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The objective of this work is twofold. First, we explore the performance of the density functional theory (DFT) when it is applied to solids with strong electronic correlations, such as transition metal compounds. Along this direction, particular effort is put into the refinement and development of parameterization techniques for deriving effective models on a basis of DFT calculations. Second, within the framework of the DFT, we address a number of questions related to the physics of Mott insulators, such as magnetic frustration and electron-phonon coupling (Cs2CuCl4 and Cs2CuBr4), high-temperature superconductivity (BSCCO) and doping of Mott insulators (TiOCl). In the frustrated antiferromagnets Cs2CuCl4 and Cs2CuBr4, we investigate the interplay between strong electronic correlations and magnetism on one hand and electron-lattice coupling on the other as well as the effect of this interplay on the microscopic model parameters. Another object of our investigations is the oxygen-doped cuprate superconductor BSCCO, where nano-scale electronic inhomogeneities have been observed in scanning tunneling spectroscopy experiments. By means of DFT and many-body calculations, we analyze the connection between the structural and electronic inhomogeneities and the superconducting properties of BSCCO. We use the DFT and molecular dynamic simulations to explain the microscopic origin of the persisting under doping Mott insulating state in the layered compound TiOCl.
Regulation of dissimilatory sulfur oxidation in the purple sulfur bacterium Allochromatium vinosum
(2011)
In the purple sulfur bacterium Allochromatium vinosum, thiosulfate oxidation is strictly dependent on the presence of three periplasmic Sox proteins encoded by the soxBXAK and soxYZ genes. It is also well documented that proteins encoded in the dissimilatory sulfite reductase (dsr) operon, dsrABEFHCMKLJOPNRS, are essential for the oxidation of sulfur that is stored intracellularly as an obligatory intermediate during the oxidation of thiosulfate and sulfide. Until recently, detailed knowledge about the regulation of the sox genes was not available. We started to fill this gap and show that these genes are expressed on a low constitutive level in A. vinosum in the absence of reduced sulfur compounds. Thiosulfate and possibly sulfide lead to an induction of sox gene transcription. Additional translational regulation was not apparent. Regulation of soxXAK is probably performed by a two-component system consisting of a multi-sensor histidine kinase and a regulator with proposed di-guanylate cyclase activity. Previous work already provided some information about regulation of the dsr genes encoding the second important sulfur-oxidizing enzyme system in the purple sulfur bacterium. The expression of most dsr genes was found to be at a low basal level in the absence of reduced sulfur compounds and enhanced in the presence of sulfide. In the present work, we focused on the role of DsrS, a protein encoded by the last gene of the dsr locus in A. vinosum. Transcriptional and translational gene fusion experiments suggest a participation of DsrS in the post-transcriptional control of the dsr operon. Characterization of an A. vinosum ΔdsrS mutant showed that the monomeric cytoplasmic 41.1-kDa protein DsrS is important though not essential for the oxidation of sulfur stored in the intracellular sulfur globules.
Forest fragmentation and selective logging are two main drivers of global environmental change and modify biodiversity and environmental conditions in many tropical forests. The consequences of these changes for the functioning of tropical forest ecosystems have rarely been explored in a comprehensive approach. In a Kenyan rainforest, we studied six animal-mediated ecosystem processes and recorded species richness and community composition of all animal taxa involved in these processes. We used linear models and a formal meta-analysis to test whether forest fragmentation and selective logging affected ecosystem processes and biodiversity and used structural equation models to disentangle direct from biodiversity-related indirect effects of human disturbance on multiple ecosystem processes. Fragmentation increased decomposition and reduced antbird predation, while selective logging consistently increased pollination, seed dispersal and army-ant raiding. Fragmentation modified species richness or community composition of five taxa, whereas selective logging did not affect any component of biodiversity. Changes in the abundance of functionally important species were related to lower predation by antbirds and higher decomposition rates in small forest fragments. The positive effects of selective logging on bee pollination, bird seed dispersal and army-ant raiding were direct, i.e. not related to changes in biodiversity, and were probably due to behavioural changes of these highly mobile animal taxa. We conclude that animal-mediated ecosystem processes respond in distinct ways to different types of human disturbance in Kakamega Forest. Our findings suggest that forest fragmentation affects ecosystem processes indirectly by changes in biodiversity, whereas selective logging influences processes directly by modifying local environmental conditions and resource distributions. The positive to neutral effects of selective logging on ecosystem processes show that the functionality of tropical forests can be maintained in moderately disturbed forest fragments. Conservation concepts for tropical forests should thus include not only remaining pristine forests but also functionally viable forest remnants.
Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points.
Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum)×PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes.
In an ongoing clinical phase I/II study, 16 pediatric patients suffering from high risk leukemia/tumors received highly purified donor natural killer (NK) cell immunotherapy (NK-DLI) at day (+3) +40 and +100 post haploidentical stem cell transplantation. However, literature about the influence of NK-DLI on recipient's immune system is scarce. Here we present concomitant results of a noninvasive in vivo monitoring approach of recipient's peripheral blood (PB) cells after transfer of either unstimulated (NK-DLI(unstim)) or IL-2 (1000 U/ml, 9–14 days) activated NK cells (NK-DLI(IL-2 stim)) along with their ex vivo secreted cytokine/chemokines. We performed phenotypical and functional characterizations of the NK-DLIs, detailed flow cytometric analyses of various PB cells and comprehensive cytokine/chemokine arrays before and after NK-DLI. Patients of both groups were comparable with regard to remission status, immune reconstitution, donor chimerism, KIR mismatching, stem cell and NK-DLI dose. Only after NK-DLI(IL-2 stim) was a rapid, almost complete loss of CD56(bright)CD16(dim/−) immune regulatory and CD56(dim)CD16(+) cytotoxic NK cells, monocytes, dendritic cells and eosinophils from PB circulation seen 10 min after infusion, while neutrophils significantly increased. The reduction of NK cells was due to both, a decrease in patients' own CD69(−) NCR(low)CD62L(+) NK cells as well as to a diminishing of the transferred cells from the NK-DLI(IL-2 stim) with the CD56(bright)CD16(+/−)CD69(+)NCR(high)CD62L(−) phenotype. All cell counts recovered within the next 24 h. Transfer of NK-DLI(IL-2 stim) translated into significantly increased levels of various cytokines/chemokines (i.e. IFN-γ, IL-6, MIP-1β) in patients' PB. Those remained stable for at least 1 h, presumably leading to endothelial activation, leukocyte adhesion and/or extravasation. In contrast, NK-DLI(unstim) did not cause any of the observed effects. In conclusion, we assume that the adoptive transfer of NK-DLI(IL-2 stim) under the influence of ex vivo and in vivo secreted cytokines/chemokines may promote NK cell trafficking and therefore might enhance efficacy of immunotherapy.
Temporal information processing in short- and long-term memory of patients with schizophrenia
(2011)
Cognitive deficits of patients with schizophrenia have been largely recognized as core symptoms of the disorder. One neglected factor that contributes to these deficits is the comprehension of time. In the present study, we assessed temporal information processing and manipulation from short- and long-term memory in 34 patients with chronic schizophrenia and 34 matched healthy controls. On the short-term memory temporal-order reconstruction task, an incidental or intentional learning strategy was deployed. Patients showed worse overall performance than healthy controls. The intentional learning strategy led to dissociable performance improvement in both groups. Whereas healthy controls improved on a performance measure (serial organization), patients improved on an error measure (inappropriate semantic clustering) when using the intentional instead of the incidental learning strategy. On the long-term memory script-generation task, routine and non-routine events of everyday activities (e.g., buying groceries) had to be generated in either chronological or inverted temporal order. Patients were slower than controls at generating events in the chronological routine condition only. They also committed more sequencing and boundary errors in the inverted conditions. The number of irrelevant events was higher in patients in the chronological, non-routine condition. These results suggest that patients with schizophrenia imprecisely access temporal information from short- and long-term memory. In short-term memory, processing of temporal information led to a reduction in errors rather than, as was the case in healthy controls, to an improvement in temporal-order recall. When accessing temporal information from long-term memory, patients were slower and committed more sequencing, boundary, and intrusion errors. Together, these results suggest that time information can be accessed and processed only imprecisely by patients who provide evidence for impaired time comprehension. This could contribute to symptomatic cognitive deficits and strategic inefficiency in schizophrenia.
Background: Oral anticoagulant therapy (OAT) with warfarin is the standard of stroke prevention in patients with atrial fibrillation. Approximately 30% of patients with cardioembolic strokes are on OAT at the time of symptom onset. We investigated whether warfarin exacerbates the risk of thrombolysis-associated hemorrhagic transformation (HT) in a mouse model of ischemic stroke.
Methods: 62 C57BL/6 mice were used for this study. To achieve effective anticoagulation, warfarin was administered orally. We performed right middle cerebral artery occlusion (MCAO) for 3 h and assessed functional deficit and HT blood volume after 24 h.
Results: In non-anticoagulated mice, treatment with rt-PA (10 mg/kg i.v.) after 3 h MCAO led to a 5-fold higher degree of HT compared to vehicle-treated controls (4.0±0.5 µl vs. 0.8±0.1, p<0.001). Mice on warfarin revealed larger amounts of HT after rt-PA treatment in comparison to non-anticoagulated mice (9.2±3.2 µl vs. 2.8±1.0, p<0.05). The rapid reversal of anticoagulation by means of prothrombin complex concentrates (PCC, 100 IU/kg) at the end of the 3 h MCAO period, but prior to rt-PA administration, neutralized the exacerbated risk of HT as compared to sham-treated controls (3.8±0.7 µl vs. 15.0±3.8, p<0.001).
Conclusion: In view of the vastly increased risk of HT, it seems to be justified to withhold tPA therapy in effectively anticoagulated patients with acute ischemic stroke. The rapid reversal of anticoagulation with PCC prior to tPA application reduces the risk attributed to warfarin pretreatment and may constitute an interesting therapeutic option.
Recent work has demonstrated that the formation of platelet neutrophil complexes (PNCs) affects inflammatory tissue injury. Vasodilator-stimulated phosphoprotein (VASP) is crucially involved into the control of PNC formation and myocardial reperfusion injury. Given the clinical importance of hepatic IR injury we pursued the role of VASP during hepatic ischemia followed by reperfusion. We report here that VASP−/− animals demonstrate reduced hepatic IR injury compared to wildtype (WT) controls. This correlated with serum levels of lactate dehydrogenase (LDH), aspartate (AST) and alanine (ALT) aminotransferase and the presence of PNCs within ischemic hepatic tissue and could be confirmed using repression of VASP through siRNA. In studies employing bone marrow chimeric mice we identified hematopoietic VASP to be of crucial importance for the extent of hepatic injury. Phosphorylation of VASP on Ser153 through Prostaglandin E1 or on Ser235 through atrial natriuretic peptide resulted in a significant reduction of hepatic IR injury. This was associated with a reduced presence of PNCs in ischemic hepatic tissue. Taken together, these studies identified VASP and VASP phosphorylation as crucial target for future hepatoprotective strategies.
Accumulating evidence indicates that increased generation of reactive oxygen species (ROS) contributes to the development of exaggerated pain hypersensitivity during persistent pain. In the present study, we investigated the antinociceptive efficacy of the antioxidants vitamin C and vitamin E in mouse models of inflammatory and neuropathic pain. We show that systemic administration of a combination of vitamins C and E inhibited the early behavioral responses to formalin injection and the neuropathic pain behavior after peripheral nerve injury, but not the inflammatory pain behavior induced by Complete Freund's Adjuvant. In contrast, vitamin C or vitamin E given alone failed to affect the nociceptive behavior in all tested models. The attenuated neuropathic pain behavior induced by the vitamin C and E combination was paralleled by a reduced p38 phosphorylation in the spinal cord and in dorsal root ganglia, and was also observed after intrathecal injection of the vitamins. Moreover, the vitamin C and E combination ameliorated the allodynia induced by an intrathecally delivered ROS donor. Our results suggest that administration of vitamins C and E in combination may exert synergistic antinociceptive effects, and further indicate that ROS essentially contribute to nociceptive processing in special pain states.
Parasites of the nematode genus Anisakis are associated with aquatic organisms. They can be found in a variety of marine hosts including whales, crustaceans, fish and cephalopods and are known to be the cause of the zoonotic disease anisakiasis, a painful inflammation of the gastro-intestinal tract caused by the accidental consumptions of infectious larvae raw or semi-raw fishery products. Since the demand on fish as dietary protein source and the export rates of seafood products in general is rapidly increasing worldwide, the knowledge about the distribution of potential foodborne human pathogens in seafood is of major significance for human health. Studies have provided evidence that a few Anisakis species can cause clinical symptoms in humans. The aim of our study was to interpolate the species range for every described Anisakis species on the basis of the existing occurrence data. We used sequence data of 373 Anisakis larvae from 30 different hosts worldwide and previously published molecular data (n = 584) from 53 field-specific publications to model the species range of Anisakis spp., using a interpolation method that combines aspects of the alpha hull interpolation algorithm as well as the conditional interpolation approach. The results of our approach strongly indicate the existence of species-specific distribution patterns of Anisakis spp. within different climate zones and oceans that are in principle congruent with those of their respective final hosts. Our results support preceding studies that propose anisakid nematodes as useful biological indicators for their final host distribution and abundance as they closely follow the trophic relationships among their successive hosts. The modeling might although be helpful for predicting the likelihood of infection in order to reduce the risk of anisakiasis cases in a given area.
Acanthocephalans are attractive candidates as model organisms for studying the ecology and co-evolutionary history of parasitic life cycles in the marine ecosystem. Adding to earlier molecular analyses of this taxon, a total of 36 acanthocephalans belonging to the classes Archiacanthocephala (3 species), Eoacanthocephala (3 species), Palaeacanthocephala (29 species), Polyacanthocephala (1 species) and Rotifera as outgroup (3 species) were analyzed by using Bayesian Inference and Maximum Likelihood analyses of nuclear 18S rDNA sequence. This data set included three re-collected and six newly collected taxa, Bolbosoma vasculosum from Lepturacanthus savala, Filisoma rizalinum from Scatophagus argus, Rhadinorhynchus pristis from Gempylus serpens, R. lintoni from Selar crumenophthalmus, Serrasentis sagittifer from Johnius coitor, and Southwellina hispida from Epinephelus coioides, representing 5 new host and 3 new locality records. The resulting trees suggest a paraphyletic arrangement of the Echinorhynchida and Polymorphida inside the Palaeacanthocephala. This questions the placement of the genera Serrasentis and Gorgorhynchoides within the Echinorhynchida and not the Polymorphida, necessitating further insights into the systematic position of these taxa based on morphology.
Recent phylogenomic studies have failed to conclusively resolve certain branches of the placental mammalian tree, despite the evolutionary analysis of genomic data from 32 species. Previous analyses of single genes and retroposon insertion data yielded support for different phylogenetic scenarios for the most basal divergences. The results indicated that some mammalian divergences were best interpreted not as a single bifurcating tree, but as an evolutionary network. In these studies the relationships among some orders of the super-clade Laurasiatheria were poorly supported, albeit not studied in detail. Therefore, 4775 protein-coding genes (6,196,263 nucleotides) were collected and aligned in order to analyze the evolution of this clade. Additionally, over 200,000 introns were screened in silico, resulting in 32 phylogenetically informative long interspersed nuclear elements (LINE) insertion events.
The present study shows that the genome evolution of Laurasiatheria may best be understood as an evolutionary network. Thus, contrary to the common expectation to resolve major evolutionary events as a bifurcating tree, genome analyses unveil complex speciation processes even in deep mammalian divergences. We exemplify this on a subset of 1159 suitable genes that have individual histories, most likely due to incomplete lineage sorting or introgression, processes that can make the genealogy of mammalian genomes complex.
These unexpected results have major implications for the understanding of evolution in general, because the evolution of even some higher level taxa such as mammalian orders may sometimes not be interpreted as a simple bifurcating pattern.
Background: Fishes show an amazing diversity in hearing abilities, inner ear structures, and otolith morphology. Inner ear morphology, however, has not yet been investigated in detail in any member of the diverse order Cyprinodontiformes. We, therefore, studied the inner ear of the cyprinodontiform freshwater fish Poecilia mexicana by analyzing the position of otoliths in situ, investigating the 3D structure of sensory epithelia, and examining the orientation patterns of ciliary bundles of the sensory hair cells, while combining μ-CT analyses, scanning electron microscopy, and immunocytochemical methods. P. mexicana occurs in different ecotypes, enabling us to study the intra-specific variability (on a qualitative basis) of fish from regular surface streams, and the Cueva del Azufre, a sulfidic cave in southern Mexico.
Results: The inner ear of Poecilia mexicana displays a combination of several remarkable features. The utricle is connected rostrally instead of dorso-rostrally to the saccule, and the macula sacculi, therefore, is very close to the utricle. Moreover, the macula sacculi possesses dorsal and ventral bulges. The two studied ecotypes of P. mexicana showed variation mainly in the shape and curvature of the macula lagenae, in the curvature of the macula sacculi, and in the thickness of the otolithic membrane.
Conclusions: Our study for the first time provides detailed insights into the auditory periphery of a cyprinodontiform inner ear and thus serves a basis—especially with regard to the application of 3D techniques—for further research on structure-function relationships of inner ears within the species-rich order Cyprinodontiformes. We suggest that other poeciliid taxa, or even other non-poeciliid cyprinodontiforms, may display similar inner ear morphologies as described here.
The duration of use is usually significantly longer for marine vessels than for roadside vehicles. Therefore, these vessels are often powered by relatively old engines which may propagate air pollution. Also, the quality of fuel used for marine vessels is usually not comparable to the quality of fuels used in the automotive sector and therefore, port areas may exhibit a high degree of air pollution. In contrast to the multitude of studies that addressed outdoor air pollution due to road traffic, only little is known about ship-related air pollution. Therefore the present article aims to summarize recent studies that address air pollution, i.e. particulate matter exposure, due to marine vessels. It can be stated that the data in this area of research is still largely limited. Especially, knowledge on the different air pollutions in different sea areas is needed.
Background: Drowning is a constant global problem which claims proximately half a million victims worldwide each year, whereas the number of near-drowning victims is considerably higher. Public health strategies to reduce the burden of death are still limited. While research activities in the subject drowning grow constantly, yet there is no scientometric evaluation of the existing literature at the present time.
Methods: The current study uses classical bibliometric tools and visualizing techniques such as density equalizing mapping to analyse and evaluate the scientific research in the field of drowning. The interpretation of the achieved results is also implemented in the context of the data collection of the WHO.
Results: All studies related to drowning and listed in the ISI-Web of Science database since 1900 were identified using the search term "drowning". Implementing bibliometric methods, a constant increase in quantitative markers such as number of publications per state, publication language or collaborations as well as qualitative markers such as citations were observed for research in the field of drowning. The combination with density equalizing mapping exposed different global patterns for research productivity and the total number of drowning deaths and drowning rates respectively. Chart techniques were used to illustrate bi- and multilateral research cooperation.
Conclusions: The present study provides the first scientometric approach that visualizes research activity on the subject of drowning. It can be assumed that the scientific approach to this topic will achieve even greater dimensions because of its continuing actuality.
Background: Closely related lineages of livebearing fishes have independently adapted to two extreme environmental factors: toxic hydrogen sulphide (H2S) and perpetual darkness. Previous work has demonstrated in adult specimens that fish from these extreme habitats convergently evolved drastically increased head and offspring size, while cave fish are further characterized by reduced pigmentation and eye size. Here, we traced the development of these (and other) divergent traits in embryos of Poecilia mexicana from benign surface habitats (“surface mollies”) and a sulphidic cave (“cave mollies”), as well as in embryos of the sister taxon, Poecilia sulphuraria from a sulphidic surface spring (“sulphur mollies”). We asked at which points during development changes in the timing of the involved processes (i.e., heterochrony) would be detectible.
Methods and Results: Data were extracted from digital photographs taken of representative embryos for each stage of development and each type of molly. Embryo mass decreased in convergent fashion, but we found patterns of embryonic fat content and ovum/embryo diameter to be divergent among all three types of mollies. The intensity of yellow colouration of the yolk (a proxy for carotenoid content) was significantly lower in cave mollies throughout development. Moreover, while relative head size decreased through development in surface mollies, it increased in both types of extremophile mollies, and eye growth was arrested in mid-stage embryos of cave mollies but not in surface or sulphur mollies.
Conclusion: Our results clearly demonstrate that even among sister taxa convergence in phenotypic traits is not always achieved by the same processes during embryo development. Furthermore, teleost development is crucially dependent on sufficient carotenoid stores in the yolk, and so we discuss how the apparent ability of cave mollies to overcome this carotenoid-dependency may represent another potential mechanism explaining the lack of gene flow between surface and cave mollies.
Background and Objective: The slow delayed rectifier current (IKs) is important for cardiac action potential termination. The underlying channel is composed of Kv7.1 α-subunits and KCNE1 β-subunits. While most evidence suggests a role of KCNE1 transmembrane domain and C-terminus for the interaction, the N-terminal KCNE1 polymorphism 38G is associated with reduced IKs and atrial fibrillation (a human arrhythmia). Structure-function relationship of the KCNE1 N-terminus for IKs modulation is poorly understood and was subject of this study.
Methods: We studied N-terminal KCNE1 constructs disrupting structurally important positively charged amino-acids (arginines) at positions 32, 33, 36 as well as KCNE1 constructs that modify position 38 including an N-terminal truncation mutation. Experimental procedures included molecular cloning, patch-clamp recording, protein biochemistry, real-time-PCR and confocal microscopy.
Results: All KCNE1 constructs physically interacted with Kv7.1. IKs resulting from co-expression of Kv7.1 with non-atrial fibrillation ‘38S’ was greater than with any other construct. Ionic currents resulting from co-transfection of a KCNE1 mutant with arginine substitutions (‘38G-3xA’) were comparable to currents evoked from cells transfected with an N-terminally truncated KCNE1-construct (‘Δ1-38’). Western-blots from plasma-membrane preparations and confocal images consistently showed a greater amount of Kv7.1 protein at the plasma-membrane in cells co-transfected with the non-atrial fibrillation KCNE1-38S than with any other construct.
Conclusions: The results of our study indicate that N-terminal arginines in positions 32, 33, 36 of KCNE1 are important for reconstitution of IKs. Furthermore, our results hint towards a role of these N-terminal amino-acids in membrane representation of the delayed rectifier channel complex.
Background: MicroRNA-21 (miR-21) is up-regulated in tumor tissue of patients with malignant diseases, including hepatocellular carcinoma (HCC). Elevated concentrations of miR-21 have also been found in sera or plasma from patients with malignancies, rendering it an interesting candidate as serum/plasma marker for malignancies. Here we correlated serum miR-21 levels with clinical parameters in patients with different stages of chronic hepatitis C virus infection (CHC) and CHC-associated HCC.
Methodology/Principal Findings: 62 CHC patients, 29 patients with CHC and HCC and 19 healthy controls were prospectively enrolled. RNA was extracted from the sera and miR-21 as well as miR-16 levels were analyzed by quantitative real-time PCR; miR-21 levels (normalized by miR-16) were correlated with standard liver parameters, histological grading and staging of CHC. The data show that serum levels of miR-21 were elevated in patients with CHC compared to healthy controls (P<0.001); there was no difference between serum miR-21 in patients with CHC and CHC-associated HCC. Serum miR-21 levels correlated with histological activity index (HAI) in the liver (r = −0.494, P = 0.00002), alanine aminotransferase (ALT) (r = −0.309, P = 0.007), aspartate aminotransferase (r = −0.495, P = 0.000007), bilirubin (r = −0.362, P = 0.002), international normalized ratio (r = −0.338, P = 0.034) and γ-glutamyltransferase (r = −0.244, P = 0.034). Multivariate analysis revealed that ALT and miR-21 serum levels were independently associated with HAI. At a cut-off dCT of 1.96, miR-21 discriminated between minimal and mild-severe necroinflammation (AUC = 0.758) with a sensitivity of 53.3% and a specificity of 95.2%.
Conclusions/Significance: The serum miR-21 level is a marker for necroinflammatory activity, but does not differ between patients with HCV and HCV-induced HCC.
Although climate is known to be one of the key factors determining animal species distributions amongst others, projections of global change impacts on their distributions often rely on bioclimatic envelope models. Vegetation structure and landscape configuration are also key determinants of distributions, but they are rarely considered in such assessments. We explore the consequences of using simulated vegetation structure and composition as well as its associated landscape configuration in models projecting global change effects on Iberian bird species distributions. Both present-day and future distributions were modelled for 168 bird species using two ensemble forecasting methods: Random Forests (RF) and Boosted Regression Trees (BRT). For each species, several models were created, differing in the predictor variables used (climate, vegetation, and landscape configuration). Discrimination ability of each model in the present-day was then tested with four commonly used evaluation methods (AUC, TSS, specificity and sensitivity). The different sets of predictor variables yielded similar spatial patterns for well-modelled species, but the future projections diverged for poorly-modelled species. Models using all predictor variables were not significantly better than models fitted with climate variables alone for ca. 50% of the cases. Moreover, models fitted with climate data were always better than models fitted with landscape configuration variables, and vegetation variables were found to correlate with bird species distributions in 26–40% of the cases with BRT, and in 1–18% of the cases with RF. We conclude that improvements from including vegetation and its landscape configuration variables in comparison with climate only variables might not always be as great as expected for future projections of Iberian bird species.
Functional near-infrared spectroscopy (fNIRS) is an established optical neuroimaging method for measuring functional hemodynamic responses to infer neural activation. However, the impact of individual anatomy on the sensitivity of fNIRS measuring hemodynamics within cortical gray matter is still unknown. By means of Monte Carlo simulations and structural MRI of 23 healthy subjects (mean age: (25.0 +- 2.8 years), we characterized the individual distribution of tissue-specific NIR-light absorption underneath 24 prefrontal fNIRS channels. We, thereby, investigated the impact of scalp-cortex distance (SCD), frontal sinus volume as well as sulcal morphology on gray matter volumes (V gray) traversed by NIR-light, i.e. anatomy-dependent fNIRS sensitivity. The NIR-light absorption between optodes was distributed describing a rotational ellipsoid with a mean penetration depth of (23.6 +- 0.7 mm) considering the deepest 5% of light. Of the detected photon packages scalp and bone absorbed (96.4 +- 9.7)% and absorbed (3,1 +- 1.8)% of the energy. The mean V gray volume (1.1 +- 0.4)cm 3 was negatively correlated (r = -.76) with the SCD and frontal sinus volume (r= -.57) and was reduced by in subjects with relatively large compared to small frontal sinus. Head circumference was significantly positively correlated with the mean SCD (r= .46) and the traversed frontal sinus volume (r= .43). Sulcal morphology had no significant impact on . Our findings suggest to consider individual SCD and frontal sinus volume as anatomical factors impacting fNIRS sensitivity. Head circumference may represent a practical measure to partly control for these sources of error variance.
Various optimality principles have been proposed to explain the characteristics of coordinated eye and head movements during visual orienting behavior. At the same time, researchers have suggested several neural models to underly the generation of saccades, but these do not include online learning as a mechanism of optimization. Here, we suggest an open-loop neural controller with a local adaptation mechanism that minimizes a proposed cost function. Simulations show that the characteristics of coordinated eye and head movements generated by this model match the experimental data in many aspects, including the relationship between amplitude, duration and peak velocity in head-restrained and the relative contribution of eye and head to the total gaze shift in head-free conditions. Our model is a first step towards bringing together an optimality principle and an incremental local learning mechanism into a unified control scheme for coordinated eye and head movements.
This paper considers the logic FOcard, i.e., first-order logic with cardinality predicates that can specify the size of a structure modulo some number. We study the expressive power of FOcard on the class of languages of ranked, finite, labelled trees with successor relations. Our first main result characterises the class of FOcard-definable tree languages in terms of algebraic closure properties of the tree languages. As it can be effectively checked whether the language of a given tree automaton satisfies these closure properties, we obtain a decidable characterisation of the class of regular tree languages definable in FOcard. Our second main result considers first-order logic with unary relations, successor relations, and two additional designated symbols < and + that must be interpreted as a linear order and its associated addition. Such a formula is called addition-invariant if, for each fixed interpretation of the unary relations and successor relations, its result is independent of the particular interpretation of < and +. We show that the FOcard-definable tree languages are exactly the regular tree languages definable in addition-invariant first-order logic. Our proof techniques involve tools from algebraic automata theory, reasoning with locality arguments, and the use of logical interpretations. We combine and extend methods developed by Benedikt and Segoufin (ACM ToCL, 2009) and Schweikardt and Segoufin (LICS, 2010).
Membrane proteins (MPs) constitute about 30% of the genome and are essential in many cellular processes. In particular structural characterisation of MPs is challenged by their hydrophobic nature resulting in expression difficulties and structural instability upon extraction from the membrane. Despite these challenges, progress in sample preparation and the techniques to solve MP structures has led to 281 unique MP structures as of January 2011. Through the combination of a cell-free expression system and selective labelling strategies, this thesis aimed to advance the structure determination of α-helical MPs by NMR spectroscopy and resulted in the structure determination of a seven-ransmembrane-helix protein. Results were obtained for the 5-lipoxygenase-activating protein (FLAP) and proteorhodopsin (PR). The detergent-based cell-free expression mode proved most efficient for production of both targets, but optimisation of FLAP and PR followed different routes. The presence of a retinal cofactor in PR greatly facilitated the search for an appropriate hydrophobic environment. For structural studies, NMR spectra of FLAP indicated favourable properties of the lysolipid LPPG. In contrast, PR was stable and homogenous in the short-chain lipid diC7PC. As NMR spectra of α-helical MPs are generally characterised by broad lines and signal overlap, selective labelling strategies were essential in the assignment process of both targets. For the backbone assignment of FLAP the transmembrane segment-enhanced (TMS) labelling was developed, employing the six amino acids AFGILV. These residues cluster predominantly in transmembrane helices and form long stretches allowing a large extent of backbone assignment. Besides that, the combinatorial labelling enables identification of unique pairs in the sequence based on a mixture of 15N and 1-13C-labelled amino acids. To find the optimal labelling pattern for a given primary structure, the UPLABEL algorithm has been made available and successfully applied in the backbone assignment of PR. Both selective labelling approaches greatly benefitted from the use of a cell-free expression system to reduce isotope scrambling. Additionally, the de novo structure of PR was determined with an average backbone rmsd of 1.2 Å based on TALOS-derived backbone torsion angles, intrahelical hydrogen bond restraints and distance restraints from the NOE and paramagnetic relaxation enhancement (PRE). A major bottleneck in the NMR structure determination of MPs concerns the number of long-range distances which are often limited. In PR, side chain assignment was enabled by stereo-array isotope labelling as well as selective labelling which provided 33 long-range NOEs. These NOEs stabilised the symmetry of the seven helix bundle. With a total number of 1031, the majority of long-range distances were derived from PREs. The structure of PR reveals differences to its homologues such as the absence of an anti-parallel β-sheet between helices B and C and allows conclusions towards the mechanism of colour tuning.
The role of small leucine-rich proteoglycans, biglycan and decorin, in podocytopathy and albuminuria
(2011)
Biglycan is a member of the small leucine-rich proteoglycan (SLRP) family and is involved in the assembly of extracellular matrix components. In macrophages soluble biglycan acts as an endogenous ligand of the innate immunity receptors TLR2 and TLR4. Data addressing the role of biglycan in renal pathology are surprisingly limited. In a normal kidney, biglycan is expressed mainly in the tubulointerstitium; however, in the course of various renal diseases its expression may be altered. The biological role and mechanisms of biglycan action in the pathology of renal diseases, especially those affecting glomeruli, remain poorly understood.
Albuminuria is the first detectable clinical abnormality in diabetic nephropathy. In this study we detected increased biglycan mRNA expression in glomeruli of renal biopsies of patients with incipient diabetic nephropathy, with predominant localization in podocytes. This novel finding raised the question about the role and mechanisms of biglycan action in diabetic podocyte injury and whether the mechanisms of biglycan signaling causing podocyte injury and albuminuria could be extrapolated to other glomerular diseases.
To investigate the role of biglycan in the cause of diabetic podocyte injury and albuminuria we used the murine model of STZ-induced diabetic nephropathy and wild type (Bgn+/0) and biglycan deficient (Bgn-/0) mice. We observed that biglycan was expressed on mRNA and protein levels in podocytes of diabetic Bgn+/0 mice and that diabetic Bgn+/0 mice also had significantly higher albuminuria compared to non-diabetic mice 6 and 12 weeks after disease induction. Biglycan deficiency was shown to be an important factor in albuminuria development. Namely, we observed that diabetic Bgn-/0 mice had significantly lower levels of urinary albumin compared to diabetic Bgn+/0 mice. We showed that less severe podocyte loss in the urine of diabetic Bgn-/0 mice was associated with significantly higher nephrin and podocin glomerular expression compared to diabetic Bgn+/0 mice. Our data suggested that biglycan deficiency was protective against podocyte loss into urine and might be beneficial against development of albuminuria in diabetes.
Biglycan contributed to podocyte actin rearrangement due to increased phosphorylation of Rac1 in vitro. Furthermore, biglycan induced caspase-3 activity and production of reactive oxygen species (ROS), thus enhancing apoptosis in cultured podocytes. Biglycan-induced ROS generation was TLR2/TLR4-dependent. Overexpression of soluble biglycan in wild type mice induced albuminuria under normal conditions and significantly increased albuminuria under pathological conditions (murine model of LPS-induced albuminuria). Inhibition of Rac1 activity in vivo decreased the albuminuria induced by biglycan overexpression. In patients with glomerular diseases, biglycan was detected in urine and was associated with nephrin appearance in the urine of these patients and with increased albuminuria. Collectively, our results elucidate a novel mechanism for biglycan-induced TLR2- and TLR4-dependent, Rac1- and ROS-mediated podocytopathy leading to podocyturia, albuminuria development and progression of glomerular diseases. Interfering with biglycan actions and blocking its signaling via TLR2 and TLR4 might be a potential therapeutic strategy against these diseases. To achieve this goal, the specific mechanisms for binding of biglycan to TLR2 and TLR4 must be elucidated and effective ways of preventing this binding must be developed. Nevertheless, biglycan remains the “danger signal” that activates innate immune receptors in non-immune cells and triggers the deleterious mechanisms leading to aggravation of renal injury.
Soil biogenic NO emissions (SNOx) play important direct and indirect roles in chemical processes of the troposphere. The most widely applied algorithm to calculate SNOx in global models was published 15 years ago by Yienger and Levy (1995), was based on very few measurements. Since then numerous new measurements have been published, which we used to build up a atabase of field measurements conducted world wide covering the period from 1978 to 2009, including 108 publications with 560 measurements.
Recently, several satellite based top-down approaches, which recalculated the different sources of NOx (fossil fuel, biomass burning, soil and lightning), have shown an underestimation of SNOx by the algorithm of Yienger and Levy (1995). Nevertheless, to our knowledge no general improvements of this algorithm have yet been published.
Here we present major improvements to the algorithm, which should help to optimize the representation of SNOx in atmospheric-chemistry global climate models, without modifying the underlying principal or mathematical equations. The changes include: 1) Using a new up to date land cover map, with twice the number of land cover classes, and using annually varying fertilizer application rates; 2) Adopting the fraction of SNOx induced by fertilizer application based on our database; 3) Switching from soil water column to volumetric soil moisture, to distinguish between the wet and dry state; 4) Tuning the emission factors to reproduce the measured emissions in our database and calculate the emissions based on their mean value. These steps lead us to increased global yearly SNOx, and our total SNOx source ends up being close to one of the top-down approaches. In some geographical regions the new results agree better with the top-down approach, but there are also distinct differences in other regions. This suggests that a ombination of both top-down and bottom-up approaches could be combined in a future attempt to provide an even better calculation of SNOx.
Biogenic NO emissions from soils (SNOx) play important direct and indirect roles in tropospheric chemistry. The most widely applied algorithm to calculate SNOx in global models was published 15 years ago by Yienger and Levy (1995), and was based on very few measurements. Since then, numerous new measurements have been published, which we used to build up a compilation of world wide field measurements covering the period from 1978 to 2010. Recently, several satellite-based top-down approaches, which recalculated the different sources of NOx (fossil fuel, biomass burning, soil and lightning), have shown an underestimation of SNOx by the algorithm of Yienger and Levy (1995). Nevertheless, to our knowledge no general improvements of this algorithm, besides suggested scalings of the total source magnitude, have yet been published. Here we present major improvements to the algorithm, which should help to optimize the representation of SNOx in atmospheric-chemistry global climate models, without modifying the underlying principals or mathematical equations. The changes include: (1) using a new landcover map, with twice the number of landcover classes, and using annually varying fertilizer application rates; (2) adopting a fraction of 1.0 % for the applied fertilizer lost as NO, based on our compilation of measurements; (3) using the volumetric soil moisture to distinguish between the wet and dry states; and (4) adjusting the emission factors to reproduce the measured emissions in our compilation (based on either their geometric or arithmetic mean values). These steps lead to increased global annual SNOx, and our total above canopy SNOx source of 8.6 Tg yr−1 (using the geometric mean) ends up being close to one of the satellite-based top-down approaches (8.9 Tg yr−1). The above canopy SNOx source using the arithmetic mean is 27.6 Tg yr−1, which is higher than all previous estimates, but compares better with a regional top-down study in eastern China. This suggests that both top-down and bottom-up approaches will be needed in future attempts to provide a better calculation of SNOx.
Which factors determine whether a stimulus is consciously perceived or unconsciously processed? Here, I investigate how previous experience on two different time scales – long term experience over the course of several days, and short term experience based on the previous trial – impact conscious perception. Regarding long term experience, I investigate how perceptual learning does not only change the capacity to process stimuli, but also the capacity to consciously perceive them. To this end, subjects are trained extensively to discriminate between masked stimuli, and concurrently rate their subjective experience. Both the ability to discriminate the stimuli as well as subjective awareness of the stimuli increase as a function of training. However, these two effects are not simple byproducts of each other. On the contrary, they display different time courses, with above chance discrimination performance emerging before subjective experience; importantly, the two learning effects also rely on different circuits in the brain: Moving the stimuli outside the trained receptive field size abolishes the learning effects on discrimination ability, but preserves the learning effects on subjective awareness.
This indicates that the receptive fields serving subjective experience are larger than the ones serving objective performance, and that the channels through which they receive their information are arranged in parallel. Regarding short term experience, I investigate how memory based predictions arising from information acquired on the trial before affect visibility and the neural correlates of consciousness. To this end, I vary stimulus evidence as well as predictability and acquire electroencephalographic data.
A comparison of the neural processes distinguishing consciously perceived from unperceived trials with and without predictions reveals that predictions speed up processing, thus shifting the neural correlates forward in time. Thus, the neural correlates of consciousness display a previously unappreciated flexibility in time and do not arise invariably late as had been predicted by some theorists.
Admittedly, however, previous experience does not always stabilize perception. Instead, previous experience can have the reverse effect: Seeing the opposite of what was there, as in so-called repulsive aftereffects. Here, I investigate what determines the direction of previous experience using multistable stimuli. In a functional magnetic resonance imaging experiment, I find that a widespread network of frontal, parietal, and ventral occipital brain areas is involved in perceptual stabilization, whereas the reverse effect is only evident in extrastriate cortex. This areal separation possibly endows the brain with the flexibility to switch between exploiting already available information and emphasizing the new.
Taken together, my data show that conscious perception and its neuronal correlates display a remarkable degree of flexibility and plasticity, which should be taken into account in future theories of consciousness.
Residual circulation trajectories and transit times into the extratropical lowermost stratosphere
(2011)
Transport into the extratropical lowermost stratosphere (LMS) can be divided into a slow part (time-scale of several months to years) associated with the global-scale stratospheric residual circulation and a fast part (time-scale of days to a few months) associated with (mostly quasi-horizontal) mixing (i.e. two-way irreversible transport, including extratropical stratosphere-troposphere exchange). The stratospheric residual circulation may be considered to consist of two branches: a deep branch more strongly associated with planetary waves breaking in the middle to upper stratosphere, and a shallow branch associated with synoptic and planetary scale waves breaking in the subtropical lower stratosphere. In this study the contribution due to the stratospheric residual circulation alone to transport into the LMS is quantified using residual circulation trajectories, i.e. trajectories driven by the (time-dependent) residual mean meridional and vertical velocities. This contribution represents the advective part of the overall transport into the LMS and can be viewed as providing a background onto which the effect of mixing has to be added. Residual mean velocities are obtained from a comprehensive chemistry-climate model as well as from reanalysis data. Transit times of air traveling from the tropical tropopause to the LMS along the residual circulation streamfunction are evaluated and compared to recent mean age of air estimates. A time-scale separation with much smaller transit times into the mid-latitudinal LMS than into polar LMS is found that is indicative of a separation of the shallow from the deep branch of the residual circulation. This separation between the shallow and the deep circulation branch is further manifested in a distinction in the aspect ratio of the vertical to meridional extent of the trajectories, the integrated mass flux along the residual circulation trajectories, as well as the stratospheric entry latitude of the trajectories. The residual transit time distribution reproduces qualitatively the observed seasonal cycle of youngest air in the extratropical LMS in fall and oldest air in spring.
Residual circulation trajectories and transit times into the extratropical lowermost stratosphere
(2010)
Transport into the extratropical lowermost stratosphere (LMS) can be divided into a slow part (time-scale of several months to years) associated with the global-scale stratospheric residual circulation and a fast part (time-scale of days to a few months) associated with (mostly quasi-horizontal) mixing (i.e. two-way irreversible transport, including stratosphere-troposphere exchange). The stratospheric residual circulation can be considered to consist of two branches: a deep branch more strongly associated with planetary waves breaking in the middle to upper stratosphere, and a shallow branch more strongly associated with synoptic-scale waves breaking in the subtropical lower stratosphere. In this study the contribution due to the stratospheric residual circulation alone to transport into the LMS is quantified using residual circulation trajectories, i.e. trajectories driven by the (time-dependent) residual mean meridional and vertical velocities. This contribution represents the advective part of the overall transport into the LMS and can be viewed as providing a background onto which the effect of mixing has to be added. Residual mean velocities are obtained from a comprehensive chemistry-climate model as well as from reanalysis data. Transit times of air traveling from the tropical tropopause to the LMS along the residual circulation streamfunction are evaluated and compared to recent mean age of air estimates. A clear time-scale separation with much smaller transit times into the mid-latitudinal LMS than into polar LMS is found that is indicative of a clear separation of the shallow from the deep branch of the residual circulation. This separation between the shallow and the deep circulation branch is further manifested in a clear distinction in the aspect ratio of the vertical to meridional extent of the trajectories as well as the integrated mass flux along the residual circulation trajectories. The residual transit time distribution reproduces qualitatively the observed seasonal cycle of youngest air in the extratropical LMS in fall and oldest air in spring.
A complete, well-preserved record of the Cenomanian/Turonian (C/T) Oceanic Anoxic Event 2 (OAE-2) was recovered from Demerara Rise in the southern North Atlantic Ocean (ODP site 1260). Across this interval, we determined changes in the stable carbon isotopic composition of sulfur-bound phytane (δ13Cphytane, a biomarker for photosynthetic algae. The δ13Cphytane record shows a positive excursion at the onset of the OAE-2 interval, with an unusually large amplitude (~7 ‰) compared to existing C/T proto-North Atlantic δ13Cphytane records (3–6 ‰). Overall, the amplitude of the excursion of δ13Cphytane decreases with latitude. Using reconstructed sea surface temperature (SST) gradients for the proto-North Atlantic, we investigated environmental factors influencing the latitudinal δ13Cphytane gradient. The observed gradient is best explained by high productivity at DSDP Site 367 and Tarfaya basin before OAE-2, which changed in overall high productivity throughout the proto-North Atlantic during OAE-2. During OAE-2, productivity at site 1260 and 603B was thus more comparable to the mid-latitude sites. Using these constraints as well as the SST and δ13Cphytane-records from Site 1260, we subsequently reconstructed pCO2 levels across the OAE-2 interval. Accordingly, pCO2 decreased from ca. 1750 to 900 ppm during OAE-2, consistent with enhanced organic matter burial resulting in lowering pCO2. Whereas the onset of OAE-2 coincided with increased pCO2, in line with a volcanic trigger for this event, the observed cooling within OAE-2 probably resulted from CO2 sequestration in black shales outcompeting CO2 input into the atmosphere. Together these results show that the ice-free Cretaceous world was sensitive to changes in pCO2 related to perturbations of the global carbon cycle.
Bioapatite in mammalian teeth is readily preserved in continental sediments and represents a very important archive for reconstructions of environment and climate evolution. This project intends to provide a detailed data base of major, minor and trace element and isotope tracers for tooth apatite using a variety of microanalytical techniques. The aim is to identify specific sedimentary environments and to improve our understanding on the interaction between internal metabolic processes during tooth formation and external nutritional control and secondary alteration effects. Here, we use the electron microprobe, to determine the major and minor element contents of fossil and modern molar enamel, cement and dentin from hippopotamids. Most of the studied specimens are from different ecosystems in Eastern Africa, representing modern and fossil lakustrine (Lake Kikorongo, Lake Albert, and Lake Malawi) and modern fluvial environments of the Nile River system.
Secondary alteration effects in particular FeO, MnO, SO3 and F concentrations, which are 2 to 10 times higher in fossil than in modern enamel; secondary enrichments in fossil dentin and cement are even higher. In modern and fossil enamel, along sections perpendicular to the enamel-dentin junction (EDJ) or along cervix-apex profiles, P2O5 and CaO contents and the CaO/P2O5 ratios are very constant (StdDev ~1 %). Linear regression analysis reveals very tight control of the MgO (R2∼0.6), Na2O and Cl variation (for both R2>0.84) along EDJ-outer enamel rim profiles, despite large concentration variations (40 % to 300 %) across the enamel. These minor elements show well defined distribution patterns in enamel, similar in all specimens regardless of their age and origin, as the concentration of MgO and Na2O decrease from the enamel-dentin junction (EDJ) towards the outer rim, whereas Cl displays the opposite variation.
Fossil enamel from hippopotamids which lived in the saline Lake Kikorongo have a much higher MgO/Na2O ratio (∼1.11) than those from the Neogene fossils of Lake Albert (MgO/Na2O∼0.4), which was a large fresh water lake like those in the western Branch of the East African Rift System today. Similarly, the MgO/Na2O ratio in modern enamel from the White Nile River (∼0.36), which has a Precambrian catchment of dominantly granite and gneisses and passes through several saline zones, is higher than that from the Blue Nile River, whose catchment is the Neogene volcanic Ethiopian Highland (MgO/Na2O∼0.22). Thus, particularly MgO/Na2O might be a sensitive fingerprint for environments where river and lake water have suffered strong evaporation.
Enamel formation in mammals takes place at successive mineralization fronts within a confined chamber where ion and molecule transport is controlled by the surrounding enamel organ. During the secretion and maturation phases the epithelium generates different fluid composition, which in principle, should determine the final composition of enamel apatite. This is supported by co-linear relationships between MgO, Cl and Na2O which can be interpreted as binary mixing lines. However, if maturation starts after secretion is completed the observed element distribution can only be explained by recrystallization of existing and addition of new apatite during maturation. Perhaps the initial enamel crystallites precipitating during secretion and the newly formed bioapatite crystals during maturation equilibrate with a continuously evolving fluid. During crystallization of bioapatite the enamel fluid becomes continuously depleted in MgO and Na2O, but enriched in Cl which results in the formation of MgO, and Na2O-rich, but Cl-poor bioapatite near the EDJ and MgO- and Na2O-poor, but Cl-rich bioapatite at the outer enamel rim.
The linkage between lake and river water composition, bioavailability of elements for plants, animal nutrition and tooth formation is complex and multifaceted. The quality and limits of the MgO/Na2O and other proxies have to be established with systematic investigations relating chemical distribution patterns to sedimentary environment and to growth structures developing as secretion and maturation proceed during tooth formation.
Ubiquitin is a highly conserved protein involved in several cellular processes like protein degradation, endocytosis, signal transduction and DNA repair. The discovery of ubiquitin-like proteins (UBL) and ubiquitin-like domains (ULD) increases the number of regulation pathways where the property of the ubiquitin-fold is profitable.
Autophagy is the catabolic pathway used in cells to deliver cytosolic components and dysfunctional organelles to the lysosome for degradation. MAP1LC3 proteins are ubiquitin-like proteins involved in one hand for the expansion of the autophagosome, which sequesters cytosolic substrates. In the other hand, these proteins (LC3- and GABARAP- subfamilies) bind to autophagic receptors linked to polyubiquitinated proteins aggregates. For this project, the 3D structure of the GABARAPL-1/NBR1-LIR complex was determined and confirmed that GABARAPL-1 belongs to the MAP1LC3 proteins family, structurally characterized by an ubiquitin-fold, consisting of a central beta-sheet formed by four beta-strands and two alpha-helices on one side of the beta-sheet, preceded N terminally by two alpha-helices, resulting in the formation of two hydrophobic pockets, hp1 and hp2. The autophagic receptor NBR1 interacts with GABARAPL-1 through the hp1 and hp2 with its LIR motif taking an extended beta conformation upon binding, forming an intermolecular beta-sheet with the second beta-strand of GABARAPL 1. This LC3- interacting region (LIR) consists of an Theta XX Gamma sequence preceded by acidic amino acids, with Theta and Gamma represented by any aromatic and hydrophobic residues, respectively. Interaction studies of the LIR domains of p62, Nix and NBR1 with different members of the MAP1LC3 proteins family indicate that the presence of a tryptophan in the LIR motif increases the binding affinity. Substitution to other aromatic amino acids or increasing the number of negatively charged residues at the N-terminus of the LIR motif, however, has little effect on the binding affinity due to enthalpy-entropy compensation, suggesting that effector proteins can interact with a wide variety of different sequences with similar and moderate binding affinities.
Additionally to be present in proteins dealing with protein folding and degradation, ubiquitin-like domain were found protein involved in the regulation of signal transduction like TBK1, a serine/threonine kinase responsible for induction of immune response. In this second project, based on the NMR chemical shifts of the TBK1 domain contained between amino acids 302 and 383, secondary structure prediction programs (TALOS and CSI) confirmed the presence of an Ubiquitin-like domain in TBK1 by identifying one alpha-helix and four beta-strands sequentially aligned like following beta-beta-alpha-beta-beta. This alignment corresponds perfectly with the secondary structure elements of Ubiquitin and proved that TBK1_ULD belongs to the UBL protein superfamily. The similarity to ubiquitin was even bigger by the presence in addition of a small beta-strand and a short helix, which are observed as the beta 5-strand and a 310-helix in Ubiquitin, respectively. The first attempts on the 3D structure determination confirmed the Ub-fold but due to the lack of assignment in TBK1_ULD, only a structure based on ubiquitin as a model was determined. Interaction studies of TBK1_ULD with the IAD-SRR domain of IRF3 showed that both side of the molecule seems involved and that the TBK1/IRF3 interaction is more complex than a one to one binding process. Unfortunately, the instability of TBK1_ULD associated to the difficulty in the purification of IAD-SRR did not allow to further study this interaction more precisely.
Finally, to overcome the difficulty encountered in NMR experiments because of low expression and/or poor solubility, an expression vector using the intrinsic property of ubiquitin was designed. Fused to proteins or peptides targets, this construct produced proteins and peptides in a larger amount than with traditional expression vectors and also with a less cost than chemical synthesis for pure labeled peptides for NMR structural studies. The presence of a hexa histidine tag was useful for the isolation and the purification of the constructs. The existence of a TEV cleavage site was created to keep the possibility of releasing the ubiquitin moiety from the expressed protein or peptide. Moreover, the ubiquitin-tag could also still be attached to the protein/peptide of interest when biophysical methods like NMR, ITC or CD spectroscopy are applied, providing the same results than for the protein/peptide moiety alone.
Tubular carbonate concretions of up to 1 m in length and perpendicular to bedding, occur abundantly in the Upper Pliensbachian (upper Amaltheus margaritatus Zone, Gibbosus Subzone) in outcrops (Fontaneilles section) in the vicinity of Rivière-sûr-Tarn, southern France. Stable isotope analyses of these concretions show negative δ13C values that decrease from the rim to the center from −18.8‰ to −25.7‰ (V-PDB), but normal marine δ18O values (−1.8‰). Carbon isotope analyses of Late Pliensbachian bulk carbonate (matrix) samples from the Fontaneilles section show clearly decreasing C-isotope values across the A. margaritatus Zone, from +1‰ to −3‰ (V-PDB). Isotope analyses of coeval belemnite rostra do not document such a negative C-isotope trend with values remaining stable around +2‰ (V-PDB). Computer tomographic (CT) scanning of the tubular concretions show multiple canals that are lined or filled entirely with pyrite. Previously, the formation of these concretions with one, two, or more central tubes, has been ascribed to the activity of an enigmatic organism, possibly with annelid or arthropod affinities, known as Tisoa siphonalis. Our results suggest tisoan structures are abiogenic. Based on our geochemical analyses and sedimentological observations we suggest that these concretions formed as a combination of the anaerobic oxidation of methane (AOM) and sulfate reduction within the sediment. Fluids rich in methane and/or hydrocarbons likely altered local bulk rock carbon isotope records, but did not affect the global carbon cycle. Interestingly, Tisoa siphonalis has been described from many locations in the Grands Causses Basin in southern France, and from northern France and Luxemburg, always occurring at the same stratigraphic level. Upper Pliensbachian authigenic carbonates thus possibly cover an area of many thousand square kilometers. Greatly reduced sedimentation rates are needed to explain the stabilization of the sulfate-methane transition zone in the sedimentary column in order for the tubular concretions to form. Late Pliensbachian cooling, reducing run-off, and/or the influx of colder water and more vigorous circulation could be responsible for a halt in sedimentation. At the same time (thermogenic) methane may have destabilized during a major phase of Late Pliensbachian sea level fall. As such Tisoa siphonalis is more than a geological curiosity, and its further study could prove pivotal in understanding Early Jurassic paleoenvironmental change.
Floodplains play an important role in the terrestrial water cycle and are very important for biodiversity. Therefore, an improved representation of the dynamics of floodplain water flows and storage in global hydrological and land surface models is required. To support model validation, we combined monthly time series of satellite-derived inundation areas (Papa et al., 2010) with data on irrigated rice areas (Portmann et al., 2010). In this way, we obtained global-scale time series of naturally inundated areas (NIA), with monthly values of inundation extent during 1993–2004 and a spatial resolution of 0.5°. For most grid cells (0.5°×0.5°), the mean annual maximum of NIA agrees well with the static open water extent of the Global Lakes and Wetlands database (GLWD) (Lehner and Döll, 2004), but in 16% of the cells NIA is larger than GLWD. In some regions, like Northwestern Europe, NIA clearly overestimates inundated areas, probably because of confounding very wet soils with inundated areas. In other areas, such as South Asia, it is likely that NIA can help to enhance GLWD. NIA data will be very useful for developing and validating a floodplain modeling algorithm for the global hydrological model WGHM. For example, we found that monthly NIAs correlate with observed river discharges.
Agriculture of crops provides more than 85% of the energy in human diet, while also securing income of more than 2.6 billion people. To investigate past, present and future changes in the domain of food security, water resources and water use, nutrient cycles, and land management it is required to know the agricultural land use, in particular which crop grows where and when. The current global land use or land cover data sets are based on remote sensing and agricultural census statistics. In general, these only contain one or very few classes of agricultural land use. When crop-specific areas are given, no distinction of irrigated and rainfed areas is made, whereas it is necessary to distinguish rainfed and irrigated crops, because crop productivity and water use differ significantly between them.
To support global-scale assessments that are sensitive to agricultural land use, the global data set of Monthly Irrigated and Rainfed Crop Areas around the year 2000 (MIRCA2000) was developed by the author. With a spatial resolution of 5 arc-minutes (approximately 9.2 km at the equator), MIRCA2000 provides for the first time, spatially explicit irrigated and rainfed crop areas separately for each of the 26 crop classes for each month of the year, and includes multi-cropping. The data set covers all major food crops as well as cotton, while the remaining crops are grouped into three categories (perennial, annual and fodder grasses). Also for the first time, crop calendars on national or sub-national level were consistently linked to annual values of harvested area at the 5 arc-minutes grid cell level, such that monthly growing areas could be computed that are representative for the time period 1998 to 2002.
The downscaling algorithm maximizes the consistency to the grid-based input data of cropland extent [Ramankutty et al., 2008], crop-specific total annual harvested area [Monfreda et al., 2008], and area equipped for irrigation [Siebert et al., 2007]. In addition to the methodology, this dissertation describes differences to other datasets and standard scaling methods, as well as some applications. For quality assessment independent datasets and newly developed quality parameters are used, and scale effects are discussed.
Supplementary Appendices document crop calendars for irrigated and rainfed crops for each of the 402 spatial units (Appendix I), data sources of harvested area and of cropping periods for irrigated crops, country by country (Appendix K), as well as data quality parameters (Appendix L, including spreadsheet files).
Introduction: Researchers experience increasing pressures to connect with bodies that finance their projects. In this climate, critical scholars face many obstacles as they seek to navigate the treacherous waters of securing external funds. To debate these challenges, the ACME Editorial Collective organized a panel for the 2009 Annual Meeting of the Association of American Geographers in Las Vegas. This intervention represents a follow-up discussion and collective writing process among some of the panelists and members of the audience who attended the panel.
Below, we examine the neoliberalization of the current funding systems, discuss the implications for research practice, and make suggestions for critical engagement and transformation. Our suggestions, however, will not be easy to implement, as we can infer from the experience of the radical scholars of the post-1968 generation whose ascension into the upper echelons of North American and European university systems was also associated with the neoliberalization of the funding systems. This intervention represents a modest contribution in the tradition of critical research practice of creating the possibilities for progressive change.
Droplets produced in a cloud condensation nuclei chamber (CCNC) as a function of supersaturation have been separated from unactivated aerosol particles using counterflow virtual impaction. Residual material after droplets were evaporated was chemically analyzed with an Aerodyne Aerosol Mass Spectrometer (AMS) and the Particle Analysis by Laser Mass Spectrometry (PALMS) instrument. Experiments were initially conducted to verify activation conditions for monodisperse ammonium sulfate particles and to determine the resulting droplet size distribution as a function of supersaturation. Based on the observed droplet size, the counterflow virtual impactor cut-size was set to differentiate droplets from unactivated interstitial particles. Validation experiments were then performed to verify that only droplets with sufficient size passed through the counterflow virtual impactor for subsequent analysis. A two-component external mixture of monodisperse particles was also exposed to a supersaturation which would activate one of the types (hygroscopic salts) but not the other (polystyrene latex spheres or adipic acid). The mass spectrum observed after separation indicated only the former, validating separation of droplets from unactivated particles. Results from ambient measurements using this technique and AMS analysis were inconclusive, showing little chemical differentiation between ambient aerosol and activated droplet residuals, largely due to low signal levels. When employing as single particle mass spectrometer for compositional analysis, however, we observed enhancement of sulfate in droplet residuals.
Droplets produced in a cloud condensation nucleus chamber as a function of supersaturation have been separated from unactivated aerosol particles using counterflow virtual impaction. Residual material after droplets were evaporated was chemically analyzed with an Aerodyne Aerosol Mass Spectrometer and the Particle Analysis by Laser Mass Spectrometry instrument. Experiments were initially conducted to verify activation conditions for monodisperse ammonium sulfate particles and to determine the resulting droplet size distribution as a function of supersaturation. Based on the observed droplet size, the counterflow virtual impactor cut-size was set to differentiate droplets from unactivated interstitial particles. Validation experiments were then performed to verify that only droplets with sufficient size passed through the counterflow virtual impactor for subsequent analysis. A two-component external mixture of monodisperse particles was also exposed to a supersaturation which would activate one of the types (ammonium sulfate) but not the other (polystyrene latex spheres). The mass spectrum observed after separation indicated only the former, validating separation of droplets from unactivated particles. Results from atmospheric measurements using this technique indicate that aerosol particles often activate predominantly as a function of particle size. Chemical composition is not irrelevant, however, and we observed enhancement of sulfate in droplet residuals using single particle analysis.
The performance of an ion source based on corona discharge has been studied. This source is used for the detection of gaseous sulfuric acid by chemical ionization mass spectrometry (CIMS) through the reaction of NO−3 ions with H2SO4. The ion source is operated under atmospheric pressure and its design is similar to the one of a radioactive (americium-241) ion source which has been used previously. The results show that the detection limit for the corona ion source is sufficiently good for most applications. For an integration time of 1 min it is ~6×104 molecule cm−3 of H2SO4. In addition, only a small cross-sensitivity to SO2 has been observed for concentrations as high as 1 ppmv in the sample gas. This low sensitivity to SO2 is achieved even without the addition of an OH scavenger. When comparing the new corona ion source with the americium ion source for the same provided H2SO4 concentration, both ion sources yield almost identical values. These features make the corona ion source investigated here favorable over the more commonly used radioactive ion sources for most applications where H2SO4 is measured by CIMS.
The performance of an ion source based on corona discharge has been studied. This source is used for the detection of gaseous sulfuric acid by chemical ionization mass spectrometry (CIMS) through the reaction of NO3– ions with H2SO4. The ion source is operated under atmospheric pressure and its design is similar to the one of a radioactive (Americium 241) ion source which has been used previously. Our results show that the detection limit for the corona ion source is sufficiently good for most applications. For an integration time of one minute it is ~6 × 104 molecules of H2SO4 per cm3. In addition, only a small cross-sensitivity to SO2 has been observed for concentrations as high as 1 ppmv in the sample gas. This low sensitivity to SO2 is achieved even without the addition of an OH scavenger. When comparing the new corona ion source with the americium ion source for the same provided H2SO4 concentration, both ion sources yield almost identical values. These features make the corona ion source investigated here favorable over the more commonly used radioactive ion sources for most applications where H2SO4 is measured by CIMS.
Critical perspectives have become more visible in German human geography. Drawing on an analysis of the debate around the German reader "Kulturgeographie" published in 2003, we suggest that this case provides new insights into the "geography of critical geography". We briefly discuss the history of critical geography in Germany, leading to a comparison of the conditions of critical geography around 1980 and in recent years. The focus is on two factors in the changed role of critical perspectives in German geography: (1) the growing internationalisation of German geography, which opened new avenues and allowed new approaches to enter the discipline; and (2) the high citation indices of "critical" journals, which leads to an enhanced reputation and a high significance of international critical geography in the German discipline. However, we draw an ambiguous conclusion: the increased role of critical approaches in German geography is linked to a growing neoliberalisation of academia and a decline of critical approaches in other disciplines.
Critical perspectives have become more visible in German human geography. Drawing on an analysis of the debate around the German reader “Kulturgeographie” published in 2003, we suggest that this case provides new insights into the “geography of critical geography”. We briefly discuss the history of left geography in Germany, leading to a comparison of the conditions of left geography around 1980 and in recent years. The focus is on two factors in the changed role of critical perspectives in German geography: (1) the growing internationalisation of German geography, which opened new avenues and allowed new approaches to enter the discipline; and (2) the high citation indices of “critical” journals, which leads to an enhanced reputation and a high significance of international critical geography in the German discipline. However, we draw an ambiguous conclusion: the increased role of critical approaches in German geography is linked to a growing neoliberalisation of academia and a decline of critical approaches in other disciplines.
The KADoNiS (Karlsruhe Astrophysical Database of Nucleosynthesis in Stars) project is an online
database (www.kadonis.org) for cross sections relevant to the s-process and the p-process.
The first version was an updated sequel to the previous Bao et al. [1] compilations from 1987
and 2000 for (n; g) cross sections relevant to Big Bang and s-process nucleosynthesis. The first
update, KADoNiS v0.2, was published in 2006 [2]. It contained mainly Maxwellian averaged
(n; g) cross sections relevant to the s-process, and some experimental charged particle induced
reaction relevant to the p-process. After that a second update was presented in 2009 [3].
Recently, we started to collect and review all existing experimental data relevant for p-process
nucleosynthesis and to provide a user-friendly database based on the KADoNiS framework. The
p-process part of the KADoNiS database is currently being extended and will include all available
experimental data from (p; g), (p;n), (p;a), (a,g), (a;n) and (a; p) reactions in or close to the
respective Gamow window.
It has been estimated that about 1% of live births carry severe congenital heart defects and 20-30% among them have valve malformations. Despite its medical importance the underlying cause of many valvular diseases remains undiscovered. Thus, it is important to identify genes that play a crucial role in cardiac valve formation and maturation.
A temporal RNA expression analysis of heart development suggested that the extracellular matrix protein Nephronectin might be a novel regulator of valve development and/or trabeculation. Nephronectin is transiently expressed during rat heart development at the time of heart valve morphogenesis and trabeculation. Moreover, the extracellular matrix is known to be crucial for organogenesis. It is a complex, dynamic and critical component that regulates cell behavior by modulating the activity, bioavailability, or presentation of growth factors to cell surface receptors.
In order to verify the hypothesis that Nephronectin is a novel regulator of valve formation and/or trabeculation the zebrafish was chosen as model system. Females are able to spawn at intervals of 5 days laying hundreds of eggs in each clutch. Development progresses rapidly with precursors to all major organs appearing within 36 hours post fertilization. Zebrafish embryos develop externally, are translucent and continue to grow for several days despite developing severely malformed, non functional hearts. In addition, gene expression can be easily modulated. During the present study it has been shown that Nephronectin expression is correlated to valve development and trabeculation. Morpholinomediated knockdown of Nephronectin in zebrafish caused failure of valve formation and trabeculation resulting in > 85% lethality at 7 days post fertilization.
Cardiac valve formation is initiated at the junction of atrium and ventricle and is characterized by extracellular matrix deposition and endocardial cell differentiation. In accordance with the above-described phenotype the earliest observed abnormality in Nephronectin morphants was an extended tube like structure at the atrio-ventricular boundary. In addition, the expression of myocardial genes involved in cardiac valve formation (cspg2, fibulin1, tbx2b, bmp4) was expanded and endocardial cells along the extended tube like structure exhibited characteristics of atrio-ventricular cells (has2, notch1b and Alcam expression, cuboidal cell shape). Inhibition of has2 in Nephronectin morphants rescued the endocardial but not the myocardial expansion. In contrast, diminishment of BMP signaling in npnt morphants resulted in reduced ectopic expression of myocardial and endocardial atrio-ventricular markers. Taken together, these results identify Nephronectin as a novel upstream regulator of BMP4-HAS2 signaling playing a crucial role in atrio-ventricular canal differentiation.
Editorial Prodigal Italy Greece Spain? Events 01
DB Prize 2011: Award Ceremony in honor of Kenneth Rogoff 02
DB Prize 2011: CFS Symposium in honor of Kenneth Rogoff 03
Is the Euro Zone on its Way to Fiscal Union? 04
CFS Visitors Program - Pistaferri 05
Krugman’s Perspective on the Crisis 06
IMF Post-Annual Meetings Policy Discussion 07
International Conference on Payout Policy – Foundations and Trends 08
MONFISPOL – Final conference 09
CFS - EIEF Conference on Household Finance
This thesis combines behavioral and cognitive approaches regarding the Web for analyzing users' behavior and supposed interests.
The work is placed in a new field of research called Web Science, which includes, but is not restricted to, the analysis of the World Wide Web. The term Web Science is affected by Tim Berners-Lee et al., who invited the researchers to "create a science of the web" [BLHH+06a]. The thesis is structured in two parts, reflecting the intersection of disciplines that is required for Web Science.
The first part is related to computer science and information systems. This part defines the Gugubarra concepts and algorithms for web user profiling and builds upon the results by Mushtaq et al. [MWTZ04]. This profiling aims at understanding the behavior and supposed interests of users. Based on these concepts, a framework was implemented to support the needs of web site owners. The core technologies used are Java, Spring, Hibernate, and content management systems. The design principles, architecture, implementation, and tests of the prototype are reported.
The second part is directly related to behavioral economics and is connected to the areas of economics, mathematics, and psychology. This part contributes to behavior models, as was claimed by Tim Berners-Lee et al.: "Though individual users may or may not be rational, it has long been noted that en masse people behave as utility maximisers. In that case, understanding the incentives that are available to web users should provide methods for generating models of behaviour..."[BLHH+06b]. The focus here is on studies that investigate the user's choice of online information services in a multi-attribute context. The introduced research framework takes into account background and local context effects and builds upon theoretical foundations by Tversky and Kahneman [TK86]. The findings provide useful insights to behavioral scientists and to practitioners on how to use framing strategies to alter the user's choice.