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In the study of relativistic jets one of the key open questions is their interaction with the environment on the microscopic level. Here, we study the initial evolution of both electron-proton (e(-)-p(+)) and electron-positron (e(+/-)) relativistic jets containing helical magnetic fields, focusing on their interaction with an ambient plasma. We have performed simulations of "global" jets containing helical magnetic fields in order to examine how helical magnetic fields affect kinetic instabilities such as the Weibel instability, the kinetic Kelvin-Helmholtz instability (kKHI) and the Mushroom instability (MI). In our initial simulation study these kinetic instabilities are suppressed and new types of instabilities can grow. In the e(-)-p(+) jet simulation a recollimation-like instability occurs and jet electrons are strongly perturbed. In the e(+/-) jet simulation a recollimation-like instability occurs at early times followed by a kinetic instability and the general structure is similar to a simulation without helical magnetic field. Simulations using much larger systems are required in order to thoroughly follow the evolution of global jets containing helical magnetic fields.
Decreasing groundwater levels in many parts of Germany and decreasing low flows in Central Europe have created a need for adaptation measures to stabilize the water balance and to increase low flows. The objective of our study was to estimate the impact of ditch water level management on stream-aquifer interactions in small lowland catchments of the mid-latitudes. The water balance of a ditch-irrigated area and fluxes between the subsurface and the adjacent stream were modeled for three runoff recession periods using the Hydrus-2D software package. The results showed that the subsurface flow to the stream was closely related to the difference between the water level in the ditch system and the stream. Evapotranspiration during the growing season additionally reduced base flow. It was crucial to stop irrigation during a recession period to decrease water withdrawal from the stream and enhance the base flow by draining the irrigated area. Mean fluxes to the stream were between 0.04 and 0.64 ls(-1) for the first 20 days of the low-flow periods. This only slightly increased the flow in the stream, whose mean was 57 ls(-1) during the period with the lowest flows. Larger areas would be necessary to effectively increase flows in mesoscale catchments.
Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter-and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A2 such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species.
Effects of data and model simplification on the results of a wetland water resource management model
(2016)
This paper presents the development of a wetland water balance model for use in a large river basin with many different wetlands. The basic model was primarily developed for a single wetland with a complex water management system involving large amounts of specialized input data and water management details. The aim was to simplify the model structure and to use only commonly available data as input for the model, with the least possible loss of accuracy. Results from different variants of the model and data adaptation were tested against results from a detailed model. This shows that using commonly available data and unifying and simplifying the input data is tolerable up to a certain level. The simplification of the model has greater effects on the evaluated water balance components than the data adaptation. Because this simplification was necessary for large-scale use, we suggest that, for reasons of comparability, simpler models should always be applied with uniform data bases for large regions, though these should only be moderately simplified. Further, we recommend using these simplified models only for large-scale comparisons and using more specific, detailed models for investigations on smaller scales.
Background:
Skewed body size distributions and the high relative richness of small-bodied taxa are a fundamental
property of a wide range of animal clades. The evolutionary processes responsible for generating these distributions
are well described in vertebrate model systems but have yet to be explored in detail for other major terrestrial
clades. In this study, we explore the macro-evolutionary patterns of body size variation across families of Hexapoda
(insects and their close relatives), using recent advances in phylogenetic understanding, with an aim to investigate
the link between size and diversity within this ancient and highly diverse lineage.
Results:
The maximum, minimum and mean-log body lengths of hexapod families are all approximately log-normally
distributed, consistent with previous studies at lower taxonomic levels, and contrasting with skewed distributions
typical of vertebrate groups. After taking phylogeny and within-tip variation into account, we find no evidence for a
negative relationship between diversification rate and body size, suggesting decoupling of the forces controlling these
two traits. Likelihood-based modeling of the log-mean body size identifies distinct processes operating within
Holometabola and Diptera compared with other hexapod groups, consistent with accelerating rates of size evolution
within these clades, while as a whole, hexapod body size evolution is found to be dominated by neutral processes
including significant phylogenetic conservatism.
Conclusions:
Based on our findings we suggest that the use of models derived from well-studied but atypical clades,
such as vertebrates may lead to misleading conclusions when applied to other major terrestrial lineages. Our results
indicate that within hexapods, and within the limits of current systematic and phylogenetic knowledge, insect
diversification is generally unfettered by size-biased macro-evolutionary processes, and that these processes over large
timescales tend to converge on apparently neutral evolutionary processes. We also identify limitations on available
data within the clade and modeling approaches for the resolution of trees of higher taxa, the resolution of which may
collectively enhance our understanding of this key component of terrestrial ecosystems.
Lake Towuti is a tectonic basin, surrounded by ultramafic rocks. Lateritic soils form through weathering and deliver abundant iron (oxy)hydroxides but very little sulfate to the lake and its sediment. To characterize the sediment biogeochemistry, we collected cores at three sites with increasing water depth and decreasing bottom water oxygen concentrations. Microbial cell densities were highest at the shallow site a feature we attribute to the availability of labile organic matter (OM) and the higher abundance of electron acceptors due to oxic bottom water conditions. At the two other sites, OM degradation and reduction processes below the oxycline led to partial electron acceptor depletion. Genetic information preserved in the sediment as extracellular DNA (eDNA) provided information on aerobic and anaerobic heterotrophs related to Nitrospirae. Chloroflexi, and Therrnoplasmatales. These taxa apparently played a significant role in the degradation of sinking OM. However, eDNA concentrations rapidly decreased with core depth. Despite very low sulfate concentrations, sulfate-reducing bacteria were present and viable in sediments at all three sites, as confirmed by measurement of potential sulfate reduction rates. Microbial community fingerprinting supported the presence of taxa related to Deltaproteobacteria and Firmicutes with demonstrated capacity for iron and sulfate reduction. Concomitantly, sequences of Ruminococcaceae, Clostridiales, and Methanornicrobiales indicated potential for fermentative hydrogen and methane production. Such first insights into ferruginous sediments showed that microbial populations perform successive metabolisms related to sulfur, iron, and methane. In theory, iron reduction could reoxidize reduced sulfur compounds and desorb OM from iron minerals to allow remineralization to methane. Overall, we found that biogeochemical processes in the sediments can be linked to redox differences in the bottom waters of the three sites, like oxidant concentrations and the supply of labile OM. At the scale of the lacustrine record, our geomicrobiological study should provide a means to link the extant subsurface biosphere to past environments.
Background:
All living cells display a rapid molecular response to adverse environmental conditions, and
the heat shock protein family reflects one such example. Hence, failing to activate heat shock proteins can impair
the cellular response. In the present study, we evaluated whether the loss of different isoforms of heat shock
protein (
hsp
) genes in
Caenorhabditis elegans
would affect their vulnerability to Manganese (Mn) toxicity.
Methods:
We exposed wild type and selected
hsp
mutant worms to Mn (30 min) and next evaluated
further the most susceptible strains. We analyzed survi
val, protein carbonylation (as a marker of oxidative
stress) and Parkinson
’
s disease related gene expression immediately after Mn exposure. Lastly, we observed
dopaminergic neurons in wild type worms and in
hsp-70
mutants following Mn treatment. Analysis of the
data was performed by one-way or two way ANOVA, depending on the case, followed by post-hoc
Bonferroni test if the overall
p
value was less than 0.05.
Results:
We verified that the loss of
hsp-70, hsp-3 and chn-1
increased the vulnerability to Mn, as
exposed mutant worms showed lower survival rate and increased protein oxidation. The importance of
hsp-70
against Mn toxicity was then corroborated in dopaminergic neurons, where Mn neurotoxicity was
aggravated. The lack of
hsp-70
also blocked the transcriptional upregulation of
pink1
, a gene that has been
linked to Parkinson
’
sdisease.
Conclusions:
Taken together, our data suggest that Mn exposu
re modulates heat shock protein expression,
particularly HSP-70, in
C. elegans
.Furthermore,lossof
hsp-70
increases protein oxidation and dopaminergic
neuronal degeneration following manganese exposure, which is associated with the inhibition of
pink1
increased expression, thus pot
entially exacerbating the v
ulnerability to this metal.
Background:
Environmental stress puts organisms at risk and requires specific stress-tailored responses to maximize
survival. Long-term exposure to stress necessitates a global reprogramming of the cellular activities at different
levels of gene expression.
Results:
Here, we use ribosome profiling and RNA sequencing to globally profile the adaptive response of
Arabidopsis thaliana
to prolonged heat stress. To adapt to long heat exposure, the expression of many genes is
modulated in a coordinated manner at a transcriptional and translational level. However, a significant group of
genes opposes this trend and shows mainly translational regulation. Different secondary structure elements are
likely candidates to play a role in regulating translation of those genes.
Conclusions:
Our data also uncover on how the subunit stoichiometry of multimeric protein complexes in plastids
is maintained upon heat exposure.
Background:
First metabolomics studies have indicated that metabolic fingerprints from accessible tissues might
be useful to better understand the etiological links between metabolism and cancer. However, there is still a lack
of prospective metabolomics studies on pre-diagnostic metabolic alterations and cancer risk.
Methods:
Associations between pre-diagnostic levels of 120 circulating metabolites (acylcarnitines, amino acids,
biogenic amines, phosphatidylcholines, sphingolipids, and hexoses) and the risks of breast, prostate, and colorectal
cancer were evaluated by Cox regression analyses using data of a prospective case-cohort study including 835
incident cancer cases.
Results:
The median follow-up duration was 8.3 years among non-cases and 6.5 years among incident cases of
cancer. Higher levels of lysophosphatidylcholines (lysoPCs), and especially lysoPC a C18:0, were consistently related
to lower risks of breast, prostate, and colorectal cancer, independent of background factors. In contrast, higher
levels of phosphatidylcholine PC ae C30:0 were associated with increased cancer risk. There was no heterogeneity
in the observed associations by lag time between blood draw and cancer diagnosis.
Conclusion:
Changes in blood lipid composition precede the diagnosis of common malignancies by several years.
Considering the consistency of the present results across three cancer types the observed alterations point to a
global metabolic shift in phosphatidylcholine metabolism that may drive tumorigenesis.
Background
Antiphospholipid antibodies (aPL) can be detected in asymptomatic carriers and infectious patients. The aim was to investigate whether a novel line immunoassay (LIA) differentiates between antiphospholipid syndrome (APS) and asymptomatic aPL+ carriers or patients with infectious diseases (infectious diseases controls (IDC)).
Methods
Sixty-one patients with APS (56 primary, 22/56 with obstetric events only, and 5 secondary), 146 controls including 24 aPL+ asymptomatic carriers and 73 IDC were tested on a novel hydrophobic solid phase coated with cardiolipin (CL), phosphatic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylserine, beta2-glycoprotein I (β2GPI), prothrombin, and annexin V. Samples were also tested by anti-CL and anti-β2GPI ELISAs and for lupus anticoagulant activity. Human monoclonal antibodies (humoAbs) against human β2GPI or PL alone were tested on the same LIA substrates in the absence or presence of human serum, purified human β2GPI or after CL-micelle absorption.
Results
Comparison of LIA with the aPL-classification assays revealed good agreement for IgG/IgM aß2GPI and aCL. Anti-CL and anti-ß2GPI IgG/IgM reactivity assessed by LIA was significantly higher in patients with APS versus healthy controls and IDCs, as detected by ELISA. IgG binding to CL and ß2GPI in the LIA was significantly lower in aPL+ carriers and Venereal Disease Research Laboratory test (VDRL) + samples than in patients with APS. HumoAb against domain 1 recognized β2GPI bound to the LIA-matrix and in anionic phospholipid (PL) complexes. Absorption with CL micelles abolished the reactivity of a PL-specific humoAb but did not affect the binding of anti-β2GPI humoAbs.
Conclusions
The LIA and ELISA have good agreement in detecting aPL in APS, but the LIA differentiates patients with APS from infectious patients and asymptomatic carriers, likely through the exposure of domain 1.
A model analysis of mechanisms for radial microtubular patterns at root hair initiation sites
(2016)
Plant cells have two main modes of growth generating anisotropic structures. Diffuse growth where whole cell walls extend in specific directions, guided by anisotropically positioned cellulose fibers, and tip growth, with inhomogeneous addition of new cell wall material at the tip of the structure. Cells are known to regulate these processes via molecular signals and the cytoskeleton. Mechanical stress has been proposed to provide an input to the positioning of the cellulose fibers via cortical microtubules in diffuse growth. In particular, a stress feedback model predicts a circumferential pattern of fibers surrounding apical tissues and growing primordia, guided by the anisotropic curvature in such tissues. In contrast, during the initiation of tip growing root hairs, a star-like radial pattern has recently been observed. Here, we use detailed finite element models to analyze how a change in mechanical properties at the root hair initiation site can lead to star-like stress patterns in order to understand whether a stress-based feedback model can also explain the microtubule patterns seen during root hair initiation. We show that two independent mechanisms, individually or combined, can be sufficient to generate radial patterns. In the first, new material is added locally at the position of the root hair. In the second, increased tension in the initiation area provides a mechanism. Finally, we describe how a molecular model of Rho-of-plant (ROP) GTPases activation driven by auxin can position a patch of activated ROP protein basally along a 2D root epidermal cell plasma membrane, paving the way for models where mechanical and molecular mechanisms cooperate in the initial placement and outgrowth of root hairs.
Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction showed a remarkable local diversity among isolates assigned to several Nostoc clades. An extensive web of negative allelopathic interactions was recorded at an agricultural site, but not at the undisturbed natural site. The cell extracts of the cyanobacteria did not show antimicrobial activities, but four isolates were shown to be cytotoxic to human cells. The secondary metabolite profiles of the isolates were mapped by MALDI-TOF MS, and the most prominent ions were further analyzed by Q-TOF for MS/MS aided identification. Symbiotic isolates produced a great variety of small peptide-like substances, most of which lack any record in the databases. Among identified compounds we found microcystin and nodularin variants toxic to eukaryotic cells. Microcystin producing chemotypes were dominating as symbiotic recruits but not in the free-living community. In addition, we were able to identify several novel aeruginosins and banyaside-like compounds, as well as nostocyclopeptides and nosperin.
Reversed predator
(2018)
Ecoevolutionary feedbacks in predator–prey systems have been shown to qualitatively alter predator–prey dynamics. As a striking example, defense–offense coevolution can reverse predator–prey cycles, so predator peaks precede prey peaks rather than vice versa. However, this has only rarely been shown in either model studies or empirical systems. Here, we investigate whether this rarity is a fundamental feature of reversed cycles by exploring under which conditions they should be found. For this, we first identify potential conditions and parameter ranges most likely to result in reversed cycles by developing a new measure, the effective prey biomass, which combines prey biomass with prey and predator traits, and represents the prey biomass as perceived by the predator. We show that predator dynamics always follow the dynamics of the effective prey biomass with a classic ¼‐phase lag. From this key insight, it follows that in reversed cycles (i.e., ¾‐lag), the dynamics of the actual and the effective prey biomass must be in antiphase with each other, that is, the effective prey biomass must be highest when actual prey biomass is lowest, and vice versa. Based on this, we predict that reversed cycles should be found mainly when oscillations in actual prey biomass are small and thus have limited impact on the dynamics of the effective prey biomass, which are mainly driven by trait changes. We then confirm this prediction using numerical simulations of a coevolutionary predator–prey system, varying the amplitude of the oscillations in prey biomass: Reversed cycles are consistently associated with regions of parameter space leading to small‐amplitude prey oscillations, offering a specific and highly testable prediction for conditions under which reversed cycles should occur in natural systems.
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.
Relatedness strongly influences social behaviors in a wide variety of species. For most species, the highest typical degree of relatedness is between full siblings with 50% shared genes. However, this is poorly understood in species with unusually high relatedness between individuals: clonal organisms. Although there has been some investigation into clonal invertebrates and yeast, nothing is known about kin selection in clonal vertebrates. We show that a clonal fish, the Amazon molly (Poecilia formosa), can distinguish between different clonal lineages, associating with genetically identical, sister clones, and use multiple sensory modalities. Also, they scale their aggressive behaviors according to the relatedness to other females: they are more aggressive to non-related clones. Our results demonstrate that even in species with very small genetic differences between individuals, kin recognition can be adaptive. Their discriminatory abilities and regulation of costly behaviors provides a powerful example of natural selection in species with limited genetic diversity.
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.
Continuing advances in 'omics methodologies and instrumentation is enhancing the understanding of how plants cope with the dynamic nature of their growing environment. 'Omics platforms have been only recently extended to cover horticultural crop species. Many of the most widely cultivated vegetable crops belong to the genus Brassica: these include plants grown for their root (turnip, rutabaga/swede), their swollen stem base (kohlrabi), their leaves (cabbage, kale, pak choi) and their inflorescence (cauliflower, broccoli). Characterization at the genome, transcript, protein and metabolite levels has illustrated the complexity of the cellular response to a whole series of environmental stresses, including nutrient deficiency, pathogen attack, heavy metal toxicity, cold acclimation, and excessive and sub optimal irradiation. This review covers recent applications of omics technologies to the brassicaceous vegetables, and discusses future scenarios in achieving improvements in crop end-use quality.
Many studies on bacterial community composition (BCC) do not distinguish between particle associated (PA) and free-living (FL) bacteria or neglect the PA fraction by pre-filtration removing most particles. Although temporal and spatial gradients in environmental variables are known to shape BCC, it remains unclear how and to what extent PA and FL bacterial diversity responds to such environmental changes. To elucidate the BCC of both bacterial fractions related to different environmental settings, we studied surface samples of three Baltic Sea stations (marine, mesohaline, and oligohaline) in two different seasons (summer and fall/winter). Amplicon sequencing of the 16S rRNA gene revealed significant differences in BCC of both bacterial fractions among stations and seasons, with a particularly high number of PA operational taxonomic units (OTUs at genus-level) at the marine station in both seasons. "Shannon and Simpson indices" showed a higher diversity of PA than FL bacteria at the marine station in both seasons and at the oligohaline station in fall/winter. In general, a high fraction of bacterial OTUs was found exclusively in the PA fraction (52% of total OTUs). These findings indicate that PA bacteria significantly contribute to overall bacterial richness and that they differ from FL bacteria. Therefore, to gain a deeper understanding on diversity and dynamics of aquatic bacteria, PA and FL bacteria should be generally studied independently.
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.
Robust appraisals of climate impacts at different levels of global-mean temperature increase are vital to guide assessments of dangerous anthropogenic interference with the climate system. The 2015 Paris Agreement includes a two-headed temperature goal: "holding the increase in the global average temperature to well below 2 degrees C above pre-industrial levels and pursuing efforts to limit the temperature increase to 1.5 degrees C". Despite the prominence of these two temperature limits, a comprehensive overview of the differences in climate impacts at these levels is still missing. Here we provide an assessment of key impacts of climate change at warming levels of 1.5 degrees C and 2 degrees C, including extreme weather events, water availability, agricultural yields, sea-level rise and risk of coral reef loss. Our results reveal substantial differences in impacts between a 1.5 degrees C and 2 degrees C warming that are highly relevant for the assessment of dangerous anthropogenic interference with the climate system. For heat-related extremes, the additional 0.5 degrees C increase in global-mean temperature marks the difference between events at the upper limit of present-day natural variability and a new climate regime, particularly in tropical regions. Similarly, this warming difference is likely to be decisive for the future of tropical coral reefs. In a scenario with an end-of-century warming of 2 degrees C, virtually all tropical coral reefs are projected to be at risk of severe degradation due to temperature-induced bleaching from 2050 onwards. This fraction is reduced to about 90% in 2050 and projected to decline to 70% by 2100 for a 1.5 degrees C scenario. Analyses of precipitation-related impacts reveal distinct regional differences and hot-spots of change emerge. Regional reduction in median water availability for the Mediterranean is found to nearly double from 9% to 17% between 1.5 degrees C and 2 degrees C, and the projected lengthening of regional dry spells increases from 7 to 11%. Projections for agricultural yields differ between crop types as well as world regions. While some (in particular high-latitude) regions may benefit, tropical regions like West Africa, South-East Asia, as well as Central and northern South America are projected to face substantial local yield reductions, particularly for wheat and maize. Best estimate sea-level rise projections based on two illustrative scenarios indicate a 50cm rise by 2100 relative to year 2000-levels for a 2 degrees C scenario, and about 10 cm lower levels for a 1.5 degrees C scenario. In a 1.5 degrees C scenario, the rate of sea-level rise in 2100 would be reduced by about 30% compared to a 2 degrees C scenario. Our findings highlight the importance of regional differentiation to assess both future climate risks and different vulnerabilities to incremental increases in global-mean temperature. The article provides a consistent and comprehensive assessment of existing projections and a good basis for future work on refining our understanding of the difference between impacts at 1.5 degrees C and 2 degrees C warming.
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.
Studies investigating the effect of increasing CO2 levels on the phosphorus cycle in natural waters are lacking although phosphorus often controls phytoplankton development in many aquatic systems. The aim of our study was to analyse effects of elevated CO2 levels on phosphorus pool sizes and uptake. The phosphorus dynamic was followed in a CO2-manipulation mesocosm experiment in the Storfjarden (western Gulf of Finland, Baltic Sea) in summer 2012 and was also studied in the surrounding fjord water. In all mesocosms as well as in surface waters of Storfjarden, dissolved organic phosphorus (DOP) concentrations of 0.26aEuro-+/- aEuro-0.03 and 0.23aEuro-+/- aEuro-0.04aEuro-A mu molaEuro-L-1, respectively, formed the main fraction of the total P-pool (TP), whereas phosphate (PO4) constituted the lowest fraction with mean concentration of 0.15aEuro-A +/- aEuro-0.02 in the mesocosms and 0.17aEuro-A +/- aEuro-0.07aEuro-A mu molaEuro-L-1 in the fjord. Transformation of PO4 into DOP appeared to be the main pathway of PO4 turnover. About 82aEuro-% of PO4 was converted into DOP whereby only 18aEuro-% of PO4 was transformed into particulate phosphorus (PP). PO4 uptake rates measured in the mesocosms ranged between 0.6 and 3.9aEuro-nmolaEuro-L(-1)aEuro-h(-1). About 86aEuro-% of them was realized by the size fraction < aEuro-3aEuro-A mu m. Adenosine triphosphate (ATP) uptake revealed that additional P was supplied from organic compounds accounting for 25-27aEuro-% of P provided by PO4 only. CO2 additions did not cause significant changes in phosphorus (P) pool sizes, DOP composition, and uptake of PO4 and ATP when the whole study period was taken into account. However, significant short-term effects were observed for PO4 and PP pool sizes in CO2 treatments > aEuro-1000aEuro-A mu atm during periods when phytoplankton biomass increased. In addition, we found significant relationships (e.g., between PP and Chl a) in the untreated mesocosms which were not observed under high fCO(2) conditions. Consequently, it can be hypothesized that the relationship between PP formation and phytoplankton growth changed with CO2 elevation. It can be deduced from the results, that visible effects of CO2 on P pools are coupled to phytoplankton growth when the transformation of PO4 into POP was stimulated. The transformation of PO4 into DOP on the other hand does not seem to be affected. Additionally, there were some indications that cellular mechanisms of P regulation might be modified under CO2 elevation changing the relationship between cellular constituents.
Introduction
Genes involved in body weight regulation that were previously investigated in genome-wide association studies (GWAS) and in animal models were target-enriched followed by massive parallel next generation sequencing.
Methods
We enriched and re-sequenced continuous genomic regions comprising FTO, MC4R, TMEM18, SDCCAG8, TKNS, MSRA and TBC1D1 in a screening sample of 196 extremely obese children and adolescents with age and sex specific body mass index (BMI) >= 99th percentile and 176 lean adults (BMI <= 15th percentile). 22 variants were confirmed by Sanger sequencing. Genotyping was performed in up to 705 independent obesity trios (extremely obese child and both parents), 243 extremely obese cases and 261 lean adults.
Results and Conclusion
We detected 20 different non-synonymous variants, one frame shift and one nonsense mutation in the 7 continuous genomic regions in study groups of different weight extremes. For SNP Arg695Cys (rs58983546) in TBC1D1 we detected nominal association with obesity (p(TDT) = 0.03 in 705 trios). Eleven of the variants were rare, thus were only detected heterozygously in up to ten individual(s) of the complete screening sample of 372 individuals. Two of them (in FTO and MSRA) were found in lean individuals, nine in extremely obese. In silico analyses of the 11 variants did not reveal functional implications for the mutations. Concordant with our hypothesis we detected a rare variant that potentially leads to loss of FTO function in a lean individual. For TBC1D1, in contrary to our hypothesis, the loss of function variant (Arg443Stop) was found in an obese individual. Functional in vitro studies are warranted.
Solving problems combining task and motion planning requires searching across a symbolic search space and a geometric search space. Because of the semantic gap between symbolic and geometric representations, symbolic sequences of actions are not guaranteed to be geometrically feasible. This compels us to search in the combined search space, in which frequent backtracks between symbolic and geometric levels make the search inefficient. We address this problem by guiding symbolic search with rich information extracted from the geometric level through culprit detection mechanisms.
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.
This study investigates the spatial and temporal distributions of 14 key arboreal taxa and their driving forces during the last 22,000 calendar years before ad 1950 (kyr BP) using a taxonomically harmonized and temporally standardized fossil pollen dataset with a 500-year resolution from the eastern part of continental Asia. Logistic regression was used to estimate pollen abundance thresholds for vegetation occurrence (presence or dominance), based on modern pollen data and present ranges of 14 taxa in China. Our investigation reveals marked changes in spatial and temporal distributions of the major arboreal taxa. The thermophilous (Castanea, Castanopsis, Cyclobalanopsis, Fagus, Pterocarya) and eurythermal (Juglans, Quercus, Tilia, Ulmus) broadleaved tree taxa were restricted to the current tropical or subtropical areas of China during the Last Glacial Maximum (LGM) and spread northward since c. 14.5 kyr BP. Betula and conifer taxa (Abies, Picea, Pinus), in contrast, retained a wider distribution during the LGM and showed no distinct expansion direction during the Late Glacial. Since the late mid-Holocene, the abundance but not the spatial extent of most trees decreased. The changes in spatial and temporal distributions for the 14 taxa are a reflection of climate changes, in particular monsoonal moisture, and, in the late Holocene, human impact. The post-LGM expansion patterns in eastern continental China seem to be different from those reported for Europe and North America, for example, the westward spread for eurythermal broadleaved taxa.
John Birks
(2015)
We describe the career of John Birks as a pioneering scientist who has, over a career spanning five decades, transformed palaeoecology from a largely descriptive to a rigorous quantitative science relevant to contemporary questions in ecology and environmental change. We review his influence on students and colleagues not only at Cambridge and Bergen Universities, his places of primary employment, but also on individuals and research groups in Europe and North America. We also introduce the collection of papers that we have assembled in his honour. The papers are written by his former students and close colleagues and span many of the areas of palaeoecology to which John himself has made major contributions. These include the relationship between ecology and palaeoecology, late-glacial and Holocene palaeoecology, ecological succession, climate change and vegetation history, the role of palaeoecological techniques in reconstructing and understanding the impact of human activity on terrestrial and freshwater ecosystems and numerical analysis of multivariate palaeoecological data.
Efficacy, Safety & Modification of Albuminuria in Type 2 Diabetes Subjects with Renal Disease with LINAgliptin (MARLINA-T2D), a multicentre, multinational, randomized, double-blind, placebo-controlled, parallel-group, phase 3b clinical trial, aims to further define the potential renal effects of dipeptidyl peptidase-4 inhibition beyond glycaemic control. A total of 350 eligible individuals with inadequately controlled type 2 diabetes and evidence of renal disease are planned to be randomized in a 1:1 ratio to receive either linagliptin 5mg or placebo in addition to their stable glucose-lowering background therapy for 24weeks. Two predefined main endpoints will be tested in a hierarchical manner: (1) change from baseline in glycated haemoglobin and (2) time-weighted average of percentage change from baseline in urinary albumin-to-creatinine ratio. Both endpoints are sufficiently powered to test for superiority versus placebo after 24weeks with =0.05. MARLINA-T2D is the first of its class to prospectively explore both the glucose- and albuminuria-lowering potential of a dipeptidyl peptidase-4 inhibitor in patients with type 2 diabetes and evidence of renal disease.
This study examines the course and driving forces of recent vegetation change in the Mongolian steppe. A sediment core covering the last 55years from a small closed-basin lake in central Mongolia was analyzed for its multi-proxy record at annual resolution. Pollen analysis shows that highest abundances of planted Poaceae and highest vegetation diversity occurred during 1977-1992, reflecting agricultural development in the lake area. A decrease in diversity and an increase in Artemisia abundance after 1992 indicate enhanced vegetation degradation in recent times, most probably because of overgrazing and farmland abandonment. Human impact is the main factor for the vegetation degradation within the past decades as revealed by a series of redundancy analyses, while climate change and soil erosion play subordinate roles. High Pediastrum (a green algae) influx, high atomic total organic carbon/total nitrogen (TOC/TN) ratios, abundant coarse detrital grains, and the decrease of C-13(org) and N-15 since about 1977 but particularly after 1992 indicate that abundant terrestrial organic matter and nutrients were transported into the lake and caused lake eutrophication, presumably because of intensified land use. Thus, we infer that the transition to a market economy in Mongolia since the early 1990s not only caused dramatic vegetation degradation but also affected the lake ecosystem through anthropogenic changes in the catchment area.
Recent research has called into question the current practice to estimate individual usual food intake in large-scale studies. In such studies, usual food intake has been defined as diet over the past year. The aim of this review is to summarise the concepts of dietary assessment methods providing food intake data over this time period. A conceptualised framework is given to help researchers to understand the more recent developments to improve dietary assessment in large-scale prospective studies, and also to help to spot the gaps that need to be addressed in future methodological research. The conceptual framework illustrates the current options for the assessment of an individual’s food consumption over 1 year. Ideally, a person’s food intake on each day of this year should be assessed. Due to participants’ burden, and organisational and financial constraints, however, the options are limited to directly requesting the long-term average (e.g. food frequency questionnaires), or selecting a few days with detailed food consumption measurements (e.g. 24-hour dietary recalls) or using snapshot techniques (e.g. barcode scanning of purchases). It seems necessary and important to further evaluate the performance of statistical modelling of the individual usual food intake from all available sources. Future dietary assessment might profit from the growing prominence of internet and telecommunication technologies to further enhance the available data on food consumption for each study participant. Research is crucial to investigate the performance of innovative assessment tools. However, the self-reported nature of the data itself will always lead to bias.
The role of serum amyloid A and sphingosine-1-phosphate on high-density lipoprotein functionality
(2017)
The high-density lipoprotein (HDL) is one of the most important endogenous cardiovascular protective markers. HDL is an attractive target in the search for new pharmaceutical therapies and in the prevention of cardiovascular events. Some of HDL’s anti-atherogenic properties are related to the signaling molecule sphingosine-1-phosphate (S1P), which plays an important role in vascular homeostasis. However, for different patient populations it seems more complicated. Significant changes in HDL’s protective potency are reduced under pathologic conditions and HDL might even serve as a proatherogenic particle. Under uremic conditions especially there is a change in the compounds associated with HDL. S1P is reduced and acute phase proteins such as serum amyloid A (SAA) are found to be elevated in HDL. The conversion of HDL in inflammation changes the functional properties of HDL. High amounts of SAA are associated with the occurrence of cardiovascular diseases such as atherosclerosis. SAA has potent pro-atherogenic properties, which may have impact on HDL’s biological functions, including cholesterol efflux capacity, antioxidative and anti-inflammatory activities. This review focuses on two molecules that affect the functionality of HDL. The balance between functional and dysfunctional HDL is disturbed after the loss of the protective sphingolipid molecule S1P and the accumulation of the acute-phase protein SAA. This review also summarizes the biological activities of lipid-free and lipid-bound SAA and its impact on HDL function.
In order to evade detection by network-traffic analysis, a growing proportion of malware uses the encrypted HTTPS protocol. We explore the problem of detecting malware on client computers based on HTTPS traffic analysis. In this setting, malware has to be detected based on the host IP address, ports, timestamp, and data volume information of TCP/IP packets that are sent and received by all the applications on the client. We develop a scalable protocol that allows us to collect network flows of known malicious and benign applications as training data and derive a malware-detection method based on a neural networks and sequence classification. We study the method's ability to detect known and new, unknown malware in a large-scale empirical study.
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.
A dramatic efficiency improvement of bulk heterojunction solar cells based on electron-donating conjugated polymers in combination with soluble fullerene derivatives has been achieved over the past years. Certified and reported power conversion efficiencies now reach over 9% for single junctions and exceed the 10% benchmark for tandem solar cells. This trend brightens the vision of organic photovoltaics becoming competitive with inorganic solar cells including the realization of low-cost and large-area organic photovoltaics. For the best performing organic materials systems, the yield of charge generation can be very efficient. However, a detailed understanding of the free charge carrier generation mechanisms at the donor acceptor interface and the energy loss associated with it needs to be established. Moreover, organic solar cells are limited by the competition between charge extraction and free charge recombination, accounting for further efficiency losses. A conclusive picture and the development of precise methodologies for investigating the fundamental processes in organic solar cells are crucial for future material design, efficiency optimization, and the implementation of organic solar cells into commercial products.
In order to advance the development of organic photovoltaics, my thesis focuses on the comprehensive understanding of charge generation, recombination and extraction in organic bulk heterojunction solar cells summarized in 6 chapters on the cumulative basis of 7 individual publications.
The general motivation guiding this work was the realization of an efficient hybrid inorganic/organic tandem solar cell with sub-cells made from amorphous hydrogenated silicon and organic bulk heterojunctions. To realize this project aim, the focus was directed to the low band-gap copolymer PCPDTBT and its derivatives, resulting in the examination of the charge carrier dynamics in PCPDTBT:PC70BM blends in relation to by the blend morphology. The phase separation in this blend can be controlled by the processing additive diiodooctane, enhancing domain purity and size. The quantitative investigation of the free charge formation was realized by utilizing and improving the time delayed collection field technique. Interestingly, a pronounced field dependence of the free carrier generation for all blends is found, with the field dependence being stronger without the additive. Also, the bimolecular recombination coefficient for both blends is rather high and increases with decreasing internal field which we suggest to be caused by a negative field dependence of mobility. The additive speeds up charge extraction which is rationalized by the threefold increase in mobility.
By fluorine attachment within the electron deficient subunit of PCPDTBT, a new polymer F-PCPDTBT is designed. This new material is characterized by a stronger tendency to aggregate as compared to non-fluorinated PCPDTBT. Our measurements show that for F-PCPDTBT:PCBM blends the charge carrier generation becomes more efficient and the field-dependence of free charge carrier generation is weakened. The stronger tendency to aggregate induced by the fluorination also leads to increased polymer rich domains, accompanied in a threefold reduction in the non-geminate recombination coefficient at conditions of open circuit. The size of the polymer domains is nicely correlated to the field-dependence of charge generation and the Langevin reduction factor, which highlights the importance of the domain size and domain purity for efficient charge carrier generation. In total, fluorination of PCPDTBT causes the PCE to increase from 3.6 to 6.1% due to enhanced fill factor, short circuit current and open circuit voltage. Further optimization of the blend ratio, active layer thickness, and polymer molecular weight resulted in 6.6% efficiency for F-PCPDTBT:PC70BM solar cells.
Interestingly, the double fluorinated version 2F-PCPDTBT exhibited poorer FF despite a further reduction of geminate and non-geminate recombination losses. To further analyze this finding, a new technique is developed that measures the effective extraction mobility under charge carrier densities and electrical fields comparable to solar cell operation conditions. This method involves the bias enhanced charge extraction technique. With the knowledge of the carrier density under different electrical field and illumination conditions, a conclusive picture of the changes in charge carrier dynamics leading to differences in the fill factor upon fluorination of PCPDTBT is attained. The more efficient charge generation and reduced recombination with fluorination is counterbalanced by a decreased extraction mobility. Thus, the highest fill factor of 60% and efficiency of 6.6% is reached for F-PCPDTBT blends, while 2F-PCPDTBT blends have only moderate fill factors of 54% caused by the lower effective extraction mobility, limiting the efficiency to 6.5%.
To understand the details of the charge generation mechanism and the related losses, we evaluated the yield and field-dependence of free charge generation using time delayed collection field in combination with sensitive measurements of the external quantum efficiency and absorption coefficients for a variety of blends. Importantly, both the yield and field-dependence of free charge generation is found to be unaffected by excitation energy, including direct charge transfer excitation below the optical band gap. To access the non-detectable absorption at energies of the relaxed charge transfer emission, the absorption was reconstructed from the CT emission, induced via the recombination of thermalized charges in electroluminescence. For a variety of blends, the quantum yield at energies of charge transfer emission was identical to excitations with energies well above the optical band-gap. Thus, the generation proceeds via the split-up of the thermalized charge transfer states in working solar cells. Further measurements were conducted on blends with fine-tuned energy levels and similar blend morphologies by using different fullerene derivatives. A direct correlation between the efficiency of free carrier generation and the energy difference of the relaxed charge transfer state relative to the energy of the charge separated state is found. These findings open up new guidelines for future material design as new high efficiency materials require a minimum energetic offset between charge transfer and the charge separated state while keeping the HOMO level (and LUMO level) difference between donor and acceptor as small as possible.
Die Ausstellung "Die Geschichte des Standortes Potsdam-Golm 1935 bis 1991" zeigt die wechselvolle Historie des jetzigen Universitäts- und Wissenschaftsstandortes. Die Ursprünge finden sich in der 1935 errichteten General-Wever-Kaserne. Nach der Beendigung des Zweiten Weltkrieges und bis zur Wende nutzten sowohl die sowjetische Armee als auch das Ministerium für Staatssicherheit das Gelände. Thematisiert werden unter anderem die militärische Zentralregion Brandenburg, die Herausbildung der Geheimdiensthochschule von 1951 bis 1990, die Lehre an dieser Einrichtung, das Studienleben und die Forschungstätigkeit sowie die Nutzung des Standortes nach 1990.
Die Ausstellung besteht aus 13 mit zahlreichen Fotos versehenen Tafeln.
Bacteria respond to changing environmental conditions by switching the global pattern of expressed genes. In response to specific environmental stresses the cell activates several stress-specific molecules such as sigma factors. They reversibly bind the RNA polymerase to form the so-called holoenzyme and direct it towards the appropriate stress response genes. In exponentially growing E. coli cells, the majority of the transcriptional activity is carried out by the housekeeping sigma factor, while stress responses are often under the control of alternative sigma factors. Different sigma factors compete for binding to a limited pool of RNA polymerase (RNAP) core enzymes, providing a mechanism for cross talk between genes or gene classes via the sharing of expression machinery. To quantitatively analyze the contribution of sigma factor competition to global changes in gene expression, we develop a thermodynamic model that describes binding between sigma factors and core RNAP at equilibrium, transcription, non-specific binding to DNA and the modulation of the availability of the molecular components.
Association of housekeeping sigma factor to RNAP is generally favored by its abundance and higher binding affinity to the core. In order to promote transcription by alternative sigma subunits, the bacterial cell modulates the transcriptional efficiency in a reversible manner through several strategies such as anti-sigma factors, 6S RNA and generally any kind of transcriptional regulators (e.g. activators or inhibitors). By shifting the outcome of sigma factor competition for the core, these modulators bias the transcriptional program of the cell. The model is validated by comparison with in vitro competition experiments, with which excellent agreement is found. We observe that transcription is affected via the modulation of the concentrations of the different types of holoenzymes, so saturated promoters are only weakly affected by sigma factor competition. However, in case of overlapping promoters or promoters recognized by two types of sigma factors, we find that even saturated promoters are strongly affected.
Active transcription effectively lowers the affinity between the sigma factor driving it and the core RNAP, resulting in complex cross talk effects and raising the question of how their in vitro measure is relevant in the cell. We also estimate that sigma factor competition is not strongly affected by non-specific binding of core RNAPs, sigma factors, and holoenzymes to DNA. Finally, we analyze the role of increased core RNAP availability upon the shut-down of ribosomal RNA transcription during stringent response. We find that passive up-regulation of alternative sigma-dependent transcription is not only possible, but also displays hypersensitivity based on the sigma factor competition. Our theoretical analysis thus provides support for a significant role of passive control during that global switch of the gene expression program and gives new insights into RNAP partitioning in the cell.
Magnetite is an iron oxide, which is ubiquitous in rocks and is usually deposited as small nanoparticulate matter among other rock material. It differs from most other iron oxides because it contains divalent and trivalent iron. Consequently, it has a special crystal structure and unique magnetic properties. These properties are used for paleoclimatic reconstructions where naturally occurring magnetite helps understanding former geological ages. Further on, magnetic properties are used in bio- and nanotechnological applications –synthetic magnetite serves as a contrast agent in MRI, is exploited in biosensing, hyperthermia or is used in storage media.
Magnetic properties are strongly size-dependent and achieving size control under preferably mild synthesis conditions is of interest in order to obtain particles with required properties. By using a custom-made setup, it was possible to synthesize stable single domain magnetite nanoparticles with the co-precipitation method. Furthermore, it was shown that magnetite formation is temperature-dependent, resulting in larger particles at higher temperatures. However, mechanistic approaches about the details are incomplete.
Formation of magnetite from solution was shown to occur from nanoparticulate matter rather than solvated ions. The theoretical framework of such processes has only started to be described, partly due to the lack of kinetic or thermodynamic data. Synthesis of magnetite nanoparticles at different temperatures was performed and the Arrhenius plot was used determine an activation energy for crystal growth of 28.4 kJ mol-1, which led to the conclusion that nanoparticle diffusion is the rate-determining step.
Furthermore, a study of the alteration of magnetite particles of different sizes as a function of their storage conditions is presented. The magnetic properties depend not only on particle size but also depend on the structure of the oxide, because magnetite oxidizes to maghemite under environmental conditions. The dynamics of this process have not been well described. Smaller nanoparticles are shown to oxidize more rapidly than larger ones and the lower the storage temperature, the lower the measured oxidation. In addition, the magnetic properties of the altered particles are not decreased dramatically, thus suggesting that this alteration will not impact the use of such nanoparticles as medical carriers.
Finally, the effect of biological additives on magnetite formation was investigated. Magnetotactic bacteria¬¬ are able to synthesize and align magnetite nanoparticles of well-defined size and morphology due to the involvement of special proteins with specific binding properties. Based on this model of morphology control, phage display experiments were performed to determine peptide sequences that preferably bind to (111)-magnetite faces. The aim was to control the shape of magnetite nanoparticles during the formation. Magnetotactic bacteria are also able to control the intracellular redox potential with proteins called magnetochromes. MamP is such a protein and its oxidizing nature was studied in vitro via biomimetic magnetite formation experiments based on ferrous ions. Magnetite and further trivalent oxides were found.
This work helps understanding basic mechanisms of magnetite formation and gives insight into non-classical crystal growth. In addition, it is shown that alteration of magnetite nanoparticles is mainly based on oxidation to maghemite and does not significantly influence the magnetic properties. Finally, biomimetic experiments help understanding the role of MamP within the bacteria and furthermore, a first step was performed to achieve morphology control in magnetite formation via co-precipitation.
In the field of disk-based parallel database management systems exists a great variety of solutions based on a shared-storage or a shared-nothing architecture. In contrast, main memory-based parallel database management systems are dominated solely by the shared-nothing approach as it preserves the in-memory performance advantage by processing data locally on each server. We argue that this unilateral development is going to cease due to the combination of the following three trends: a) Nowadays network technology features remote direct memory access (RDMA) and narrows the performance gap between accessing main memory inside a server and of a remote server to and even below a single order of magnitude. b) Modern storage systems scale gracefully, are elastic, and provide high-availability. c) A modern storage system such as Stanford's RAMCloud even keeps all data resident in main memory. Exploiting these characteristics in the context of a main-memory parallel database management system is desirable. The advent of RDMA-enabled network technology makes the creation of a parallel main memory DBMS based on a shared-storage approach feasible.
This thesis describes building a columnar database on shared main memory-based storage. The thesis discusses the resulting architecture (Part I), the implications on query processing (Part II), and presents an evaluation of the resulting solution in terms of performance, high-availability, and elasticity (Part III).
In our architecture, we use Stanford's RAMCloud as shared-storage, and the self-designed and developed in-memory AnalyticsDB as relational query processor on top. AnalyticsDB encapsulates data access and operator execution via an interface which allows seamless switching between local and remote main memory, while RAMCloud provides not only storage capacity, but also processing power. Combining both aspects allows pushing-down the execution of database operators into the storage system. We describe how the columnar data processed by AnalyticsDB is mapped to RAMCloud's key-value data model and how the performance advantages of columnar data storage can be preserved.
The combination of fast network technology and the possibility to execute database operators in the storage system opens the discussion for site selection. We construct a system model that allows the estimation of operator execution costs in terms of network transfer, data processed in memory, and wall time. This can be used for database operators that work on one relation at a time - such as a scan or materialize operation - to discuss the site selection problem (data pull vs. operator push). Since a database query translates to the execution of several database operators, it is possible that the optimal site selection varies per operator. For the execution of a database operator that works on two (or more) relations at a time, such as a join, the system model is enriched by additional factors such as the chosen algorithm (e.g. Grace- vs. Distributed Block Nested Loop Join vs. Cyclo-Join), the data partitioning of the respective relations, and their overlapping as well as the allowed resource allocation.
We present an evaluation on a cluster with 60 nodes where all nodes are connected via RDMA-enabled network equipment. We show that query processing performance is about 2.4x slower if everything is done via the data pull operator execution strategy (i.e. RAMCloud is being used only for data access) and about 27% slower if operator execution is also supported inside RAMCloud (in comparison to operating only on main memory inside a server without any network communication at all). The fast-crash recovery feature of RAMCloud can be leveraged to provide high-availability, e.g. a server crash during query execution only delays the query response for about one second. Our solution is elastic in a way that it can adapt to changing workloads a) within seconds, b) without interruption of the ongoing query processing, and c) without manual intervention.
Pulsar wind nebulae (PWNe) are the most abundant TeV gamma-ray emitters in the Milky Way. The radiative emission of these objects is powered by fast-rotating pulsars, which donate parts of their rotational energy into winds of relativistic particles. This thesis presents an in-depth study of the detected population of PWNe at high energies. To outline general trends regarding their evolutionary behaviour, a time-dependent model is introduced and compared to the available data. In particular, this work presents two exceptional PWNe which protrude from the rest of the population, namely the Crab Nebula and N 157B. Both objects are driven by pulsars with extremely high rotational energy loss rates. Accordingly, they are often referred to as energetic twins. Modelling the non-thermal multi-wavelength emission of N157B gives access to specific properties of this object, like the magnetic field inside the nebula. Comparing the derived parameters to those of the Crab Nebula reveals large intrinsic differences between the two PWNe. Possible origins of these differences are discussed in context of the resembling pulsars.
Compared to the TeV gamma-ray regime, the number of detected PWNe is much smaller in the MeV-GeV gamma-ray range. In the latter range, the Crab Nebula stands out by the recent detection of gamma-ray flares. In general, the measured flux enhancements on short time scales of days to weeks were not expected in the theoretical understanding of PWNe. In this thesis, the variability of the Crab Nebula is analysed using data from the Fermi Large Area Telescope (Fermi-LAT). For the presented analysis, a new gamma-ray reconstruction method is used, providing a higher sensitivity and a lower energy threshold compared to previous analyses. The derived gamma-ray light curve of the Crab Nebula is investigated for flares and periodicity. The detected flares are analysed regarding their energy spectra, and their variety and commonalities are discussed. In addition, a dedicated analysis of the flare which occurred in March 2013 is performed. The derived short-term variability time scale is roughly 6h, implying a small region inside the Crab Nebula to be responsible for the enigmatic flares. The most promising theories explaining the origins of the flux eruptions and gamma-ray variability are discussed in detail.
In the technical part of this work, a new analysis framework is presented. The introduced software, called gammalib/ctools, is currently being developed for the future CTA observa- tory. The analysis framework is extensively tested using data from the H. E. S. S. experiment. To conduct proper data analysis in the likelihood framework of gammalib/ctools, a model describing the distribution of background events in H.E.S.S. data is presented. The software provides the infrastructure to combine data from several instruments in one analysis. To study the gamma-ray emitting PWN population, data from Fermi-LAT and H. E. S. S. are combined in the likelihood framework of gammalib/ctools. In particular, the spectral peak, which usually lies in the overlap energy regime between these two instruments, is determined with the presented analysis framework. The derived measurements are compared to the predictions from the time-dependent model. The combined analysis supports the conclusion of a diverse population of gamma-ray emitting PWNe.