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- Mathematisch-Naturwissenschaftliche Fakultät (70) (remove)
Siberian arctic vegetation and lake water communities, known for their temperature dependence, are expected to be particularly impacted by recent climate change and high warming rates. However, decadal information on the nature and strength of recent vegetation change and its time lag to climate signals are rare. In this study, we present a Pb-210/Cs-137 dated pollen and Pediastrum species record from a unnamed lake in the south of the Taymyr peninsula covering the period from AD 1706 to 2011. Thirty-nine palynomorphs and 10 morphotypes of Pediastrum species were studied to assess changes in vegetation and lake conditions as probable responses to climate change. We compared the pollen record with Pediastrum species, which we consider to be important proxies of climate changes. Three pollen assemblage zones characterised by Betula nana, Alnus viridis and Larix gmelinii (1706-1808); herbs such as Cyperaceae, Artemisia or Senecio (1808-1879), and higher abundance of Larix pollen (1955-2011) are visible. Also, three Pediastrum assemblage zones show changes of aquatic conditions: higher abundances of Pediastrum boryanum var. brevicorne (1706-1802); medium abundances of P. kawraiskyi and P. integrum (1802-1840 and 1920-1980), indicating cooler conditions while less eutrophic conditions are indicated by P. boryanum, and a mainly balanced composition with only small changes of cold- and warm-adapted Pediastrum species (1965-2011). In general, compositional Pediastrum species turnover is slightly higher than that indicated by pollen data (0.54 vs 0.34 SD), but both are only minor for this treeline location. In conclusion, the relevance of differentiation of Pediastrum species is promising and can give further insights into the relationship between lakes and their surrounding vegetation transferred onto climatic conditions.
By overcoming the diffraction limit in light microscopy, super-resolution techniques, such as stimulated emission depletion (STED) microscopy, are experiencing an increasing impact on life sciences. High costs and technically demanding setups, however, may still hinder a wider distribution of this innovation in biomedical research laboratories. As far-field microscopy is the most widely employed microscopy modality in the life sciences, upgrading already existing systems seems to be an attractive option for achieving diffraction-unlimited fluorescence microscopy in a cost-effective manner. Here, we demonstrate the successful upgrade of a commercial time-resolved confocal fluorescence microscope to an easy-to-align STED microscope in the single-beam path layout, previously proposed as "easy-STED", achieving lateral resolution <lambda/10 corresponding to a five-fold improvement over a confocal modality. For this purpose, both the excitation and depletion laser beams pass through a commercially available segmented phase plate that creates the STED-doughnut light distribution in the focal plane, while leaving the excitation beam unaltered when implemented into the joint beam path. Diffraction-unlimited imaging of 20 nm-sized fluorescent beads as reference were achieved with the wavelength combination of 635 nm excitation and 766 nm depletion. To evaluate the STED performance in biological systems, we compared the popular phalloidin-coupled fluorescent dyes Atto647N and Abberior STAR635 by labeling F-actin filaments in vitro as well as through immunofluorescence recordings of microtubules in a complex epithelial tissue. Here, we applied a recently proposed deconvolution approach and showed that images obtained from time-gated pulsed STED microscopy may benefit concerning the signal-to-background ratio, from the joint deconvolution of sub-images with different spatial information which were extracted from offline time gating.
Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement.
Towards the assimilation of tree-ring-width records using ensemble Kalman filtering techniques
(2015)
This paper investigates the applicability of the Vaganov–Shashkin–Lite (VSL) forward model for tree-ring-width chronologies as observation operator within a proxy data assimilation (DA) setting. Based on the principle of limiting factors, VSL combines temperature and moisture time series in a nonlinear fashion to obtain simulated TRW chronologies. When used as observation operator, this modelling approach implies three compounding, challenging features: (1) time averaging, (2) “switching recording” of 2 variables and (3) bounded response windows leading to “thresholded response”. We generate pseudo-TRW observations from a chaotic 2-scale dynamical system, used as a cartoon of the atmosphere-land system, and attempt to assimilate them via ensemble Kalman filtering techniques. Results within our simplified setting reveal that VSL’s nonlinearities may lead to considerable loss of assimilation skill, as compared to the utilization of a time-averaged (TA) linear observation operator. In order to understand this undesired effect, we embed VSL’s formulation into the framework of fuzzy logic (FL) theory, which thereby exposes multiple representations of the principle of limiting factors. DA experiments employing three alternative growth rate functions disclose a strong link between the lack of smoothness of the growth rate function and the loss of optimality in the estimate of the TA state. Accordingly, VSL’s performance as observation operator can be enhanced by resorting to smoother FL representations of the principle of limiting factors. This finding fosters new interpretations of tree-ring-growth limitation processes.
XopJ is a Xanthomonas type III effector protein that promotes bacterial virulence on susceptible pepper plants through the inhibition of the host cell proteasome and a resultant suppression of salicylic acid (SA) - dependent defense responses. We show here that Nicotiana benthamiana leaves transiently expressing XopJ display hypersensitive response (HR) -like symptoms when exogenously treated with SA. This apparent avirulence function of XopJ was further dependent on effector myristoylation as well as on an intact catalytic triad, suggesting a requirement of its enzymatic activity for HR-like symptom elicitation. The ability of XopJ to cause a HR-like symptom development upon SA treatment was lost upon silencing of SGT1 and NDR1, respectively, but was independent of EDS1 silencing, suggesting that XopJ is recognized by an R protein of the CC-NBS-LRR class. Furthermore, silencing of NPR1 abolished the elicitation of HR-like symptoms in XopJ expressing leaves after SA application. Measurement of the proteasome activity indicated that proteasome inhibition by XopJ was alleviated in the presence of SA, an effect that was not observed in NPR1 silenced plants. Our results suggest that XopJ - triggered HR-like symptoms are closely related to the virulence function of the effector and that XopJ follows a two-signal model in order to elicit a response in the non-host plant N. benthamiana.
Mitogen-activated dual-specificity MAPK phosphatases are important negative regulators in the MAPK signalling pathways responsible for many essential processes in plants. In a screen for mutants with reduced organ size we have identified a mutation in the active site of the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) that we named tinkerbell (tink) due to its small size. Analysis of the tink mutant indicates that IBR5 acts as a novel regulator of organ size that changes the rate of growth in petals and leaves. Organ size and shape regulation by IBR5 acts independently of the KLU growth-regulatory pathway. Microarray analysis of tink/ibr5-6 mutants identified a likely role for this phosphatase in male gametophyte development. We show that IBR5 may influence the size and shape of petals through auxin and TCP growth regulatory pathways.
There is growing recognition of strong periglacial control on bedrock erosion in mountain landscapes, including the shaping of low-relief surfaces at high elevations (summit flats). But, as yet, the hypothesis that frost action was crucial to the assumed Late Cenozoic rise in erosion rates remains compelling and untested. Here we present a landscape evolution model incorporating two key periglacial processes - regolith production via frost cracking and sediment transport via frost creep - which together are harnessed to variations in temperature and the evolving thickness of sediment cover. Our computational experiments time-integrate the contribution of frost action to shaping mountain topography over million-year timescales, with the primary and highly reproducible outcome being the development of flattish or gently convex summit flats. A simple scaling of temperature to marine delta O-18 records spanning the past 14 Myr indicates that the highest summit flats in mid-to high-latitude mountains may have formed via frost action prior to the Quaternary. We suggest that deep cooling in the Quaternary accelerated mechanical weathering globally by significantly expanding the area subject to frost. Further, the inclusion of subglacial erosion alongside periglacial processes in our computational experiments points to alpine glaciers increasing the long-term efficiency of frost-driven erosion by steepening hillslopes.
With accelerating climate cooling in the late Cenozoic, glacial and periglacial erosion became more widespread on the surface of the Earth. The resultant shift in erosion patterns significantly changed the large-scale morphology of many mountain ranges worldwide. Whereas the glacial fingerprint is easily distinguished by its characteristic fjords and U-shaped valleys, the periglacial fingerprint is more subtle but potentially prevails in some mid- to high-latitude landscapes. Previous models have advocated a frost-driven control on debris production at steep headwalls and glacial valley sides. Here we investigate the important role that periglacial processes also play in less steep parts of mountain landscapes. Understanding the influences of frost-driven processes in low-relief areas requires a focus on the consequences of an accreting soil mantle, which characterises such surfaces. We present a new model that quantifies two key physical processes: frost cracking and frost creep, as a function of both temperature and sediment thickness. Our results yield new insights into how climate and sediment transport properties combine to scale the intensity of periglacial processes. The thickness of the soil mantle strongly modulates the relation between climate and the intensity of mechanical weathering and sediment flux. Our results also point to an offset between the conditions that promote frost cracking and those that promote frost creep, indicating that a stable climate can provide optimal conditions for only one of those processes at a time. Finally, quantifying these relations also opens up the possibility of including periglacial processes in large-scale, long-term landscape evolution models, as demonstrated in a companion paper.
The Global Terrestrial Network for Permafrost (GTN-P) provides the first dynamic database associated with the Thermal State of Permafrost (TSP) and the Circumpolar Active Layer Monitoring (CALM) programs, which extensively collect permafrost temperature and active layer thickness (ALT) data from Arctic, Antarctic and mountain permafrost regions. The purpose of GTN-P is to establish an early warning system for the consequences of climate change in permafrost regions and to provide standardized thermal permafrost data to global models. In this paper we introduce the GTN-P database and perform statistical analysis of the GTN-P metadata to identify and quantify the spatial gaps in the site distribution in relation to climate-effective environmental parameters. We describe the concept and structure of the data management system in regard to user operability, data transfer and data policy. We outline data sources and data processing including quality control strategies based on national correspondents. Assessment of the metadata and data quality reveals 63% metadata completeness at active layer sites and 50% metadata completeness for boreholes.
Voronoi tessellation analysis on the spatial sample distribution of boreholes and active layer measurement sites quantifies the distribution inhomogeneity and provides a potential method to locate additional permafrost research sites by improving the representativeness of thermal monitoring across areas underlain by permafrost. The depth distribution of the boreholes reveals that 73% are shallower than 25m and 27% are deeper, reaching a maximum of 1 km depth. Comparison of the GTN-P site distribution with permafrost zones, soil organic carbon contents and vegetation types exhibits different local to regional monitoring situations, which are illustrated with maps. Preferential slope orientation at the sites most likely causes a bias in the temperature monitoring and should be taken into account when using the data for global models. The distribution of GTN-P sites within zones of projected temperature change show a high representation of areas with smaller expected temperature rise but a lower number of sites within Arctic areas where climate models project extreme temperature increase.
The future of ancient DNA
(2015)
Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.
The recently proposed global monsoon hypothesis interprets monsoon systems as part of one global-scale atmospheric overturning circulation, implying a connection between the regional monsoon systems and an in-phase behaviour of all northern hemispheric monsoons on annual timescales (Trenberth et al., 2000). Whether this concept can be applied to past climates and variability on longer timescales is still under debate, because the monsoon systems exhibit different regional characteristics such as different seasonality (i. e. onset, peak and withdrawal). To investigate the interconnection of different monsoon systems during the pre-industrial Holocene, five transient global climate model simulations have been analysed with respect to the rainfall trend and variability in different sub-domains of the Afro-Asian monsoon region. Our analysis suggests that on millennial timescales with varying orbital forcing, the monsoons do not behave as a tightly connected global system. According to the models, the Indian and North African monsoons are coupled, showing similar rainfall trend and moderate correlation in centennial rainfall variability in all models. The East Asian monsoon changes independently during the Holocene. The dissimilarities in the seasonality of the monsoon sub-systems lead to a stronger response of the North African and Indian monsoon systems to the Holocene insolation forcing than of the East Asian monsoon and affect the seasonal distribution of Holocene rainfall variations. Within the Indian and North African monsoon domain, precipitation solely changes during the summer months, showing a decreasing Holocene precipitation trend. In the East Asian monsoon region, the precipitation signal is determined by an increasing precipitation trend during spring and a decreasing precipitation change during summer, partly balancing each other. A synthesis of reconstructions and the model results do not reveal an impact of the different seasonality on the timing of the Holocene rainfall optimum in the different sub-monsoon systems. Rather they indicate locally inhomogeneous rainfall changes and show that single palaeo-records should not be used to characterise the rainfall change and monsoon evolution for entire monsoon sub-systems.
Background
The flowering plant Primula veris is a common spring blooming perennial that is widely cultivated throughout Europe. This species is an established model system in the study of the genetics, evolution, and ecology of heterostylous floral polymorphisms. Despite the long history of research focused on this and related species, the continued development of this system has been restricted due the absence of genomic and transcriptomic resources.
Results
We present here a de novo draft genome assembly of P. veris covering 301.8 Mb, or approximately 63% of the estimated 479.22 Mb genome, with an N50 contig size of 9.5 Kb, an N50 scaffold size of 164 Kb, and containing an estimated 19,507 genes. The results of a RADseq bulk segregant analysis allow for the confident identification of four genome scaffolds that are linked to the P. veris S-locus. RNAseq data from both P. veris and the closely related species P. vulgaris allow for the characterization of 113 candidate heterostyly genes that show significant floral morph-specific differential expression. One candidate gene of particular interest is a duplicated GLOBOSA homolog that may be unique to Primula (PveGLO2), and is completely silenced in L-morph flowers.
Conclusions
The P. veris genome represents the first genome assembled from a heterostylous species, and thus provides an immensely important resource for future studies focused on the evolution and genetic dissection of heterostyly. As the first genome assembled from the Primulaceae, the P. veris genome will also facilitate the expanded application of phylogenomic methods in this diverse family and the eudicots as a whole.
In this paper, I review observational evidence from spectroscopy and polarimetry for the presence of small and large scale structure in the winds of Wolf-Rayet (WR) stars. Clumping is known to be ubiquitous in the winds of these stars and many of its characteristics can be deduced from spectroscopic time-series and polarisation lightcurves. Conversely, a much smaller fraction of WR stars have been shown to harbour larger scale structures in their wind (∼ 1/5) while they are thought to be present is the winds of most of their O-star ancestors. The reason for this difference is still unknown.
The stress field at depth is a relevant parameter for the design of subsurface constructions and reservoir management. Yet the distortion of the regional stress field due to local-scale features such as sedimentary and tectonic structures or topography is often poorly constrained. We conduct a stress sensitivity analysis using 3-D numerical geomechanical modelling with an elasto-plastic material law to explore the impact of such site-specific features on the stress field in a sedimentary sequence of the Swiss Alpine foreland. The model's dimensions are 14 x 14 x 3 km(3) and it contains 10 units with different mechanical properties, intersected by two regional fault zones. An initial stress state is established involving a semi-empirical relationship between the ratio of horizontal to vertical stress and the overconsolidation ratio of argillaceous sediments. The model results indicate that local topography can affect the stress field significantly to depths greater than the relief contrasts at the surface, especially in conjunction with horizontal tectonic loading. The complexity and frictional properties of faults are also relevant. The greatest variability of the stress field arises across the different sedimentary units. Stress magnitudes and stress anisotropy are much larger in stiffer formations such as massive limestones than in softer argillaceous formations. The stiffer formations essentially carry the load of the far-field forces and are therefore more sensitive to changes of the boundary conditions. This general characteristic of stress distribution in the stiff and soft formations is broadly maintained also with progressive loading towards the plastic limit. The stress field in argillaceous sediments within a stack of formations with strongly contrasting mechanical properties like in the Alpine foreland appears to be relatively insensitive to changes in the tectonic boundary conditions and is largely controlled by the maximum stiffness contrast with respect to the load-bearing formations.
State-dependent foraging
(2015)
Parental care often produces a trade-off between meeting nutritional demands of offspring and the duties of offspring protection, especially in altricial species. Parents have to leave their young unattended for foraging trips, during which nestlings are exposed to predators. We investigated how rodent mothers of altricial young respond to risk of nest predation in their foraging decisions. We studied foraging behavior of lactating bank voles (Myodes glareolus) exposed to a nest predator, the common shrew (Sorex araneus). We conducted the experiment in summer (high resource provisioning for both species) and autumn (less food available) in 12 replicates with fully crossed factors “shrew presence” and “season.” We monitored use of feeding stations near and far from the nest as measurement of foraging activity and strategic foraging behavior. Vole mothers adapted their strategies to shrew presence and optimized their foraging behavior according to seasonal constraints, resulting in an interaction of treatment and season. In summer, shrew presence reduced food intake from feeding stations, while it enhanced intake in autumn. Shrew presence decreased the number of visited feeding stations in autumn and concentrated mother’s foraging efforts to fewer stations. Independent of shrew presence or season, mothers foraged more in patches further away from the nest than near the nest. Results indicate that females are not investing in nest guarding but try to avoid the accumulation of olfactory cues near the nest leading a predator to the young. Additionally, our study shows how foraging strategies and nest attendance are influenced by seasonal food provision.
The Smoothing Spline ANOVA (SS-ANOVA) requires a specialized construction of basis and penalty terms in order to incorporate prior knowledge about the data to be fitted. Typically, one resorts to the most general approach using tensor product splines. This implies severe constraints on the correlation structure, i.e. the assumption of isotropy of smoothness can not be incorporated in general. This may increase the variance of the spline fit, especially if only a relatively small set of observations are given. In this article, we propose an alternative method that allows to incorporate prior knowledge without the need to construct specialized bases and penalties, allowing the researcher to choose the spline basis and penalty according to the prior knowledge of the observations rather than choosing them according to the analysis to be done. The two approaches are compared with an artificial example and with analyses of fixation durations during reading.
Setting the PAS, the role of circadian PAS domain proteins during environmental adaptation in plants
(2015)
The per-ARNT-sim (PAS) domain represents an ancient protein module that can be found across all kingdoms of life. The domain functions as a sensing unit for a diverse array of signals, including molecular oxygen, small metabolites, and light. In plants, several PAS domain-containing proteins form an integral part of the circadian clock and regulate responses to environmental change. Moreover, these proteins function in pathways that control development and plant stress adaptation responses. Here, we discuss the role of PAS domain-containing proteins in anticipation, and adaptation to environmental changes in plants.
Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation.
Roads at risk
(2015)
Globalisation and interregional exchange of people, goods, and services has boosted the importance of and reliance on all kinds of transport networks. The linear structure of road networks is especially sensitive to natural hazards. In southern Norway, steep topography and extreme weather events promote frequent traffic disruption caused by debris flows. Topographic susceptibility and trigger frequency maps serve as input into a hazard appraisal at the scale of first-order catchments to quantify the impact of debris flows on the road network in terms of a failure likelihood of each link connecting two network vertices, e.g. road junctions. We compute total additional traffic loads as a function of traffic volume and excess distance, i.e. the extra length of an alternative path connecting two previously disrupted network vertices using a shortest-path algorithm. Our risk metric of link failure is the total additional annual traffic load, expressed as vehicle kilometres, because of debris-flow-related road closures. We present two scenarios demonstrating the impact of debris flows on the road network and quantify the associated path-failure likelihood between major cities in southern Norway. The scenarios indicate that major routes crossing the central and north-western part of the study area are associated with high link-failure risk. Yet options for detours on major routes are manifold and incur only little additional costs provided that drivers are sufficiently well informed about road closures. Our risk estimates may be of importance to road network managers and transport companies relying on speedy delivery of services and goods.