CYNTENATOR: Progressive Gene Order Alignment of 17 Vertebrate Genomes

Whole genome gene order evolution in higher eukaryotes was initially considered as a random process. Gene order conservation or conserved synteny was seen as a feature of common descent and did not imply the existence of functional constraints. This view had to be revised in the light of results from sequencing dozens of vertebrate genomes

Atmospheric rivers in CMIP5 climate ensembles downscaled with a high-resolution regional climate model

Atmospheric rivers (ARs) are important drivers of hazardous precipitation levels and are often associated with intense floods. So far, the response of ARs to climate change in Europe has been investigated using global climate models within the CMIP5 framework. However, the spatial resolution of those models (1–3∘) is too coarse for an adequate assessment of local to regional precipitation patterns. Using a regional climate model with 0.22∘ resolution, we downscaled an ensemble consisting of 1 ERA-Interim (ERAI) reanalysis data hindcast simulation, 9 global historical, and 24 climate scenario simulations following greenhouse gas emission scenarios RCP2.6, RCP4.5, and RCP8.5. The performance of the climate model to simulate AR frequencies and AR-induced precipitation was tested against ERAI. Overall, we find a good agreement between the downscaled CMIP5 historical simulations and ERAI. However, the downscaled simulations better represented small-scale spatial characteristics. This was most evident over the terrain of the Iberian Peninsula, where the AR-induced precipitation pattern clearly reflected prominent east–west topographical elements, resulting in zonal bands of high and low AR impact. Over central Europe, the models simulated a smaller propagation distance of ARs toward eastern Europe than obtained using the ERAI data. Our models showed that ARs in a future warmer climate will be more frequent and more intense, especially in the higher-emission scenarios (RCP4.5, RCP8.5). However, assuming low emissions (RCP2.6), the related changes can be mostly mitigated. According to the high-emission scenario RCP8.5, AR-induced precipitation will increase by 20 %–40 % in western central Europe, whereas mean precipitation rates increase by a maximum of only 12 %. Over the Iberian Peninsula, AR-induced precipitation will slightly decrease (∼6 %) but the decrease in the mean rate will be larger (∼15 %). These changes will lead to an overall increased fractional contribution of ARs to heavy precipitation, with the greatest impact over the Iberian Peninsula (15 %–30 %) and western France (∼15 %). Likewise, the fractional share of yearly maximum precipitation attributable to ARs will increase over the Iberian Peninsula, the UK, and western France. Over Norway, average AR precipitation rates will decline by −5 % to −30 %, most likely due to dynamic changes, with ARs originating from latitudes > 60∘ N decreasing by up to 20 % and those originating south of 45∘ N increasing. This suggests that ARs over Norway will follow longer routes over the continent, such that additional moisture uptake will be impeded. By contrast, ARs from >60∘ N will take up moisture from the North Atlantic before making landfall over Norway. The found changes in the local AR pathway are probably driven by larger-scale circulation changes such as a change in dominating weather regimes and/or changes in the winter storm track over the North Atlantic

Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus

BACKGROUND: The development of multicellular organisms is accompanied by gene expression changes in differentiating cells. Profiling stage-specific expression during development may reveal important insights into gene sets that contributed to the morphological diversity across the animal kingdom. RESULTS: We sequenced RNA-seq libraries throughout a developmental timecourse of the nematode Pristionchus pacificus. The transcriptomes reflect early larval stages, adult worms including late larvae, and growth-arrested dauer larvae and allowed the identification of developmentally regulated gene clusters. Our data reveals similar trends as previous transcriptome profiling of dauer worms and represents the first expression data for early larvae in P. pacificus. Gene expression clusters characterizing early larval stages show most significant enrichments of chaperones, while collagens are most significantly enriched in transcriptomes of late larvae and adult worms. By combining expression data with phylogenetic analysis, we found that developmentally regulated genes are found in paralogous clusters that have arisen through lineage-specific duplications after the split from the Caenorhabditis elegans branch. CONCLUSIONS: We propose that gene duplications of developmentally regulated genes represent a plausible evolutionary mechanism to increase the dosage of stage-specific expression. Consequently, this may contribute to the substantial divergence in expression profiles that has been observed across larger evolutionary time scales

Baltic Sea ecosystem response to various nutrient load scenarios in present and future climates

The Baltic Sea is a shallow, semi-enclosed brackish sea suffering like many other coastal seas from eutrophication caused by human impact. Hence, nutrient load abatement strategies are intensively discussed. With the help of a high-resolution, coupled physical-biogeochemical circulation model we investigate the combined impact of changing nutrient loads from land and changing climate during the 21st century as projected from a global climate model regionalized to the Baltic Sea region. Novel compared to previous studies are an extraordinary spin-up based upon historical reconstructions of atmospheric, nutrient load and runoff forcing, revised nutrient load scenarios and a comparison of nutrient load scenario simulations with and without changing climate. We found in almost all scenario simulations, with differing nutrient inputs, reduced eutrophication and improved ecological state compared to the reference period 1976–2005. This result is a long-lasting consequence of ongoing nutrient load reductions since the 1980s. Only in case of combined high-end nutrient load and climate scenarios, eutrophication is reinforced. Differences compared to earlier studies are explained by the experimental setup including nutrient loads during the historical period and by the projected nutrient loads. We found that the impact of warming climate may amplify the effects of eutrophication and primary production. However, effects of changing climate, within the range of considered greenhouse gas emission scenarios, are smaller than effects of considered nutrient load changes, in particular under low nutrient conditions. Hence, nutrient load reductions following the Baltic Sea Action Plan will lead to improved environmental conditions independently of future climate change.publishedVersio

Uncertainties in projections of the baltic sea ecosystem driven by an ensemble of global climate models

Many coastal seas worldwide are affected by human impacts such as eutrophication causing, inter alia, oxygen depletion, and extensive areas of hypoxia. Depending on the region, global warming may reinforce these environmental changes by reducing air-sea oxygen fluxes, intensifying internal nutrient cycling, and increasing river-borne nutrient loads. The development of appropriate management plans to effectively protect the marine environment requires projections of future marine ecosystem states. However, projections with regional climate models commonly suffer from shortcomings in the driving global General Circulation Models (GCMs). The differing sensitivities of GCMs to increased greenhouse gas concentrations affect regional projections considerably. In this study, we focused on one of the most threatened coastal seas, the Baltic Sea, and estimated uncertainties in projections due to climate model deficiencies and due to unknown future greenhouse gas concentration, nutrient load and sea level rise scenarios. To address the latter, simulations of the period 1975–2098 were performed using the initial conditions from an earlier reconstruction with the same Baltic Sea model (starting in 1850). To estimate the impacts of climate model uncertainties, dynamical downscaling experiments with four driving global models were carried out for two greenhouse gas concentration scenarios and for three nutrient load scenarios, covering the plausible range between low and high loads. The results suggest that changes in nutrient supply, in particular phosphorus, control the long-term (centennial) response of eutrophication, biogeochemical fluxes and oxygen conditions in the deep water. The analysis of simulated primary production, nitrogen fixation, and hypoxic areas shows that uncertainties caused by the various nutrient load scenarios are greater than the uncertainties due to climate model uncertainties and future greenhouse gas concentrations. In all scenario simulations, a proposed nutrient load abatement strategy, i.e., the Baltic Sea Action Plan, will lead to a significant improvement in the overall environmental state. However, the projections cannot provide detailed information on the timing and the reductions of future hypoxic areas, due to uncertainties in salinity projections caused by uncertainties in projections of the regional water cycle and of the mean sea level outside the model domain.publishedVersio

Wirtschaften. Kulturwissenschaftliche Perspektiven.

Unter dem Titel „Wirtschaften. Kulturwissenschaftliche Perspektiven“ fand 2017 in Marburg der 41. Kongress der Deutschen Gesellschaft für Volkskunde (dgv) auf Einladung des Instituts für Europäische Ethnologie / Kulturwissenschaft der Philipps-Universität Marburg statt. Die vorliegende Publikation liefert eine umfassende Dokumentation der auf dem Kongress diskutierten Beiträge

Hydroxyproline-containing collagen analogs trigger the release and activation of collagen-sequestered proMMP-2 by competition with prodomain-derived peptide P33-42.

BACKGROUND: Fibrolytic and profibrotic activities of the matrix metalloproteinases (MMPs)-2 and -9 play a central role in liver fibrosis. Since binding to the extracellular matrix influences the activity of both gelatinases, here the role of fibrillar collagens as the most abundant matrix components in fibrotic tissue was investigated. RESULTS: In situ zymography and immunohistology showed association of enzymatically inactive prodomain-containing proMMP-2 and proMMP-9 but not of their activated forms to fibrillar collagen structures, which are not substrates of these gelatinases. In solid-phase binding studies with human collagens and collagen fragments, up to 45% of [125I]-labeled proMMP-2 and proMMP-9 but not of active (act)MMP-2 and actMMP-9 were retained by natural collagenous molecules and by synthetic analogs containing repeated Gly-Pro-Hyp triplets (GPO). Surface plasmon resonance yielded binding constants for the interaction of collagen type I (CI) with proMMP-2 and proMMP-9 in a nanomolar range. Values for actMMP-2 and actMMP-9 were 30-40 times higher. Tenfold molar excesses of (GPO)10 reduced the interaction of CI with pro- and actMMP-2 by 22- or 380-fold and resulted in prodomain release accompanied by high enzymatic activation and activity. Pointing to gelatine substrate displacement, higher (GPO)10 concentrations blocked the enzymatic activity. The MMP-2 prodomain-derived collagen-binding domain peptide (P33-42) binds to the collagen-binding domain of MMP-2, thereby preserving enzymatic inactivity. Synthetic P33-42 peptide competed with proMMP-2 binding to CI and prevented (GPO)10-mediated proMMP-2 activation. In contrast to (GPO)10, P33-42 did not activate proMMP-2, making triple helical and hydroxyproline-containing (GPO)10 unique in modulating gelatinase availability and activity. CONCLUSIONS: These findings suggest novel strategies using collagen analogs for the resolution of liver fibrosis via fibrotic matrix-sequestered gelatinases.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

N-Acetyl-L-Leucine Accelerates Vestibular Compensation after Unilateral Labyrinthectomy by Action in the Cerebellum and Thalamus

An acute unilateral vestibular lesion leads to a vestibular tone imbalance with nystagmus, head roll tilt and postural imbalance. These deficits gradually decrease over days to weeks due to central vestibular compensation (VC). This study investigated the effects of i.v. N-acetyl-DL-leucine, N-acetyl-L-leucine and N-acetyl-D-leucine on VC using behavioural testing and serial [18F]-Fluoro-desoxyglucose ([18F]-FDG)-mu PET in a rat model of unilateral chemical labyrinthectomy (UL). Vestibular behavioural testing included measurements of nystagmus, head roll tilt and postural imbalance as well as sequential whole-brain [18F]FDG-mu PET was done before and on days 1, 3, 7 and 15 after UL. A significant reduction of postural imbalance scores was identified on day 7 in the N-acetyl-DL-leucine (p < 0.03) and the N-acetyl-L-leucine groups (p < 0.01),compared to the sham treatment group, but not in the N-acetyl-D-leucine group (comparison for applied dose of 24 mg i.v. per rat, equivalent to 60 mg/kg body weight, in each group). The course of postural compensation in the DL-and L-group was accelerated by about 6 days relative to controls. The effect of N-acetyl-L-leucine on postural compensation depended on the dose: in contrast to 60 mg/kg, doses of 15 mg/kg and 3.75 mg/kg had no significant effect. N-acetyl-L-leucine did not change the compensation of nystagmus or head roll tilt at any dose. Measurements of the regional cerebral glucose metabolism (rCGM) by means of mu PET revealed that only N-acetyl-L-leucine but not N-acetyl-D-leucine caused a significant increase of rCGM in the vestibulocerebellum and a decrease in the posterolateral thalamus and subthalamic region on days 3 and 7. A similar pattern was found when comparing the effect of N-acetyl-L-leucine on rCGM in an UL-group and a sham UL-group without vestibular damage. In conclusion, N-acetyl-L-leucine improves compensation of postural symptoms after UL in a dose-dependent and specific manner, most likely by activating the vestibulocerebellum and deactivating the posterolateral thalamus

Simulational study of anomalous tracer diffusion in hydrogels

In this article, we analyze different factors that affect the diffusion behavior of small tracer particles (as they are used e.g.in fluorescence correlation spectroscopy (FCS)) in the polymer network of a hydrogel and perform simulations of various simplified models. We observe, that under certain circumstances the attraction of a tracer particle to the polymer network strands might cause subdiffusive behavior on intermediate time scales. In theory, this behavior could be employed to examine the network structure and swelling behavior of weakly crosslinked hydrogels with the help of FCS.Comment: 11 pages, 11 figure