here we report details of the European research initiative “Soil Crust International” (SCIN) focusing on the biodiversity of biological soil crusts (BSC, composed of bacteria, algae, lichens, and bryophytes) and on functional aspects in their specific environment. Known as the so-called “colored soil lichen community” (Bunte Erdflechtengesellschaft), these BSCs occur all over Europe, extending into subtropical and arid regions. Our goal is to study the uniqueness of these BSCs on the regional scale and investigate how this community can cope with large macroclimatic differences. One of the major aims of this project is to develop biodiversity conservation and sustainable management strategies for European BSCs. To achieve this, we established a latitudinal transect from the Great Alvar of Öland, Sweden in the north over Gössenheim, Central Germany and Hochtor in the Hohe Tauern National Park, Austria down to the badlands of Tabernas, Spain in the south. The transect stretches over 20° latitude and 2,300 m in altitude, including natural (Hochtor, Tabernas) and semi-natural sites that require maintenance such as by grazing activities (Öland, Gössenheim). At all four sites BSC coverage exceeded 30 % of the referring landscape, with the alpine site (Hochtor) reaching the highest cyanobacterial cover and the two semi-natural sites (Öland, Gössenheim) the highest bryophyte cover. Although BSCs of the four European sites share a common set of bacteria, algae (including cyanobacteria) lichens and bryophytes, first results indicate not only climate specific additions of species, but also genetic/phenotypic uniqueness of species between the four sites. While macroclimatic conditions are rather different, microclimatic conditions and partly soil properties seem fairly homogeneous between the four sites, with the exception of water availability. Continuous activity monitoring of photosystem II revealed the BSCs of the Spanish site as the least active in terms of photosynthetic active periods. 相似文献
998.
David Lyon Maria Angeles Castillejo Christiana Staudinger Wolfram Weckwerth Stefanie Wienkoop Volker Egelhofer 《PloS one》2014,9(4)
Protein turnover is a well-controlled process in which polypeptides are constantly being degraded and subsequently replaced with newly synthesized copies. Extraction of composite spectral envelopes from complex LC/MS shotgun proteomics data can be a challenging task, due to the inherent complexity of biological samples. With partial metabolic labeling experiments this complexity increases as a result of the emergence of additional isotopic peaks. Automated spectral extraction and subsequent protein turnover calculations enable the analysis of gigabytes of data within minutes, a prerequisite for systems biology high throughput studies. Here we present a fully automated method for protein turnover calculations from shotgun proteomics data. The approach enables the analysis of complex shotgun LC/MS 15N partial metabolic labeling experiments. Spectral envelopes of 1419 peptides can be extracted within an hour. The method quantifies turnover by calculating the Relative Isotope Abundance (RIA), which is defined as the ratio between the intensity sum of all heavy (15N) to the intensity sum of all light (14N) and heavy peaks. To facilitate this process, we have developed a computer program based on our method, which is freely available to download at http://promex.pph.univie.ac.at/protover. 相似文献
999.
Taxonomy, the science of describing and naming of the living world, is recognized as an important and relevant field in modern biological science. While there is wide agreement on the importance of a complete inventory of all organisms on Earth, the public is partly unaware of the amount of known and unknown biodiversity. Out of the enormous number of undescribed (but already recognized) species in natural history museum collections, we selected an attractive example of a wasp, which was presented to museum visitors at a special museum event. We asked 300 visitors to vote on a name for the new species and out of four preselected options, Ampulex dementor Ohl n. sp. was selected. The name, derived from the ‘soul sucking’ dementors from the popular Harry Potter books is an allusion to the wasps'' behavior to selectively paralyze its cockroach prey. In this example, public voting on a scientific name has been shown to be an appropriate way to link museum visitors emotionally to biodiversity and its discovery. 相似文献
1000.
Anja Urbschat Kai Zacharowski Nicholas Obermüller Katrin Rupprecht Daniela Penzkofer Carla Jennewein Nguyen Tran Bertram Scheller Stefanie Dimmeler Patrick Paulus 《PloS one》2014,9(1)
Disruption of the renal endothelial integrity is pivotal for the development of a vascular leak, tissue edema and consequently acute kidney injury. Kidney ischemia amplifies endothelial activation and up-regulation of pro-inflammatory mechanisms. After restoring a sufficient blood flow, the kidney is damaged through complex pathomechanisms that are classically referred to as ischemia and reperfusion injury, where the disruption of the inter-endothelial connections seems to be a crucial step in this pathomechanism. Focusing on the molecular cell-cell interaction, the fibrinopeptide Bβ15–42 prevents vascular leakage by stabilizing these inter-endothelial junctions. The peptide associates with vascular endothelial-cadherin, thus preventing early kidney dysfunction by preserving blood perfusion efficacy, edema formation and thus organ dysfunction. We intended to demonstrate the early therapeutic benefit of intravenously administered Bβ15–42 in a mouse model of renal ischemia and reperfusion. After 30 minutes of ischemia, the fibrinopeptide Bβ15–42 was administered intravenously before reperfusion was commenced for 1 and 3 hours. We show that Bβ15–42 alleviates early functional and morphological kidney damage as soon as 1 h and 3 h after ischemia and reperfusion. Mice treated with Bβ15–42 displayed a significantly reduced loss of VE-cadherin, indicating a conserved endothelial barrier leading to less neutrophil infiltration which in turn resulted in significantly reduced structural renal damage. The significant reduction in tissue and serum neutrophil gelatinase-associated lipocalin levels reinforced our findings. Moreover, renal perfusion analysis by color duplex sonography revealed that Bβ15–42 treatment preserved resistive indices and even improved blood velocity. Our data demonstrate the efficacy of early therapeutic intervention using the fibrinopeptide Bβ15–42 in the treatment of acute kidney injury resulting from ischemia and reperfusion. In this context Bβ15–42 may act as a potent renoprotective agent by preserving the endothelial and vascular integrity. 相似文献