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The recent financial crisis has highlighted the limits of the “originate to distribute” model of banking, but its nexus with the macroeconomy and monetary policy remains unexplored. I build a DSGE model with banks (along the lines of Holmström and Tirole [28] and Parlour and Plantin [39] and examine its properties with and without active secondary markets for credit risk transfer. The possibility of transferring credit reduces the impact of liquidity shocks on bank balance sheets, but also reduces the bank incentive to monitor. As a result, secondary markets allow to release bank capital and exacerbate the effect of productivity and other macroeconomic shocks on output and inflation. By offering a possibility of capital recycling and by reducing bank monitoring, secondary credit markets in general equilibrium allow banks to take on more risk. Keywords: Credit Risk Transfer , Dual Moral Hazard , Monetary Policy , Liquidity , Welfare JEL Classification: E3, E5, G3 First Draft: December 2009, This Draft: September 2010
Exit strategies
(2010)
We study alternative scenarios for exiting the post-crisis fiscal and monetary accommodation using the model of Angeloni and Faia (2010), that combines a standard DSGE framework with a fragile banking sector, suitably modified and calibrated for the euro area. Credibly announced and fast fiscal consolidations dominate – based on simple criteria – alternative strategies incorporating various degrees of gradualism and surprise. The fiscal adjustment should be based on spending cuts or else be relatively skewed towards consumption taxes. The phasing out of monetary accommodation should be simultaneous or slightly delayed. We also find that, contrary to widespread belief, Basel III may well have an expansionary macroeconomic effect. Keywords: Exit Strategies , Debt Consolidation , Fiscal Policy , Monetary Policy , Capital Requirements , Bank Runs JEL Classification: G01, E63, H12
We show that if an agent is uncertain about the precise form of his utility function, his actual relative risk aversion may depend on wealth even if he knows his utility function lies in the class of constant relative risk aversion (CRRA) utility functions. We illustrate the consequences of this result for asset allocation: poor agents that are uncertain about their risk aversion parameter invest less in risky assets than wealthy investors with identical risk aversion uncertainty. Keywords: Risk Aversion , Preference Uncertainty , Risk-taking , Asset Allocation JEL Classification: D81, D84, G11 This Version: November 25, 2010
According to disposition effect theory, people hold losing investments too long. However, many investors eventually sell at a loss, and little is known about which psychological factors contribute to these capitulation decisions. This study integrates prospect theory, utility maximization theory, and theory on reference point adaptation to argue that the combination of a negative expectation about an investment’s future performance and a low level of adaptation to previous losses leads to a greater capitulation probability. The test of this hypothesis in a dynamic experimental setting reveals that a larger total loss and longer time spent in a losing position lead to downward adaptations of the reference point. Negative expectations about future investment performance lead to a greater capitulation probability. Consistent with the theoretical framework, empirical evidence supports the relevance of the interaction between adaptation and expectation as a determinant of capitulation decisions. Keywords: Investments , Adaptation , Reference Point , Capitulation , Selling Decisions , Disposition Effect , Financial Markets JEL Classification: D91, D03, D81
We investigate the incentives for vertical or horizontal integration in the financial security service industry, consisting of trading, clearing and settlement. We thereby focus on firms’ decisions but also look on the implications of these decisions on competition and welfare. Our analysis shows that the incentives for vertical integration crucially depend on industry as well as market characteristics. A more pronounced demand for liquidity clearly favors vertical integration whereas deeper financial integration increases the incentives to undertake vertical integration only if the efficiency gains associated with vertical integration are sufficiently large. Furthermore, we show that market forces can suffer from a coordination problem that end in vertically integrated structures that are not in the best interest of the firms. We believe this problem can be addressed by policy measures such as the TARGET2-Securities program. Furthermore, we use our framework to discuss major industry trends and policy initiatives. Keywords: Vertical Integration , Horizontal Integration , Competition , Trading , Settlement JEL Classification: G15, L13, L22
During the last decades households in the U.S. have experienced that residential house prices move in a persistent manner, i.e. that returns are positively serially correlated. Since an owner-occupied home is usually the largest investment of a household it is important to understand how households act when they base their consumption and investment decisions on this experience. We show in a setting with housing market cycles and households who can decide whether they rent or own the home, that - besides the consumption and the precautionary savings motive - serial correlation in house prices generates a new speculative motive for homeownership. In particular, we show how good and bad housing market cycles affect homeownership rates, leverage, stock investments and consumption and can explain empirically observed household behavior during housing market boom and bust periods. Keywords: Asset Allocation , Portfolio Choice , Housing Market Cycles , Real Estate JEL Classification: G11, D91
We test whether asymmetric preferences for losses versus gains as in Ang, Chen, and Xing (2006) also affect the pricing of cash flow versus discount rate news as in Campbell and Vuolteenaho (2004). We construct a new four-fold beta decomposition, distinguishing cash flow and discount rate betas in up and down markets. Using CRSP data over 1963–2008, we find that the downside cash flow beta and downside discount rate beta carry the largest premia. We subject our result to an extensive number of robustness checks. Overall, downside cash flow risk is priced most consistently across different samples, periods, and return decomposition methods, and is the only component of beta that has significant out-of-sample predictive ability. The downside cash flow risk premium is mainly attributable to small stocks. The risk premium for large stocks appears much more driven by a compensation for symmetric, cash flow related risk. Finally, we multiply our premia estimates by average betas to compute the contribution of the different risk components to realized average returns. We find that up and down discount rate components dominate the contribution to average returns of downside cash flow risk. Keywords: Asset Pricing, Beta, Downside Risk, Upside Risk, Cash Flow Risk, Discount Rate Risk JEL Classification: G11, G12, G14
Capturing the zero: a new class of zero-augmented distributions and multiplicative error processes
(2010)
We propose a novel approach to model serially dependent positive-valued variables which realize a non-trivial proportion of zero outcomes. This is a typical phenomenon in financial time series observed on high frequencies, such as cumulated trading volumes or the time between potentially simultaneously occurring market events. We introduce a flexible pointmass mixture distribution and develop a semiparametric specification test explicitly tailored for such distributions. Moreover, we propose a new type of multiplicative error model (MEM) based on a zero-augmented distribution, which incorporates an autoregressive binary choice component and thus captures the (potentially different) dynamics of both zero occurrences and of strictly positive realizations. Applying the proposed model to high-frequency cumulated trading volumes of liquid NYSE stocks, we show that the model captures both the dynamic and distribution properties of the data very well and is able to correctly predict future distributions. Keywords: High-frequency Data , Point-mass Mixture , Multiplicative Error Model , Excess Zeros , Semiparametric Specification Test , Market Microstructure JEL Classification: C22, C25, C14, C16, C51
Despite sensible guidelines for the use of opioid analgesics, respiratory depression remains a significant risk with a possibility of fatal outcomes. Clinicians need to find a balance of analgesia with manageable respiratory effects. The ampakine CX717 (Cortex Pharmaceuticals, Irvine, CA, USA), an allosteric enhancer of glutamate-stimulated AMPA receptor activation, has been shown to counteract opioid-induced respiratory depression in rats while preserving opioid-induced analgesia. Adopting a translational approach, we orally administered 1500 mg of CX717 to 16 male healthy volunteers in a placebo controlled double-blind study. Starting 100 min after CX717 or placebo intake, alfentanil was administered by computerized intravenous infusion targeting a plateau of effective alfentanil plasma concentrations of 100 ng/ml. One hour after start of opioid infusion, its effects were antagonized by intravenous injection of 1.6 mg of the classical opioid antidote naloxone. Respiration was quantified prior to drug administration (baseline), during alfentanil infusion and after naloxone administration by (i) counting the spontaneous respiratory frequency at rest and (ii) by employing hypercapnic challenge with CO2 rebreathing that assessed the expiratory volume at a carbon dioxide concentration in the breathable air of 55% (VE55). Pain was quantified at the same time points, immediately after assessment of respiratory parameters, by (i) measuring the tolerance to electrical stimuli (5 Hz sine increased by 0.2 mA/s from 0 to 20 mA and applied via two gold electrodes placed on the medial and lateral side of the mid-phalanx of the right middle finger) and (ii) by measuring the tolerance to heat (increased by 0.3°C/s from 32 to 52.5°C applied to a 3 x 3 cm2 skin area of the left volar forearm, after sensitization with 0.15 g capsaicin cream 0.1%). CX717 was tolerated by all subjects without side effects that would have required medical intervention. We observed that CX717 was approximately as effective as naloxone in reversing the opioid induced reduction of the respiratory frequency. Despite the presence of high plasma alfentanil concentrations, the respiratory frequency decreased only by 8.9 ± 22.4% when CX717 was pre-administered, which was comparable to the 7.0 ± 19.3% decrease observed after administration of naloxone. In contrast, after placebo pre-administration the respiratory rate decreased by 30.0 ± 21.3% (p=0.0054 for CX717 versus placebo). In agreement with this, periods of a very low respiratory frequency of <= 4 min-1 under alfentanil alone were shortened by ampakine pre-dosing by 52.9% (p=0.0182 for CX717 versus placebo). Furthermore, VE55 was decreased during alfentanil infusion by 55.9 ± 16.7% under placebo preadministration but only by 46.0 ± 18.1% under CX717 pre-administration (p=0.017 for CX717 versus placebo). Most importantly, in contrast to naloxone, CX717 had no effect on opioid induced analgesia. Alfentanil increased the pain tolerance to electrical stimuli by 68.7 ± 59.5% with placebo pre-administration. With CX717 pre-administration, the increase of the electrical pain tolerance was similar (54.6 ± 56.7%, p=0.1 for CX717 versus placebo). Similarly, alfentanil increased the heat pain tolerance threshold by 24.6 ± 10.0% with placebo pre-administration. Ampakine co-administration had also no effect on the increase of the heat pain tolerance of the capsaicin-sensitized skin (23.1 ± 8.3%, p=0.46 for CX717 versus placebo). The results of this study allow us to draw the conclusion, that opioid induced ventilatory depression can be selectively antagonized in humans by co-administering an ampakine. This is the first successful translation of a selective antagonism of opioidinduced respiratory depression from animal research into application in humans. Ampakines, namely CX717, thus are the first selective antidote for opioid-induced respiratory depression without loss of analgesia, available for the use in humans.
Within this thesis, an experimental study of the photo double ionization (PDI) and the simultaneous ionization-excitation is performed for lithium in different initial states Li (1s22l) (l = s, p). The excess energy of the linearly polarized VUV-light is between 4 and 12 eV above the PDI-threshold. Three forefront technologies are combined: a magneto-optical trap (MOT) for lithium generating an ultra-cold and, by means of optical pumping, a state-prepared target; a reaction microscope (ReMi), enabling the momentum resolved detection of all reaction fragments with high-resolution and the free-electron laser in Hamburg (FLASH), providing an unprecedented brilliant photon beam at favourable time structure to access small cross sections. Close to threshold the total as well as differential PDI cross sections are observed to critically depend on the excitation level and the symmetry of the initial state. For the excited state Li (1s22p) the PDI dynamics strongly depends on the alignment of the 2p-orbital with respect to the VUV-light polarization and, thus, from the population of the magnetic substates (mp = 0, ±1). This alignment sensitivity decreases for increasing excess energy and is completely absent for ionization-excitation. Time-dependent close-coupling calculations are able to reproduce the experimental total cross sections with deviations of at most 30%. All the experimental observations can be consistently understood in terms of the long range electron correlation among the continuum electrons which gives rise to their preferential back-to-back emission. This alignment effect, which is observed here for the first time, allows controlling the PDI dynamics through a purely geometrical modification of the target initial state without changing its internal energy.
Transmissible spongiform encephalopathies (TSEs) are rare but fatal neurodegenerative diseases affecting human and animals. The prion protein which is the causative agent, according to “protein-only” hypothesis misfold in to rogue amyloid conformer. Despite several years of studies, the atomic structural details of the rogue conformers have not been clearly understood. This study focused on developing an in-vitro conversion method, which allows us to monitor the transition from unfolded state of prion protein to fibril state. In order to reach maximal unfolded state, we have used 8 M urea as chemical denaturant, pH 2 and prion fragment 90-230 as the model. It has been demonstrated earlier that acidic pH and mild denaturant induce the fibril formation. The mechanism underlying the structural transition from monomeric state to polymeric form is largely unknown. We have confirmed by EM and AFM that fibrils are formed in our conditions, which resemble to naturally occurring fibrils in morphologies observed. The agitation accelerates the rate of fibril formation and, which allow us to do time-resolved NMR on these preparations. The conformational flexibility is inherent to amyloid fibrils and has been observed in our preparations. We aimed to map the important segment of prion protein, which forms the rigid core in its fibrillar structured form. Our time-resolved NMR studies allowed us to monitor the changes happening from unfolded state to fibrillar state. Analysis of data identified the segment between residues 145 to 223 forming the rigid core in these fibrils, which correspond to β strand 2, helix 2 and major part of helix 3 of native prion monomeric structure. Most of the point mutations which are associated with hereditary prion disease are part of rigid core, which undergo a refolding on fibril formation. The C-terminal residues from 224 to 230 displayed peak shifting and therefore, indicate the adaptation to a fibril specific conformation. The major part of N-terminal 90-144 segment, remains dynamic, which can be understood by their accessibility to amyloid specific antibodies. This provides novel structural insight to the amyloid formation from unfolded state of prion protein fragment 90-230, which represents the proteinase-K resistant part naturally occurring prions. Earlier studies have established the core to 160-220 where hydrogen-deuterium exchange mass spectrometry or site-directed spin labeling EPR spectroscopy was used for analysis. Those studies have been initiated from either native-like or partially unfolded state of recombinant prion protein, and therefore, it is quite striking to find out that fibrils initiated from unfolded monomeric state share the same “amyloid core”. This structural insight has important implications for understanding the molecular basis of prion propagation.
The first part of the following paper deals with varying points of criticism forwarded against Ordoliberalism. Here, it is not the aim to directly falsify each argument on its own; rather, the author tries to give a precise overview of the spectrum of critique. The second section picks out one argument of critical review – namely that the ordoliberal concept of the state is somewhat elitist and grounded on intellectual experts. Based on the previous sections, the final part differentiates two kinds of genesis of norms: an evolutionary and an elitist one – both (latently) present within Ordoliberalism. In combination with the two-level differentiation between individual and regulatory ethics, the essay allows for a distinction between individual-ethical norms based on an evolutionary genesis of norms and regulatory-ethical norms based on an elitist understanding of norms. A by-product of the author’s argument is a (further) demarcation within neoliberalism.
Iron uptake is an essential process in all Gram-negative bacteria including cyanobacteria and therefore different transport systems evolved during evolution. In cyanobacteria, however, the iron demand is higher than in proteobacteria due to the function of iron as cofactor in e.g. photosynthesis and nitrogen fixation. Most of the transport systems depend on outer membrane localized TonB-dependent transporters (TBDTs), a periplasma-facing TonB protein and a plasma membrane localized machinery (ExbBD). So far, iron chelators (siderophores), oligosaccharides and polypeptides have been identified as substrates of TBDTs. However, in proteobacteria TonB-dependent outer membrane transporter represent a well-explored subject whereas for cyanobacteria almost nothing is known about possible TonB-dependent uptake systems for iron or other substrates. The heterocyst-forming filamentous cyanobacterium Anabaena sp. PCC 7120 is known to secrete the siderophore schizokinen, but its transport system has remained unidentified. For Anabaena sp. PCC 7120 22 genes were identified as putative TBDTs covering almost all known TBDT subclasses. This is a high number of TBDTs compared to other cyanobacteria. The expression of the 22 putative TBDTs individually depends on the presence of iron, copper or nitrogen. The atypical dependence of TBDT gene expression on different nutrition points to a yet unknown regulatory mechanism. In addition, the hypothesis of the absence of TonB in Anabaena sp. PCC 7120 was clarified by the identification of an according sequence, all5036. Inspection of the genome of Anabaena sp. PCC 7120 shows that only one gene encoding a putative TonB-dependent iron transporter, namely alr0397, is positioned close to genes encoding enzymes involved in the biosynthesis of a hydroxamate siderophore. The expression of alr0397 was elevated under iron-limited conditions. Inactivation of this gene caused a moderate phenotype of iron starvation in the mutant cells. The characterization of the mutant strain showed that Alr0397 is a TonB-dependent schizokinen transporter (SchT) of the outer membrane and that alr0397 expression and schizokinen production are regulated by the iron homeostasis of the cell. Additional two genes of Anabaena sp. PCC 7120 involved in this process were identified. SchE encoded by all4025 is a putative cytoplasmic membrane-localized transporter involved in TolC-dependent siderophore secretion. The mutation of schE resulted in an enhanced sensitivity to high metal concentrations and in drastically reduction of secretion of hydroxamate-type siderophores. IacT coded by all4026 is a predicted outer membrane-localized TonB-dependent iron transporter. Inactivation of iacT resulted in reduced sensitivity to elevated iron and copper levels, whereas decoupling the expression from putative regulation by exchange of the promoter resulted in sensitization against tested metals. Further analysis showed that iron and copper effects are synergistic because decrease of iron induced a significant decrease of copper levels in the iacT insertion mutant but an increase of those levels in Anabaena sp. PCC 7120 where expression of all4026 is under the trc-promoter. In consequence, the results unravel a link between iron and copper homeostasis.
Acute myeloid/lymphoid leukemia is a fatal hematological malignancy characterized by accumulation of nonfunctional, immature blasts, which interferes with the production of normal blood cells. Activating mutations of receptor tyrosine kinases are common genetic lesions in leukemia. FLT3-ITD is a frequent activating mutation found in AML patients, leading to uncontrolled proliferation of leukemic blasts. FLT3-ITD directly activates STAT5, leading to the induction of STAT5 target gene expression like PIM kinases and SOCS genes. STAT5 and PIM kinases have been shown to play a crucial role in the FLT3-ITD mediated transformation. On the other hand, the role of SOCS proteins in FLT3-ITD mediated transformation has not been studied to date. SOCS proteins are part of a negative feedback mechanism that controls Jak kinases downstream of cytokine receptors. One of the SOCS family members, SOCS1 has been reported to suppress oncogenecity of several activating kinases implicated in hematologic malignancies. In this thesis the role of these SOCS proteins in FLT3-ITD mediated transformation (in vitro) and leukemogenesis (in vivo) is systematically explored. Expression of FLT3-ITD in cell lines of myeloid (32D) and lymphoid (Ba/F3) origin, led to CIS, SOCS1 and SOCS2 expression. FLT3-ITD expression in primary murine bone marrow stem/progenitor cells led to a 59 fold induction of SOCS1 expression. Furthermore, FLT3-ITD positive AML cell lines (MV4-11, MOLM-13) show kinase dependent CIS, SOCS1, and SOCS3 expression. Importantly SOCS1 is highly expressed in AML patients with FLT3-ITD compared to healthy individuals. SOCS1 protein was expressed in FLT3-ITD transduced murine bone marrow stem cells and SOCS1 expression was abolished with kinase inhibition in MOLM-13 cell line. In conclusion, SOCS1 was highly regulated by FLT3-ITD in myeloid, lymphoid cell lines, in bone marrow stem/progenitors and in AML patient samples. SOCS1 co-expression did not affect FLT3-ITD mediated signaling and proliferation, but abolished IL-3 mediated proliferation and protected 32D cells from interferon-α and interferon-γ mediated growth inhibition. FLT3-ITD expressing 32D cells showed diminished STAT1 activation in response to interferons (α and γ). Alone, SOCS1 strongly inhibited cytokine induced colony formation of bone marrow stem and progenitors, but not FLT3-ITD induced colony formation. Most importantly, in the presence of growth inhibitory interferon-γ, SOCS1 co-expression with FLT3-ITD led to increased colony formation compared to FLT3-ITD alone. Taken together, FLT3-ITD induced and exogenously expressed SOCS1, shielded cells from external cytokines, signals, while not affecting FLT3-ITD induced proliferation/signaling. In further experiments the in vivo effects of SOCS1 were studied in a bone marrow transplantation model. SOCS1 bone marrow transplants were unable to engraft/proliferate in mice. FLT3-ITD was shown to induce a myeloproliferative disease. Both control (empty vector), SOCS1 transplanted mice were normal and did not show any disease phenotype. FLT3-ITD alone and SOCS1 co-expressing FLT3-ITD developed either myeloproliferative disease or acute lymphoblastic leukemia with equal distribution. SOCS1 co-expression with FLT3-ITD led to a decreased latency. Mice transplanted with FLT3-ITD alone and SOCS1 co-expressing FLT3-ITD displayed enlarged spleens, liver and hypercellular bone marrow indicating infiltration of leukemic cells. Mice were also anemic and showed decreased platelet counts. Importantly SOCS1 co-expression particularly shortened the latency of myeloproliferative disease but not of acute lymphoblastic leukemia. In summary, in the context of FLT3-ITD, SOCS1 acts as a ‘conditional oncogene’ and cooperates with FLT3-ITD in the development of myeloproliferative disease. With these data we propose the following model: FLT3-ITD induces SOCS gene expression, which shields cells against proliferation and differentiation signals from cytokines, while not affecting FLT3-ITD mediated proliferative signals. This leaves cells under the dictate of FLT3-ITD thereby contributing to leukemogenesis. Similar to FLT3-ITD, BCR/ABL (P190) (an oncogenic fusion kinase often found in acute lymphoblastic leukemia) induces SOCS gene expression in K562 and long-term cultured cells from patients with acute lymphoblastic leukemia. SOCS1 co-expression does not affect BCR/ABL mediated proliferation while abrogating IL-3 mediated proliferation. These findings suggest that SOCS proteins may play a general co-operative role in the context of oncogenes which aberrantly activate STAT3/5 independently of JAK kinases. This study reveals a novel molecular mechanism of FLT3-ITD mediated leukemogenesis and suggests SOCS genes as potential therapeutic targets.
Relational data exchange deals with translating relational data according to a given specification. This problem is one of the many tasks that arise in data integration, for example, in data restructuring, in ETL (Extract-Transform-Load) processes used for updating data warehouses, or in data exchange between different, possibly independently created, applications. Systems for relational data exchange exist for several decades now. Motivated by their experiences with one of those systems, Fagin, Kolaitis, Miller, and Popa (2003) studied fundamental and algorithmic issues arising in relational data exchange. One of these issues is how to answer queries that are posed against the target schema (i.e., against the result of the data exchange) so that the answers are consistent with the source data. For monotonic queries, the certain answers semantics proposed by Fagin, Kolaitis, Miller, and Popa (2003) is appropriate. For many non-monotonic queries, however, the certain answers semantics was shown to yield counter-intuitive results. This thesis deals with computing the certain answers for monotonic queries on the one hand, and on the other hand, it deals with the issue of which semantics are appropriate for answering non-monotonic queries, and how hard it is to evaluate non-monotonic queries under these semantics. As shown by Fagin, Kolaitis, Miller, and Popa (2003), computing the certain answers for unions of conjunctive queries - a subclass of the monotonic queries - basically reduces to computing universal solutions, provided the data transformation is specified by a set of tgds (tuple-generating dependencies) and egds (equality-generating dependencies). If M is such a specification and S is a source database, then T is called a solution for S under M if T is a possible result of translating S according to M. Intuitively, universal solutions are most general solutions. Since the above-mentioned work by Fagin, Kolaitis, Miller, and Popa it was unknown whether it is decidable if a source database has a universal solution under a given data exchange specification. In this thesis, we show that this problem is undecidable. More precisely, we construct a specification M that consists of tgds only so that it is undecidable whether a given source database has a universal solution under M. From the proof it also follows that it is undecidable whether the chase procedure - by which universal models can be obtained - terminates on a given source database and the set of tgds in M. The above results in particular strengthen results of Deutsch, Nash, and Remmel (2008). Concerning the issue of which semantics are appropriate for answering non-monotonic queries, we study several semantics for answering such queries. All of these semantics are based on the closed world assumption (CWA). First, the CWA-semantics of Libkin (2006) are extended so that they can be applied to specifications consisting of tgds and egds. The key is to extend the concept of CWA-solution, on which the CWA-semantics are based. CWA-solutions are characterized as universal solutions that are derivable from the source database using a suitably controlled version of the chase procedure. In particular, if CWA-solutions exist, then there is a minimal CWA-solution that is unique up to isomorphism: the core of the universal solutions introduced by Fagin, Kolaitis, and Popa (2003). We show that evaluation of a query under some of the CWA-semantics reduces to computing the certain answers to the query on the minimal CWA-solution. The CWA-semantics resolve some the known problems with answering non-monotonic queries. There are, however, two natural properties that are not possessed by the CWA-semantics. On the one hand, queries may be answered differently with respect to data exchange specifications that are logically equivalent. On the other hand, there are queries whose answer under the CWA-semantics intuitively contradicts the information derivable from the source database and the data exchange specification. To find an alternative semantics, we first test several CWA-based semantics from the area of deductive databases for their suitability regarding non-monotonic query answering in relational data exchange. More precisely, we focus on the CWA-semantics by Reiter (1978), the GCWA-semantics (Minker 1982), the EGCWA-semantics (Yahya, Henschen 1985) and the PWS-semantics (Chan 1993). It turns out that these semantics are either too weak or too strong, or do not possess the desired properties. Finally, based on the GCWA-semantics we develop the GCWA*-semantics which intuitively possesses the desired properties. For monotonic queries, some of the CWA-semantics as well as the GCWA*-semantics coincide with the certain answers semantics, that is, results obtained for the certain answers semantics carry over to those semantics. When studying the complexity of evaluating non-monotonic queries under the above-mentioned semantics, we focus on the data complexity, that is, the complexity when the data exchange specification and the query are fixed. We show that in many cases, evaluating non-monotonic queries is hard: co-NP- or NP-complete, or even undecidable. For example, evaluating conjunctive queries with at least one negative literal under simple specifications may be co-NP-hard. Notice, however, that this result only says that there is such a query and such a specification for which the problem is hard, but not that the problem is hard for all such queries and specifications. On the other hand, we identify a broad class of queries - the class of universal queries - which can be evaluated in polynomial time under the GCWA*-semantics, provided the data exchange specification is suitably restricted. More precisely, we show that universal queries can be evaluated on the core of the universal solutions, independent of the source database and the specification.
Fas Ligand (FasL; CD95L; CD178; TNSF6) is a 40 kDa glycosylated type II transmembrane protein with 279 aa in mice and 281 aa in humans that belongs to the tumor necrosis factor (TNF) family. The extracellular domain (ECD) harbors a TNF homology domain, the receptor binding site, a motif for self assembly and trimerization, and several putative N-glycosylation and a metalloprotease cleavage site/s. The cytoplasmic tail of FasL is the longest of all TNFL family members and contains several conserved signaling motifs, such as a putative tandem Casein kinase I phosphorylation site, a unique proline-rich domain (PRD) and phosphorylatable tyrosine residues (Y7 in mice; Y7, Y9, Y13 in human). The FasL/Fas system is renowned for the potent induction of apoptosis in the receptor-bearing cell and is especially important for immune system functions. It is involved in the killing of target cells by natural killer (NK) and cytotoxic T cells, in the (self) elimination of effector cells following the proliferative phase of an immune response (activation-induced cell death; AICD), in the maintenance of immuneprivileged sites and in the induction and maintenance of peripheral tolerance. Owing to its potent pro-apoptotic signaling capacity and important functions, FasL expression and activity are tightly regulated at transcriptional and posttranscriptional levels and restricted to few cell types, such as immune effector cells and cells of immune-privileged sites. In contrast, Fas is expressed in a variety of tissues including lymphoid tissues, liver, heart, kidney, pancreas, brain and ovary. In addition to its pro-apoptotic function, the FasL/Fas system can also elicit nonapoptotic signals in the receptor-expressing cell. Among others, Fas-signaling exerts co-stimulatory functions in the immune system, e.g. by promoting survival, activation and proliferation of T cells. Besides the capacity to deliver a signal into receptor-bearing cells (‘forward signal’), FasL can receive and transmit signals into the ligand-expressing cell. This phenomenon has been described for several TNF family ligands and is known as ‘reverse signaling’. The first evidence for the existence of reverse signaling into FasL-bearing cells stems from two studies that demonstrated either co-stimulation of murine CD8+ T cell lines by FasL cross-linking or inhibition of activation-induced proliferation of murine CD4+ T cells. In both cases, the observed changes of proliferative behaviour critically depended on the presence of a signaling-competent FasL. Almost certainly, the FasL ICD is functionally involved in signal-transmission: (i) The ICD is highly conserved across species and harbors several signaling motifs, most notably a unique PRD. (ii) Numerous proteins have been identified which interact with the FasL PRD via their SH3 or WW domains and regulate various aspects of FasL biology, such as FasL sorting, storage, cell surface expression and the linkage of FasL to intracellular signaling pathways. (iii) Post-translational modifications of the ICD have been implicated in the sorting of FasL to vesicles and the FasL-dependent activation of Nuclear factor of activated T cells (NFAT). (iv) Proteolytic processing of FasL liberates the ICD and allows its translocation into the nucleus where it might influence gene transcription. (v) It could be shown that overexpression of the FasL ICD is sufficient to initiate reverse signaling upon concomitant T cell receptor (TCR) stimulation and ICD cross-linking. Conflicting data on the consequences of FasL reverse signaling exist, and costimulatory as well as inhibitory functions have been reported. These discrepancies probably reflect the use of artificial experimental systems. Neither the precise molecular mechanism underlying FasL reverse signaling, nor its physiological relevance have been addressed at the endogenous protein level in vivo. Therefore, a ‘knockout/knockin’ mouse model in which wildtype FasL was replaced with a deletion mutant lacking the intracellular portion (FasL Delta Intra) was established in the group of PD Dr. Martin Zörnig. In the present study, FasL Delta Intra mice were phenotypically characterized and were employed to investigate the physiological consequences of FasL reverse signaling at the molecular and cellular level. To ensure that FasL Delta Intra mice represent a suitable model to study the consequences of FasL reverse signaling, we demonstrated that activated lymphocytes from homozygous FasL Delta Intra or wildtype mice express comparable amounts of (truncated) FasL at the cell surface. The truncated protein retains the capacity to induce apoptosis in Fas receptor-positive target cells, as co-culture assays with FasL-expressing activated lymphocytes and Fas-sensitive target cells showed. Additionally, systematic screening of unchallenged mice did not reveal any phenotypic abnormalities. Notably, signs of a lymphoproliferative autoimmune disease associated with FasL-deficiency could not be detected. As several reports have implicated FasL reverse signaling in the regulation of T cell expansion and activation, proliferation of lymphocytes isolated from FasL Delta Intra and wildtype mice in response to antigen receptor stimulation was investigated. Using CFSE dilution assays it could be demonstrated that the proliferative response of CD4+ T cells, CD8+ T cells and of B cells was enhanced in the absence of the FasL ICD. Interestingly, this effect was most pronounced in B cells and could only be detected in CD4+ T cells after depletion of CD4+CD25+ regulatory T cells. To our Summary knowledge, this is the first time that FasL reverse signaling has been demonstrated in B cells. In a series of experiments, the activation of several pathways that are known to play important roles in signal-transmission initiated upon antigen receptor triggering was assessed. As a molecular correlate for the observed enhancement of activation-induced proliferation, Extracellular signal regulated kinase (ERK1/2) phosphorylation was significantly increased in FasL Delta Intra mice following antigen receptor crosslinking. Surprisingly, B cell stimulation lead to a comparable extent of activating phosphorylations on S38 in c-Raf and S218/S222 in MEK1/2 in cells isolated from wildtype and FasL Delta Intra mice, indicating that Mitogen activated protein kinases (MAPKs) upstream of ERK1/2 (Raf-1 and MEK1/2) apparently do not contribute to the differential regulation of ERK1/2. Experiments in which activation-induced Akt phosphorylation (S473) was quantified also did not suggest a participation of Phosphoinositol specific kinase 3 (PI3K)/Akt signals in this process. Instead, further characterization of the upstream pathway revealed an involvement of Phospholipase C gamma (PLC gamma) and Protein kinase C (PKC) signals in FasL-dependent ERK1/2- regulation. Previous studies in our group revealed a Notch-like processing of FasL, resulting in the transcriptional regulation of a reporter gene. Furthermore, an interaction of the FasL ICD with the transcription factor Lymphoid-enhancer binding factor-1 (Lef-1) that affected Lef-1-dependent reporter gene transcription could be demonstrated. Therefore, a molecular analysis of activated lymphocytes was performed to identify FasL reverse signaling target genes. The differential expression of promising candidates was verified by quantitative real-time PCR (qRT-PCR), which showed that the transcription of genes associated with lymphocyte proliferation and activation was increased in FasL Delta Intra mice compared to wildtype mice. Interestingly, an extensive regulation of Lef-1-dependent Wnt/beta-Catenin signalingrelated genes was found. Lef-1 mRNA (RT-PCR) and protein (intracellular FACS staining) could be detected in mature B cells, suggesting the possibility of FasL ICD-mediated inhibition of Lef-1-dependent gene expression in these cells, initiated by Notch-like processing of FasL. To investigate the consequences of FasL reverse signaling in vivo, a potential participation of the FasL ICD in the regulation of immune responses upon various challenges was analyzed. In experiments in which thymocyte proliferation or the expansion of antigen-specific T cells following a challenge with the superantigen Staphylococcus enterotoxin B (SEB), with Lymphocytic choriomeningitis virus (LCMV) or with Listeria monocytogenes were investigated, comparable results were obtained with wildtype and FasL Delta Intra mice. Likewise, the recruitment of neutrophils in a thioglycollate-induced model of peritonitis was not affected by deletion of the FasL ICD. These findings might reflect regulatory mechanisms operating in vivo, such as control exerted by regulatory T cells. Along these lines, proliferative differences in CD4+ T cells could only be detected ex vivo after depletion of CD4+CD25+ regulatory T cells. Furthermore, several in vitro studies indicate that retrograde FasL signals can be observed under conditions of suboptimal lymphocyte stimulation, but not when the TCR is optimally stimulated. Therefore, the potent initiation of antigen receptor signaling by stimuli like SEB or LCMV might have masked inhibitory FasL reverse signaling in these experiments. In agreement with the observed hyperactivation of lymphocytes in the absence of the ICD ex vivo, the increase in germinal center B cells (GCs) following immunization with the hapten 3-hydroxy 4-nitrophenylacetyl (NP) and the number of antibody-secreting PCs was significantly higher in FasL Delta Intra mice. The larger quantity of PCs correlated with increased titers of NP-binding, i.e. antigen-specific, IgM and IgG1 antibodies in the serum of FasL Delta Intra mice after immunization. These data suggest that FasL reverse signaling exerts immunmodulatory functions. Supporting this notion, a model of Ovalbumin-induced allergic airway inflammation revealed an involvement of retrograde FasL-signals in the recruitment of immune effector cells into the lung and in the activation of T cells following exposure of mice to Ovalbumin. Together, our ex vivo and in vivo findings based on endogenous FasL protein levels demonstrate that FasL ICD-mediated reverse signaling is a negative modulator of certain immune responses. It is tempting to speculate that FasL reverse signaling might be a fine-tuning mechanism to prevent autoimmune diseases, a theory which will be tested in adequate mouse models in the future.
Lattice Yang-Mills theories at finite temperature can be mapped onto effective 3d spin systems, thus facilitating their numerical investigation. Using strong-coupling expansions we derive effective actions for Polyakov loops in the SU(2) and SU(3) cases and investigate the effect of higher order corrections. Once a formulation is obtained which allows for Monte Carlo analysis, the nature of the phase transition in both classes of models is investigated numerically, and the results are then used to predict – with an accuracy within a few percent – the deconfinement point in the original 4d Yang-Mills pure gauge theories, for a series of values of Nt at once.
To investigate the formation and the propagation of relativistic shock waves in viscous gluon matter we solve the relativistic Riemann problem using a microscopic parton cascade. We demonstrate the transition from ideal to viscous shock waves by varying the shear viscosity to entropy density ratio n/s. Furthermore we compare our results with those obtained by solving the relativistic causal dissipative fluid equations of Israel and Stewart (IS), in order to show the validity of the IS hydrodynamics. Employing the parton cascade we also investigate the formation of Mach shocks induced by a high-energy gluon traversing viscous gluon matter. For n/s = 0.08 a Mach cone structure is observed, whereas the signal smears out for n/s >=0.32.
Starting from a classical picture of shear viscosity we construct a steady velocity gradient in the partonic cascade BAMPS. Using the Navier-Stokes-equation we calculate the shear viscosity coefficient. For elastic isotropic scatterings we find a very good agreement with the analytic values. For both elastic and inelastic scatterings with pQCD cross sections we find good agreement with previously published calculations.
This paper shows the equivalence of applicative similarity and contextual approximation, and hence also of bisimilarity and contextual equivalence, in the deterministic call-by-need lambda calculus with letrec. Bisimilarity simplifies equivalence proofs in the calculus and opens a way for more convenient correctness proofs for program transformations. Although this property may be a natural one to expect, to the best of our knowledge, this paper is the first one providing a proof. The proof technique is to transfer the contextual approximation into Abramsky’s lazy lambda calculus by a fully abstract and surjective translation. This also shows that the natural embedding of Abramsky’s lazy lambda calculus into the call-by-need lambda calculus with letrec is an isomorphism between the respective term-models. We show that the equivalence property proven in this paper transfers to a call-by-need letrec calculus developed by Ariola and Felleisen. 1998 ACM Subject Classification: F.4.2, F.3.2, F.3.3, F.4.1. Key words and phrases: semantics, contextual equivalence, bisimulation, lambda calculus, call-by-need, letrec.
Introduction: In the large-scale case-control study EPILIFT, we investigated the dose-response relationship between lifestyle factors (weight, smoking amount, cumulative duration of different sports activities) and lumbar disc disease. Methods: In four German study regions (Frankfurt am Main, Freiburg, Halle/Saale, Regensburg), 564 male and female patients with lumbar disc herniation and 351 patients with lumbar disc narrowing (chondrosis) aged 25 to 70 years were prospectively recruited. From the regional population registers, 901 population control subjects were randomly selected. In a structured personal interview, we enquired as to body weight at different ages, body height, cumulative smoking amount and cumulative duration of different sports activities. Confounders were selected according to biological plausibility and to the change-in-estimate criterion. Adjusted, gender-stratified odds ratios with 95% confidence intervals were calculated using unconditional logistic regression analysis. Results: The results of this case-control study reveal a positive association between weight and lumbar disc herniation as well as lumbar disc narrowing among men and women. A medium amount of pack-years was associated with lumbar disc herniation and narrowing in men and women. A non-significantly lowered risk of lumbar disc disease was found in men with high levels of cumulative body building and strength training. Conclusions: According to our multi-center case-control study, body weight might be related to lumbar disc herniation as well as to lumbar disc narrowing. Further research should clarify the potential protective role of body building or strength training on lumbar disc disease.
Background: Descending inhibitory pain control contributes to the endogenous defense against chronic pain and involves noradrenergic and serotonergic systems. The clinical efficacy of antidepressants suggests that serotonin may be particularly relevant for neuropathic pain conditions. Serotonergic signaling is regulated by synthesis, metabolisms, reuptake and receptors. To address the complexity, we used inbred mouse strains, C57BL/6J, 129 Sv, DBA/2J and Balb/c, which differ in brain serotonin levels. Results: Serotonin analysis after nerve injury revealed inter-strain differences in the adaptation of descending serotonergic fibers. Upregulation of spinal cord and midbrain serotonin was apparent only in 129 Sv mice and was associated with attenuated nerve injury evoked hyperalgesia and allodynia in this strain. The increase of dorsal horn serotonin was blocked by hemisectioning of descending fibers but not by rhizotomy of primary afferents indicating a midbrain source. Para-chlorophenylalanine-mediated serotonin depletion in spinal cord and midbrain intensified pain hypersensitivity in the nerve injury model. In contrast, chronic inflammation of the hindpaw did not evoke equivalent changes in serotonin levels in the spinal cord and midbrain and nociceptive thresholds dropped in a parallel manner in all strains. Conclusion: The results suggest that chronic nerve injury evoked hypernociception may be contributed by genetic differences of descending serotonergic inhibitory control.
In this chapter we develop an agenda for future research on the personalization of politics. To do so, we clarify the propositions of the personalization hypothesis, critically discuss the normative standard on which most studies base their evaluation of personalization, and systematically summarize empirical research findings. We show that the condemnation of personalization is based on a trivial logic and on a maximalist definition of democracy. The review of empirical studies leads us to question the assumption that personalization has steadily increased in all areas of politics. Finally, our normative considerations help us develop new research questions on how personalized politics affects democracy. Moreover, this review also makes clear that another weakness of today's empirical research on the personalization of politics lies in methodological problems and a lack of analysis of the impacts of systemic and contextual variables. Consequently, we suggest methodological pathways and possible explanatory factors for the study of personalization.
On the backdrop of the 2008 financial crisis this paper introduces an understanding of societal crises as a reduction in the meaning production of social entities, which can either be internally or externally provoked. The emergence of constitutions and, more generally, constitutional structures, can be understood as responses to both forms of crisis. This is the case because they are double-edged structures which are simultaneously oriented towards the maintenance of internal order and stability within a given social entity at the same time as they frame the transfer of the meaning components between the social entities and their environments. Thus, the 2008 financial crisis indicates a failure of constitutional bonding. When observed from an overall structural perspective, the reasons for this failure can be traced back to an increased discrepancy between the structural composition of world society and the constitutional structures in place. The crisis reflects a failure to respond to two simultaneous, inter-related and mutually re-inforcing structural transformations. First, there is the increased globalisation, which has led to massive dis-locations in the relative centrality of the different national configurations for the reproductive processes of functional systems. Second, there is a structural transformation of the transnational layer of world society through a reduced reliance on the centre/periphery differentiation and an increased reliance on functional differentiation. One of the many consequences of this development is the emergence of new forms of transnational law and politics. A new constitutional architecture which reflects these transformations is needed in order to ensure an adequate constitutional bonding of economic processes, as well as of other social processes.
Background: Haemostasis in liver surgery remains a challenge despite improved resection techniques. Oozing from blood vessels too small to be ligated necessitate a treatment with haemostats in order to prevent complications attributed to bleeding. There is good evidence from randomised trials for the efficacy of fibrin sealants, on their own or in combination with a carrier material. A new haemostatic device is Sangustop(R). It is a collagen based material without any coagulation factors. Pre-clinical data for Sangustop(R) showed superior haemostatic effect. This present study aims to show that in the clinical situation Sangustop(R) is not inferior to a carrier-bound fibrin sealant (Tachosil(R)) as a haemostatic treatment in hepatic resection. Methods: This is a multi-centre, patient-blinded, intra-operatively randomised controlled trial. A total of 126 patients planned for an elective liver resection will be enrolled in eight surgical centres. The primary objective of this study is to show the non-inferiority of Sangustop(R) versus a carrier-bound fibrin sealant (Tachosil(R)) in achieving haemostasis after hepatic resection. The surgical intervention is standardised with regard to devices and techniques used for resection and primary haemostasis. Patients will be followed-up for three months for complications and adverse events. Discussion: This randomised controlled trial (ESSCALIVER) aims to compare the new collagen haemostat Sangustop(R) with a carrier-bound fibrin sealant which can be seen as a "gold standard" in hepatic and other visceral organ surgery. If non-inferiority is shown other criteria than the haemostatic efficacy (e.g. costs, adverse events rate) may be considered for the choice of the most appropriate treatment. Trial Registration: NCT00918619
Current theories of schizophrenia suggest that the pathophysiology of the disorder may be the result of a deficit in the coordination of neural activity within and between areas of the brain, which may lead to impairments in basic cognitive functions such as contextual disambiguation and dynamic grouping (Phillips and Silverstein, 2003). This notion has been supported by recent studies showing that patients with schizophrenia are characterized by reduced synchronous, oscillatory activity in the gamma-frequency band during sensory processing (Spencer et al. 2003, Green et al. 2003, Wynn et al. 2005). However, it is currently unclear to what extent high-frequency gamma-band oscillations (> 60 Hz) contribute to impaired neural synchronization as research has so far focussed on gamma-band oscillations between 30 and 60 Hz. In addition, it is not known whether deficits in high-frequency oscillations are already present at the onset of the disorder and to what extent reductions may be related to the confounding influence of antipsychotic medication. Finally, the neural generators underlying impairments in synchronous oscillatory activity in schizophrenia have not been investigated yet. To address these questions, we recorded MEG activity during a visual closure task (Mooney faces task) in medicated chronic schizophrenia patients, drug-naive first-episode schizophrenia patients and healthy controls. MEG data were analysed for spectral power between 25 and 150 Hz, and beamforming techniques were used to localize the sources of oscillatory gamma-band activity. In healthy controls, we observed that the processing of Mooney faces was associated with sustained high-frequency gamma-band activity (> 60 Hz). A time-resolved analysis of the neural generators underlying perceptual closure revealed a network of distributed sources in occipito-temporal, parietal and frontal regions, which were differentially activated during specific time intervals. In chronic schizophrenia patients, we found a pronounced reduction of high-frequency gamma-band oscillatory activity that was accompanied by an impairment in perceptual organization and involved reduced source power in various brain regions associated with perceptual closure. First-episode patients were also characterized by a deficit in high-frequency gamma-band activity and reductions of source power in multiple areas; these impairments, however, were less pronounced than in chronic patients. Regarding behavioral performance, first-episode patients were not impaired in their ability to detect Mooney faces, but exhibited a loss in specificity of face detection. In conclusion, our results suggest that schizophrenia is associated with a widespread reduction in high-frequency oscillations that indicate local network abnormalities. These dysfunctions are independent of medication status and already present at illness onset, suggesting a possible progressive deficit during the course of the disorder.
Dessins d'enfants (children's drawings) may be defined as hypermaps, i.e. as bipartite graphs embedded in compact Riemann surfaces. They are very important objects in order to describe the surface of the embedding as an algebraic curve. Knowing the combinatorial properties of the dessin may, in fact, help us determining defining equations or the field of definition of the surface. This task is easier if the automorphism group of the dessin is "large". In this thesis we consider a special type of dessins, so-called Wada dessins, for which the underlying graph illustrates the incidence structure of points and of hyperplanes of projective spaces. We determine under which conditions they have a large orientation-preserving automorphism group. We show that applying algebraic operations called "mock" Wilson operations to the underlying graph we may obtain new dessins. We study the automorphism group of the new dessins and we show that the dessins we started with are coverings of the new ones.
The concept of embeddedness plays a central role in the segment of economic sociology and social theory which is inspired by the works of Karl Polanyi. But to the extent that embeddedness is understood in a substantialist manner, implying the existence of a unitary lifeworld, the desire for embeddedness is an impossible aspiration under modern conditions. Throughout the modern era it is however possible to observe the emergence of complex societal stabilization mechanisms, which serve as substitutes to traditional forms of embeddedness. The emergence of function specific cultures, in the form of, for example, legal, political and scientific cultures, establishing a ‘second nature’ in the Hegelian sense, is one example of this. Other examples are (neo-)corporatist institutions which fulfilled a central stabilising role in classical modernity and the kind of network based governance arrangements which fulfil a similar position in today’s radicalised modernity.
Leukotrienes (LTs) are pro-inflammatory lipid mediators that belong to the group of eicosanoids, which are oxygenated metabolites of one common precursor, the aracidonic acid (AA). This polyunsaturated fatty acid is esterified at the sn-2 position of cellular membrane phospholipids and can be released by cytosolic phospholipase A2 alpha (cPLA2alpha) enzymatic deacylation. AA can be converted into LTs by the catalytic reaction of 5-lipoxygenase (5-LO). Enzymatic activation of cPLA2alpha as well as of 5-LO is regulated by similar determinants. In response to cellular stimuli that elevate the intracellular Ca2+ level and/or activate MAP kinase pathways, cPLA2alpha and 5-LO comigrate from a soluble cell compartment (mainly the cytosol) to the nuclear membrane, where AA is released und converted into LTs. LTs play a significant role in promoting inflammatory reactions and immune processes. They have been shown to be released from leukocytes in response to bacterial and viral infections and substantially contribute to an effective immune reaction for host defense. Innate immune pathogen recognition is mediated to a substantial part by the Toll-like receptor (TLR) family. So far, 10 human TLR subtypes have been identified, all of which detect distinct highly conserved microbial structures and trigger the induction of signaling pathways that lead to the expression of numerous immune and inflammatory genes. TLR signaling culminates in the activation NF-kappaB and/or MAP kinases, which as well are known to be involved in the regulation of cellular LT biosynthesis. In this regard, it seemed conceivable that the release of LTs might be regulated by TLR activation. Present studies were undertaken in order to verify and characterize a possible influence of TLR activation on the LT biosynthesis, and furthermore to identify the involved signaling pathways and underlying mechanisms. First experiments revealed that pre-incubation of differentiated Mono Mac 6 (MM6) cells with a TLR4 ligand, a TLR5 ligand, as well as with different TLR2 ligands led to an about 2-fold enhancement of Ca2+ ionophore induced LT biosynthesis. Ligands of other TLR subtypes did not show any influence. These observations could also be confirmed in primary human monocytes stimulated with ionophore or fMLP. With focus on TLR2 ligands, further studies were carried out to characterize the observed enhancement of LT biosynthesis in MM6 cells. It was demonstrated that the extent of LT formation was dependent on the ligand concentration used, but was also dependent on the duration of pre-incubation. Ligand pre-incubation of 15 minutes was optimal to maximally enhance LT formation and further prolongation of pre-incubation decreased LT formation again. Moreover, simultaneous addition of TLR2 ligands with ionophore did also not enhance LT formation. These results indicated that TLR2 ligands seemed to prime human monocytes for an enhanced response upon ionophore stimulation, but did not act as costimuli, which per se were not capable of directly stimulating the biosynthesis of LTs. To analyze the underlying mechanism, the impact of TLR2 ligands on the two key enzymes of the LT biosynthesis pathway, cPLA2alpha and 5-LO, was investigated. In this regard, 5-LO could not been shown to be positively regulated by TLR ligand priming. Neither a direct stimulation, nor an enhancement of 5-LO activity by TLR ligands was detectable in MM6 cells. Similarly, TLR2 ligands did also not enhance ionophore induced 5-LO translocation to the nuclear membrane. However, it was shown that TLR2 ligands enhanced ionophore induced release of AA in MM6 cells, which occurred with a similar time course as LT formation, displaying a maximum at 10 minutes of pre-incubation. A direct stimulation of AA release, however, could not been detected. Inhibitor studies revealed cPLA2alpha to be essential for AA release in TLR2 ligand primed, ionophore stimulated MM6 cells, but also sPLA2 was found to be involved. However, the priming effect of TLR2 ligands was mediated exclusively by cPLA2alpha. Western Blot analyses revealed that p38 MAP kinase, as well as ERK1/2, are activated in MM6 cells in response to TLR2 ligands, and also Ser-505 phosphorylation of cPLA2alpha was detected, which is known to be mediated by MAP kinases and to increase cPLA2alpha activity in vitro. Maximal cPLA2alpha phosphorylation occurred after 5-10 minutes of TLR2 ligand incubation, slightly preceding maximal AA release at 10 minutes and maximal LT formation at 15 minutes of priming. The combined use of a specific p38 MAPK inhibitor with an inhibitor of the ERK1/2 signaling pathway resulted in a complete prevention of cPLA2alpha phosphorylation and TLR2 ligand mediated enhancement of AA release. Thus, both MAPK pathways seem to play a role for TLR2 ligand mediated priming effects on the release of AA. An impact of other kinases such as Mnk-1 and CamKII, which can also regulate cPLA2alpha by phosphorylation, was excluded. Finally, an anti-hTLR2 antibody significantly reduced enhanced AA release, confirming the priming effects to be dependent on TLR2 activation. In summary, it was concluded that the increase of LT biosynthesis by TLR2 ligand priming is considerably due to an enhanced cellular AA supply, which arises from a MAPK mediated phosphorylation and up-regulation of cPLA2alpha. TLR dependent enhancement of LT biosynthesis represents an interesting link between activation of innate immune receptors and the rapid formation of pro-inflammatory lipid mediators. On the one hand, this support the role of LTs in host defence and infectious diseases, but may also be relevant in pathophysiological processes, which involve TLRs as well as LTs, as it has been shown for the pathogenesis of atherosclerosis or allergic diseases.
Genes coding for membrane proteins make up 25%-30% of the genome in most organisms. Membrane proteins play an important role in cell functioning and their importance is enhanced by the fact that a large number of drugs are targeted at membrane proteins. Paradoxically, experimentally determined structures of membrane protein correspond to only about 1.7% of protein structures deposited in the protein data bank (PDB). This is largely due to the fact that membrane proteins are difficult to deal with owing to their amphipathic nature. The low abundance of membrane proteins in native tissue makes heterologous overexpression of these genes a necessity. This thesis work aimed at heterologous production of several secondary active transporter proteins for structural and functional characterizations and establishing alternative strategies to overcome the obstacles associated with heterologous overproduction. Four members of the heavy metal transporting cation diffusion facilitator (CDF) family from S. typhimurium and A. aeolicus were heterologously overproduced in E. coli and functionally characterized by an in vivo complementation assay using the zinc transport deficient E. coli GG48 strain. Out of these four, Aq_2073 from A. aeolicus was produced in large scale with substantial yield and purity sufficient to carry out structural studies. After extensive stability studies with different detergents, pHs and temperatures, the protein was subjected to 3D and 2D crystallization trials. Several C- terminal truncated constructs were made and the simultaneous crystallization screenings were carried out. These resulted in initial needle like crystals in 3D crystallization trials or optimum sized vesicles with crystalline patches in 2D crystallization trials but no obvious crystal. The protein showed significant increase in melting temperature in the presence of cadmium, when tested by differential scanning calorimetry. Another transporter, STM3880 of the potassium uptake permease (KUP) family from S. typhimurium, was heterologously overproduced in E. coli, purified by affinity chromatography, reconstituted into artificial liposome and functionally characterized by solid supported membrane based electrophysiology. In order to establish alternative expression strategies, continuous exchange cell free expression (CECF) of proteins from four different families was carried out. This method found to be aptly complementing the cell-based production approach. Targets from resistance to homoserine/threonine (RhtB) family not expressing in vivo could be expressed and purified using CECF. STM1781 of the sulfate permease (SulP) family was expressed, purified and characterized for stability while the cell-based production resulted in extensive degradation. PF0780 of multidrug/oligosaccharidyllipid/polysaccharide flippase (MOP) family was also purified to homogeneity and the stability was comparable to in vivo produced protein. Moreover, the effect of maltose binding protein (MBP) fusion at N-terminus on production and membrane integration was tested with three selected targets. The analysis revealed decreased yields in the presence of MBP if the protein had both termini in the cytoplasm. This work succeed in heterologously overproducing and establishing purification protocols for several secondary active transporters aiming at structural and functional characterization in a structural genomics framework. It also showed that integration of alternative strategies, like employing both cell-based and cell-free heterologous expression systems, expands the overall expression space coverage and in turn increases the chance of success of a structural genomics styled project.
This dissertation consists of three essays, which study the relation between stock prices and the macroeconomy using vector autoregressions (VARs). The first essay focuses on the link between stock prices and the current account. I find that stock markets provide a channel, in addition to the traditional exchange rate channel, through which external balance for a country with a current account imbalance can be restored. The second essay explores the transmission of U.S. stock price shocks to real activity and prices in G-7 countries. I achieve identification by imposing a small number of sign restrictions on impulse responses, while controlling for monetary policy, business cycle and government spending shocks. The results suggest that stock price movements are important for fluctuations in G-7 real activity and prices, but do not qualify as demand side business cycle shocks. The third essay investigates the impact of monetary and technology shocks on the stock market. I find an important role for technology shocks, but not monetary shocks, in explaining variations in real stock prices. The identification method is flexible enough to study the effects of technology news shocks. The responses are consistent with the idea that news on technology improvements have an immediate impact on stock prices.
Plasticity supports the remarkable adaptability and robustness of cortical processing. It allows the brain to learn and remember patterns in the sensory world, to refine motor control, to predict and obtain reward, or to recover function after injury. Behind this great flexibility hide a range of plasticity mechanisms, affecting different aspects of neuronal communication. However, little is known about the precise computational roles of some of these mechanisms. Here, we show that the interaction between spike-timing dependent plasticity (STDP), intrinsic plasticity and synaptic scaling enables neurons to learn efficient representations of their inputs. In the context of reward-dependent learning, the same mechanisms allow a neural network to solve a working memory task. Moreover, although we make no any apriori assumptions on the encoding used for representing inputs, the network activity resembles that of brain regions known to be associated with working memory, suggesting that reward-dependent learning may be a central force in working memory development. Lastly, we investigated some of the clinical implications of synaptic scaling and showed that, paradoxically, there are situations in which the very mechanisms that normally are required to preserve the balance of the system, may act as a destabilizing factor and lead to seizures. Our model offers a novel explanation for the increased incidence of seizures following chronic inflammation.
The physical and functional borders of transit peptide-like sequences in secondary endosymbionts
(2010)
Background: Plastids rely on protein supply by their host cells. In plastids surrounded by two membranes (primary plastids) targeting of these proteins is facilitated by an N-terminal targeting signal, the transit peptide. In secondary plastids (surrounded by three or four membranes), transit peptide-like regions are an essential part of a bipartite topogenic signal sequence (BTS), and generally found adjacent to a N-terminally located signal peptide of the plastid pre-proteins. As in primary plastids, for which no wealth of functional information about transit peptide features exists, the transit peptide-like regions used for import into secondary ones show some common features only, which are also poorly characterised. Results: We modified the BTS (in the transit peptide-like region) of the plastid precursor fucoxanthin-chlorophyll a/c binding protein D (FcpD) fused to GFP as model substrate for the characterisation of pre-protein import into the secondary plastids of diatoms. Thereby we show that (i) pre-protein import is highly charge dependent. Positive net charge is necessary for transport across the plastid envelope, but not across the periplastid membrane. Acidic net charge perturbs pre-protein import within the ER. Moreover, we show that (ii) the mature domain of the pre-protein can provide intrinsic transit peptide functions. Conclusions: Our results indicate important characteristics of targeting signals of proteins imported into secondary plastids surrounded by four membranes. In addition, we show a self-targeting mechanism, in which the mature protein domain contributes to the transit peptide function. Thus, this phenomenon lowers the demand for pre-sequences evolved during the course of endosymbiosis.
This essay examines the differing contexts and modes of encounter with Islamic culture in the travel writing of two contrasting women, the Prussian Countess Ida Hahn-Hahn and the Austrian Maria Schuber: both travelled to and wrote from the Middle East in the 1830s and 1840s and published their letters as collections. The encounters both women had with Islam were conditioned, at least in part, by their respective stance on religion, issues of gender and social class, and by the obligations of patronage and the expectations of distinct readerships. Whilst both women can be seen to write about Islam as a religion and culture defined by its difference to Christianity, both can also be seen in differing ways and to differing extents to represent Islam and Muslims as simultaneously belonging to a universal and inclusive notion of humanity and human religion. Thus, without embracing high philosophical discourse of Kant or Hegel, both women can be seen to demonstrate cosmopolitan impulses towards Islam, although these jostle for ascendancy with a more Eurocentric, Christian and indeed völkisch vision of the relationship between cultures.
Within the visual cortex, it has been proposed that interhemispheric interactions serve to re-establish the continuity of the visual field across its vertical meridian (VM) by mechanisms similar to those used by intrinsic connections within a hemisphere. However, other specific functions of transcallosal projections have also been proposed, including contributing to disparity tuning and depth perception. Here, we consider whether interhemispheric connections modulate specific response properties, orientation and direction selectivity, of neurons in areas 17 and 18 of the ferret by combining reversible thermal deactivation in one hemisphere with optical imaging of intrinsic signals and single-cell electrophysiology in the other hemisphere. We found interhemispheric influences on both the strength and specificity of the responses to stimulus orientation and direction of motion, predominantly at the VM. However, neurons and domains preferring cardinal contours, in particular vertical contours, seem to receive stronger interhemispheric input than others. This finding is compatible with interhemispheric connections being involved in horizontal disparity tuning. In conclusion, our results support the view that interhemispheric interactions mainly perform integrative functions similar to those of connections intrinsic to one hemisphere. Key words: cooling deactivation , corpus callosum , ferret , optical imaging , orientation selectivity
Studying the role of human parietal cortex in visuospatial attention with concurrent TMS-fMRI
(2010)
Combining transcranial magnetic stimulation (TMS) with concurrent functional magnetic resonance imaging (fMRI) allows study of how local brain stimulation may causally affect activity in remote brain regions. Here, we applied bursts of high- or low-intensity TMS over right posterior parietal cortex, during a task requiring sustained covert visuospatial attention to either the left or right hemifield, or in a neutral control condition, while recording blood oxygenation-level–dependent signal with a posterior MR surface coil. As expected, the active attention conditions activated components of the well-described “attention network,” as compared with the neutral baseline. Also as expected, when comparing left minus right attention, or vice versa, contralateral occipital visual cortex was activated. The critical new finding was that the impact of high- minus low-intensity parietal TMS upon these visual regions depended on the currently attended side. High- minus low-intensity parietal TMS increased the difference between contralateral versus ipsilateral attention in right extrastriate visual cortex. A related albeit less pronounced pattern was found for left extrastriate visual cortex. Our results confirm that right human parietal cortex can exert attention-dependent influences on occipital visual cortex and provide a proof of concept for the use of concurrent TMS–fMRI in studying how remote influences can vary in a purely top–down manner with attentional demands. Key words: concurrent TMS--fMRI, posterior parietal cortex, statedependence, visuospatial attention
Gamma synchronization has generally been associated with grouping processes in the visual system. Here, we examine in monkey V1 whether gamma oscillations play a functional role in segmenting surfaces of plaid stimuli. Local field potentials (LFPs) and spiking activity were recorded simultaneously from multiple sites in the opercular and calcarine regions while the monkeys were presented with sequences of single and superimposed components of plaid stimuli. In accord with the previous studies, responses to the single components (gratings) exhibited strong and sustained gamma-band oscillations (30–65 Hz). The superposition of the second component, however, led to profound changes in the temporal structure of the responses, characterized by a drastic reduction of gamma oscillations in the spiking activity and systematic shifts to higher frequencies in the LFP (~10% increase). Comparisons between cerebral hemispheres and across monkeys revealed robust subject-specific spectral signatures. A possible interpretation of our results may be that single gratings induce strong cooperative interactions among populations of cells that share similar response properties, whereas plaids lead to competition. Overall, our results suggest that the functional architecture of the cortex is a major determinant of the neuronal synchronization dynamics in V1. Key words: attention , gamma , gratings , oscillation , visual cortex
Understanding how temperature affects cod (Gadus morhua) ecology is important for forecasting how populations will develop as climate changes in future. The effects of spawning-season temperature and habitat size on cod recruitment dynamics have been investigated across the North Atlantic. Ricker and Beverton and Holt stock–recruitment (SR) models were extended by applying hierarchical methods, mixed-effects models, and Bayesian inference to incorporate the influence of these ecosystem factors on model parameters representing cod maximum reproductive rate and carrying capacity. We identified the pattern of temperature effects on cod productivity at the species level and estimated SR model parameters with increased precision. Temperature impacts vary geographically, being positive in areas where temperatures are <5°C, and negative for higher temperatures. Using the relationship derived, it is possible to predict expected changes in population-specific reproductive rates and carrying capacities resulting from temperature increases. Further, carrying capacity covaries with available habitat size, explaining at least half its variability across stocks. These patterns improve our understanding of environmental impacts on key population parameters, which is required for an ecosystem approach to cod management, particularly under ocean-warming scenarios. Key words: carrying capacity , cod , hierarchical models , North Atlantic , temperature , uncertainty
The massive amount of genomic sequence data that is now available for analyzing evolutionary relationships among 31 placental mammals reduces the stochastic error in phylogenetic analyses to virtually zero. One would expect that this would make it possible to finally resolve controversial branches in the placental mammalian tree. We analyzed a 2,863,797 nucleotide-long alignment (3,364 genes) from 31 placental mammals for reconstructing their evolution. Most placental mammalian relationships were resolved, and a consensus of their evolution is emerging. However, certain branches remain difficult or virtually impossible to resolve. These branches are characterized by short divergence times in the order of 1-4 million years. Computer simulations based on parameters from the real data show that as little as about 12,500 amino acid sites could be sufficient to confidently resolve short branches as old as about 90 million years ago. Thus, the amount of sequence data should no longer be a limiting factor in resolving the relationships among placental mammals. The timing of the early radiation of placental mammals coincides with a period of climate warming some 100 - 80 million years ago and with continental fragmentation. These global processes may have triggered the rapid diversification of placental mammals. However, the rapid radiations of certain mammalian groups complicate phylogenetic analyses, possibly due to incomplete lineage sorting and introgression. These speciation-related processes led to a mosaic genome and conflicting phylogenetic signals. Split network methods are ideal for visualizing these problematic branches and can therefore depict data conflict and possibly the true evolutionary history better than strictly bifurcating trees. Given the timing of tectonics, of placental mammalian divergences, and the fossil record, a Laurasian rather than Gondwanan origin of placental mammals seems the most parsimonious explanation. Key words: continental drift , Cretaceous warming , genome analysis , hybridization , phylogenomics , split decomposition
Fucoxanthin chlorophyll proteins (Fcps), the light-harvesting antennas of heterokont algae, are encoded by a multigene family and are highly similar with respect to their molecular masses as well as to their pigmentation, making it difficult to purify single Fcps. In this study, a hexa-histidine tag was genetically added to the C-terminus of the FcpA protein of the pennate diatom Phaeodactylum tricornutum. A transgenic strain expressing the recombinant His-tagged FcpA protein in addition to the endogenous wild type Fcps was created. This strategy allowed, for the first time, the purification of a specific, stable trimeric Fcp complex. In addition, a pool of various trimeric Fcps was also purified from the wild-type cells using sucrose density gradient ultracentrifugation and gel filtration. In both the His-tagged and the wild-type Fcps, excitation energy coupling between fucoxanthin and chlorophyll a was intact and the existence of a chlorophyll a/fucoxanthin excitonic dimer was demonstrated using circular dichroism spectroscopy. Mass spectrometric analyses of the trimeric His-tagged complex indicated that it is composed of FcpA and FcpE polypeptides. It is confirmed here that a trimer is the basic organizational unit of Fcps in P. tricornutum. From circular dichroism spectra, it is proposed that the organization of the pigments on the polypeptide backbone of Fcps is a conserved feature in the case of chlorophyll a/c containing algae.
Transcripts of NANOG and OCT4 have been recently identified in human t(4;11) leukemia and in a model system expressing both t(4;11) fusion proteins. Moreover, downstream target genes of NANOG/OCT4/SOX2 were shown to be transcriptionally activated. However, the NANOG1 gene belongs to a gene family, including a gene tandem duplication (named NANOG2 or NANOGP1) and several pseudogenes (NANOGP2-P11). Thus, it was unclear which of the NANOG family members were transcribed in t(4;11) leukemia cells. 5'-RACE experiments revealed novel 5'-exons of NANOG1 and NANOG2, which could give rise to the expression of two different NANOG1 and three different NANOG2 protein variants. Moreover, a novel PCR-based method was established that allows distinguishing between transcripts deriving from NANOG1, NANOG2 and all other NANOG pseudogenes (P2–P11). By applying this method, we were able to demonstrate that human hematopoietic stem cells and different leukemic cells transcribe NANOG2. Furthermore, we functionally tested NANOG1 and NANOG2 protein variants by recombinant expression in 293 cells. These studies revealed that NANOG1 and NANOG2 protein variants are functionally equivalent and activate a regulatory circuit that activates specific stem cell genes. Therefore, we pose the hypothesis that the transcriptional activation of NANOG2 represents a ‘gain-of-stem cell function’ in acute leukemia.
Recombinase-mediated cassette exchange (RMCE) exploits the possibility to unidirectionally exchange any genetic material flanked by heterotypic recombinase recognition sites (RRS) with target sites in the genome. Due to a limited number of available pre-fabricated target sites, RMCE in mouse embryonic stem (ES) cells has not been tapped to its full potential to date. Here, we introduce a universal system, which allows the targeted insertion of any given transcriptional unit into 85 742 previously annotated retroviral conditional gene trap insertions, representing 7013 independent genes in mouse ES cells, by RMCE. This system can be used to express any given cDNA under the control of endogenous trapped promoters in vivo, as well as for the generation of transposon ‘launch pads’ for chromosomal region-specific ‘Sleeping Beauty’ insertional mutagenesis. Moreover, transcription of the gene-of-interest is only activated upon Cre-recombinase activity, a feature that adds conditionality to this expression system, which is demonstrated in vivo. The use of the RMCE system presented in this work requires one single-cloning step followed by one overnight gateway clonase reaction and subsequent cassette exchange in ES cells with efficiencies of 40% in average.
Human Transformer2-beta (hTra2-beta) is an important member of the serine/arginine-rich protein family, and contains one RNA recognition motif (RRM). It controls the alternative splicing of several pre-mRNAs, including those of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Accordingly, the RRM of hTra2-beta specifically binds to two types of RNA sequences [the CAA and (GAA)2 sequences]. We determined the solution structure of the hTra2-beta RRM (spanning residues Asn110–Thr201), which not only has a canonical RRM fold, but also an unusual alignment of the aromatic amino acids on the beta-sheet surface. We then solved the complex structure of the hTra2-beta RRM with the (GAA)2 sequence, and found that the AGAA tetra-nucleotide was specifically recognized through hydrogen-bond formation with several amino acids on the N- and C-terminal extensions, as well as stacking interactions mediated by the unusually aligned aromatic rings on the beta-sheet surface. Further NMR experiments revealed that the hTra2-beta RRM recognizes the CAA sequence when it is integrated in the stem-loop structure. This study indicates that the hTra2-beta RRM recognizes two types of RNA sequences in different RNA binding modes.
We present here a set of 13C-direct detected NMR experiments to facilitate the resonance assignment of RNA oligonucleotides. Three experiments have been developed: (1) the (H)CC-TOCSY-experiment utilizing a virtual decoupling scheme to assign the intraresidual ribose 13C-spins, (2) the (H)CPC-experiment that correlates each phosphorus with the C40 nuclei of adjacent nucleotides via J(C,P) couplings and (3) the (H)CPC-CCH-TOCSY-experiment that correlates the phosphorus nuclei with the respective C10,H10 ribose signals. The experiments were applied to two RNA hairpin structures. The current set of 13C-direct detected experiments allows direct and unambiguous assignment of the majority of the hetero nuclei and the identification of the individual ribose moieties following their sequential assignment. Thus, 13C-direct detected NMR methods constitute useful complements to the conventional 1H-detected approach for the resonance assignment of oligonucleotides that is often hindered by the limited chemical shift dispersion. The developed methods can also be applied to large deuterated RNAs. Keywords: NMR spectroscopy , Direct carbon , detection , RNA
The Nep1 (Emg1) SPOUT-class methyltransferase is an essential ribosome assembly factor and the human Bowen–Conradi syndrome (BCS) is caused by a specific Nep1D86G mutation. We recently showed in vitro that Methanocaldococcus jannaschii Nep1 is a sequence-specific pseudouridine-N1-methyltransferase. Here, we show that in yeast the in vivo target site for Nep1-catalyzed methylation is located within loop 35 of the 18S rRNA that contains the unique hypermodification of U1191 to 1-methyl-3-(3-amino-3-carboxypropyl)-pseudouri-dine (m1acp3Psi). Specific 14C-methionine labelling of 18S rRNA in yeast mutants showed that Nep1 is not required for acp-modification but suggested a function in Psi1191 methylation. ESI MS analysis of acp-modified Psi-nucleosides in a DeltaNep1-mutant showed that Nep1 catalyzes the Psi1191 methylation in vivo. Remarkably, the restored growth of a nep1-1ts mutant upon addition of S-adenosylmethionine was even observed after preventing U1191 methylation in a deltasnr35 mutant. This strongly suggests a dual Nep1 function, as Psi1191-methyltransferase and ribosome assembly factor. Interestingly, the Nep1 methyltransferase activity is not affected upon introduction of the BCS mutation. Instead, the mutated protein shows enhanced dimerization propensity and increased affinity for its RNA-target in vitro. Furthermore, the BCS mutation prevents nucleolar accumulation of Nep1, which could be the reason for reduced growth in yeast and the Bowen-Conradi syndrome.
Long-range tertiary interactions determine the three-dimensional structure of a number of metabolite-binding riboswitch RNA elements and were found to be important for their regulatory function. For the guanine-sensing riboswitch of the Bacillus subtilis xpt-pbuX operon, our previous NMR-spectroscopic studies indicated pre-formation of long-range tertiary contacts in the ligand-free state of its aptamer domain. Loss of the structural pre-organization in a mutant of this RNA (G37A/C61U) resulted in the requirement of Mg2+ for ligand binding. Here, we investigate structural and stability aspects of the wild-type aptamer domain (Gsw) and the G37A/C61U-mutant (Gswloop) of the guanine-sensing riboswitch and their Mg2+-induced folding characteristics to dissect the role of long-range tertiary interactions, the link between pre-formation of structural elements and ligand-binding properties and the functional stability. Destabilization of the long-range interactions as a result of the introduced mutations for Gswloop or the increase in temperature for both Gsw and Gswloop involves pronounced alterations of the conformational ensemble characteristics of the ligand-free state of the riboswitch. The increased flexibility of the conformational ensemble can, however, be compensated by Mg2+. We propose that reduction of conformational dynamics in remote regions of the riboswitch aptamer domain is the minimal pre-requisite to pre-organize the core region for specific ligand binding.
In prokaryotes, RNA thermometers regulate a number of heat shock and virulence genes. These temperature sensitive RNA elements are usually located in the 5'-untranslated regions of the regulated genes. They repress translation initiation by base pairing to the Shine–Dalgarno sequence at low temperatures. We investigated the thermodynamic stability of the temperature labile hairpin 2 of the Salmonella fourU RNA thermometer over a broad temperature range and determined free energy, enthalpy and entropy values for the base-pair opening of individual nucleobases by measuring the temperature dependence of the imino proton exchange rates via NMR spectroscopy. Exchange rates were analyzed for the wild-type (wt) RNA and the A8C mutant. The wt RNA was found to be stabilized by the extraordinarily stable G14–C25 base pair. The mismatch base pair in the wt RNA thermometer (A8–G31) is responsible for the smaller cooperativity of the unfolding transition in the wt RNA. Enthalpy and entropy values for the base-pair opening events exhibit linear correlation for both RNAs. The slopes of these correlations coincide with the melting points of the RNAs determined by CD spectroscopy. RNA unfolding occurs at a temperature where all nucleobases have equal thermodynamic stabilities. Our results are in agreement with a consecutive zipper-type unfolding mechanism in which the stacking interaction is responsible for the observed cooperativity. Furthermore, remote effects of the A8C mutation affecting the stability of nucleobase G14 could be identified. According to our analysis we deduce that this effect is most probably transduced via the hydration shell of the RNA.
BACKGROUND: Parkinson's disease (PD), the second most frequent neurodegenerative disorder at old age, can be caused by elevated expression or the A53T missense mutation of the presynaptic protein alpha-synuclein (SNCA). PD is characterized pathologically by the preferential vulnerability of the dopaminergic nigrostriatal projection neurons. METHODOLOGY/PRINCIPAL FINDINGS: Here, we used two mouse lines overexpressing human A53T-SNCA and studied striatal dysfunction in the absence of neurodegeneration to understand early disease mechanisms. To characterize the progression, we employed young adult as well as old mice. Analysis of striatal neurotransmitter content demonstrated that dopamine (DA) levels correlated directly with the level of expression of SNCA, an observation also made in SNCA-deficient (knockout, KO) mice. However, the elevated DA levels in the striatum of old A53T-SNCA overexpressing mice may not be transmitted appropriately, in view of three observations. First, a transcriptional downregulation of the extraneural DA degradation enzyme catechol-ortho-methytransferase (COMT) was found. Second, an upregulation of DA receptors was detected by immunoblots and autoradiography. Third, extensive transcriptome studies via microarrays and quantitative real-time RT-PCR (qPCR) of altered transcript levels of the DA-inducible genes Atf2, Cb1, Freq, Homer1 and Pde7b indicated a progressive and genotype-dependent reduction in the postsynaptic DA response. As a functional consequence, long term depression (LTD) was absent in corticostriatal slices from old transgenic mice. CONCLUSIONS/SIGNIFICANCE: Taken together, the dysfunctional neurotransmission and impaired synaptic plasticity seen in the A53T-SNCA overexpressing mice reflect early changes within the basal ganglia prior to frank neurodegeneration. As a model of preclinical stages of PD, such insights may help to develop neuroprotective therapeutic approaches.
Hollywood musicals combine two distinctive features: narrative and musical numbers, also referred to as “the real and the expressive” (Telotte 1980a, 4). These two equally important parts of any successful musical have to harmonize such that both seem appropriate in each scene and, ideally, supportive of each other. As musical numbers are traditionally seen as a “source of a tension” (ibid., 2) within the narrative, harmonization is not easy to achieve, and different directors as well as different sub-genres of the film musical have found different ways to deal with this tension. In this work, I will discuss two methods of integrating musical numbers into the plot of Hollywood musicals: the stage-worlds and the world-stages. While the former entails a certain kind of storyline, the latter refers to the setting of single numbers within the plot.
Introduction: Acute lung injury (ALI) is an inflammatory disorder of pulmonary or extrapulmonary origin. We have previously demonstrated that netrin-1 dampens murine ALI, and in an attempt to advance this finding into future clinical practice we evaluated whether netrin-1 would reduce alveolar inflammation during porcine ALI. Methods: This was a controlled in vivo experimental study in pigs. We induced ALI through lipoploysaccharide (LPS) infusion (50 micro g/kg) for 2 hours. Following this, we exposed animals to either vehicle, intravenous netrin-1 (netrin-1 i.v.) or inhaled netrin-1 (netrin-1 inh.). Serum samples and bronchoalveolar lavage (BAL) were obtained to determine levels of tumor necrosis factor-alpha (TNF-alpha), interleukin (IL)-1beta, interleukin-6 and interleukin-8 at baseline and 6 hours following treatment. Myeloperoxidase activity (MPO) and protein levels were determined in the BAL, and tissue samples were obtained for histological evaluation. Finally, animals were scanned with spiral CT. Results: Following LPS infusion, animals developed acute pulmonary injury. Serum levels of TNF-alpha and IL-6 were significantly reduced in the netrin-1 i.v. group. BAL demonstrated significantly reduced cytokine levels 6 hours post-netrin-1 treatment (TNF-alpha: vehicle 633 ± 172 pg/ml, netrin-1 i.v. 84 ± 5 pg/ml, netrin-1 inh. 168 ± 74 pg/ml; both P < 0.05). MPO activity and protein content were significantly reduced in BAL samples from netrin-1-treated animals. Histological sections confirmed reduced inflammatory changes in the netrin-1-treated animals. Computed tomography corroborated reduced pulmonary damage in both netrin-1-treated groups. Conclusions: We conclude that treatment with the endogenous anti-inflammatory protein netrin-1 reduces pulmonary inflammation during the initial stages of ALI and should be pursued as a future therapeutic option.
The goal of this project is to develop a framework for a cell that takes in consideration its internal structure, using an agent-based approach. In this framework, a cell was simulated as many sub-particles interacting to each other. This sub-particles can, in principle, represent any internal structure from the cell (organelles, etc). In the model discussed here, two types of sub-particles were used: membrane sub-particles and cytosolic elements. A kinetic and dynamic Delaunay triangulation was used in order to define the neighborhood relations between the sub-particles. However, it was soon noted that the relations defined by the Delaunay triangulation were not suitable to define the interactions between membrane sub-particles. The cell membrane is a lipid bilayer, and does not present any long range interactions between their sub-particles. This means that the membrane particles should not be able to interact in a long range. Instead, their interactions should be confined to the two-dimensional surface supposedly formed by the membrane. A method to select, from the original three-dimensional triangulations, connections restricted to the two-dimensional surface formed by the cell membrane was then developed. The algorithm uses as starting point the three-dimensional Delaunay triangulation involving both internal and membrane sub-particles. From this triangulation, only the subset of connections between membrane sub-particles was considered. Since the cell is full of internal particles, the collection of the membrane particles' connections will resemble the surface to be obtained, even though it will still have many connections that do not belong to the restricted triangulation on the surface. This "thick surface" was called a quasi-surface. The following step was to refine the quasi-surface, cutting out some of the connections so that the ones left made a proper surface triangulation with the membrane points. For that, the quasi-surface was separated in clusters. Clusters are defined as areas on the quasi-surface that are not yet properly triangulated on a two-dimensional surface. Each of the clusters was then re-triangulated independently, using re-triangulation methods also developed during this work. The interactions between cytosolic elements was given by a Lennard-Jones potential, as well as the interactions between cytosolic elements and membrane particles. Between only membrane particles, the interactions were given by an elastic interaction. For each particle, the equation of motion was written. The algorithm chosen to solve the equations of motion was the Verlet algorithm. Since the cytosol can be approximated as a gel, it is reasonable to suppose that the sub-cellular particles are moving in an overdamped environment. Therefore, an overdamped approximation was used for all interactions. Additionally, an adaptive algorithm was used in order to define the size of the time step used in each interaction. After the method to re-triangulate the membrane points was implemented, the time needed to re-triangulate a single cluster was studied, followed by an analysis on how the time needed to re-triangulate each point in a cluster varied with the cluster size. The frequency of appearance for each cluster size was also compared, as this information is necessary to guarantee that the total time needed by to re-triangulate a cell is convergent. At last, the total time spent re-triangulating a surface was plotted, as well as a scaling for the total re-triangulation time with the variation. Even though there is still a lot to be done, the work presented here is an important step on the way to the main goal of this project: to create an agent-based framework that not only allows the simulation of any sub-cellular structure of interest but also provides meaningful interaction relations to particles belonging to the cell membrane.
During a 4-week run in October–November 2006, a pilot experiment was performed at the CERN Proton Synchrotron in preparation for the Cosmics Leaving OUtdoor Droplets (CLOUD) experiment, whose aim is to study the possible influence of cosmic rays on clouds. The purpose of the pilot experiment was firstly to carry out exploratory measurements of the effect of ionising particle radiation on aerosol formation from trace H2SO4 vapour and secondly to provide technical input for the CLOUD design. A total of 44 nucleation bursts were produced and recorded, with formation rates of particles above the 3 nm detection threshold of between 0.1 and 100 cm -3 s -1, and growth rates between 2 and 37 nm h -1. The corresponding H2O concentrations were typically around 106 cm -3 or less. The experimentally-measured formation rates and htwosofour concentrations are comparable to those found in the atmosphere, supporting the idea that sulphuric acid is involved in the nucleation of atmospheric aerosols. However, sulphuric acid alone is not able to explain the observed rapid growth rates, which suggests the presence of additional trace vapours in the aerosol chamber, whose identity is unknown. By analysing the charged fraction, a few of the aerosol bursts appear to have a contribution from ion-induced nucleation and ion-ion recombination to form neutral clusters. Some indications were also found for the accelerator beam timing and intensity to influence the aerosol particle formation rate at the highest experimental SO2 concentrations of 6 ppb, although none was found at lower concentrations. Overall, the exploratory measurements provide suggestive evidence for ion-induced nucleation or ion-ion recombination as sources of aerosol particles. However in order to quantify the conditions under which ion processes become significant, improvements are needed in controlling the experimental variables and in the reproducibility of the experiments. Finally, concerning technical aspects, the most important lessons for the CLOUD design include the stringent requirement of internal cleanliness of the aerosol chamber, as well as maintenance of extremely stable temperatures (variations below 0.1 °C)
Aging of biological systems ultimately leads to death of the individual. In humans, organ failure as the result of functional impairments after stroke, cardio-vascular disease, tumor development, neurodegeneration and other diseases are certainly crucial in bringing life to an end. But what happens in individuals with no obvious disease or disorders?
Plasticity resembling spike-timing dependent synaptic plasticity: the evidence in human cortex
(2010)
Spike-timing dependent plasticity (STDP) has been studied extensively in a variety of animal models during the past decade but whether it can be studied at the systems level of the human cortex has been a matter of debate. Only recently newly developed non-invasive brain stimulation techniques such as transcranial magnetic stimulation (TMS) have made it possible to induce and assess timing dependent plasticity in conscious human subjects. This review will present a critical synopsis of these experiments, which suggest that several of the principal characteristics and molecular mechanisms of TMS-induced plasticity correspond to those of STDP as studied at a cellular level. TMS combined with a second phasic stimulation modality can induce bidirectional long-lasting changes in the excitability of the stimulated cortex, whose polarity depends on the order of the associated stimulus-evoked events within a critical time window of tens of milliseconds. Pharmacological evidence suggests an NMDA receptor mediated form of synaptic plasticity. Studies in human motor cortex demonstrated that motor learning significantly modulates TMS-induced timing dependent plasticity, and, conversely, may be modulated bidirectionally by prior TMS-induced plasticity, providing circumstantial evidence that long-term potentiation-like mechanisms may be involved in motor learning. In summary, convergent evidence is being accumulated for the contention that it is now possible to induce STDP-like changes in the intact human central nervous system by means of TMS to study and interfere with synaptic plasticity in neural circuits in the context of behavior such as learning and memory. Keywords: spike-timing dependent plasticity, long-term potentiation, long-term depression, paired associative stimulation, transcranial magnetic stimulation, human, cortex, translational neuroscience
Potentiation of glycine-gated NR1/NR3A NMDA receptors relieves Ca2+-dependent outward rectification
(2010)
Glycine has diverse functions within the mammalian central nervous system. It inhibits postsynaptic neurons via strychnine-sensitive glycine receptors (GlyRs) and enhances neuronal excitation through co-activation of N-methyl-D-aspartate (NMDA) receptors. Classical Ca2+-permeable NMDA receptors are composed of glycine-binding NR1 and glutamate-binding NR2 subunits, and hence require both glutamate and glycine for efficient activation. In contrast, recombinant receptors composed of NR1 and the glycine binding NR3A and/or NR3B subunits lack glutamate binding sites and can be activated by glycine alone. Therefore these receptors are also named “excitatory glycine receptors”. Co-application of antagonists of the NR1 glycine-binding site or of the divalent cation Zn2+ markedly enhances the glycine responses of these receptors. To gain further insight into the properties of these glycine-gated NMDA receptors, we investigated their current-voltage (I–V) dependence. Whole-cell current-voltage relations of glycine currents recorded from NR1/NR3B and NR1/NR3A/NR3B expressing oocytes were found to be linear under our recording conditions. In contrast, NR1/NR3A receptors displayed a strong outwardly rectifying I–V relation. Interestingly, the voltage-dependent inward current block was abolished in the presence of NR1 antagonists, Zn2+ or a combination of both. Further analysis revealed that Ca2+ (1.8 mM) present in our recording solutions was responsible for the voltage-dependent inhibition of ion flux through NR1/NR3A receptors. Since physiological concentrations of the divalent cation Mg2+ did not affect the I–V dependence, our data suggest that relief of the voltage-dependent Ca2+ block of NR1/NR3A receptors by Zn2+ may be important for the regulation of excitatory glycinergic transmission, according to the Mg2+-block of conventional NR1/NR2 NMDA receptors. Keywords: NMDA receptor, excitatory glycine receptor, voltage block, NR3 subunit, supralinear potentiation, Zn2+, NR1 antagonist, ligand-binding domain
Although models based on independent component analysis (ICA) have been successful in explaining various properties of sensory coding in the cortex, it remains unclear how networks of spiking neurons using realistic plasticity rules can realize such computation. Here, we propose a biologically plausible mechanism for ICA-like learning with spiking neurons. Our model combines spike-timing dependent plasticity and synaptic scaling with an intrinsic plasticity rule that regulates neuronal excitability to maximize information transmission. We show that a stochastically spiking neuron learns one independent component for inputs encoded either as rates or using spike-spike correlations. Furthermore, different independent components can be recovered, when the activity of different neurons is decorrelated by adaptive lateral inhibition.
We examined whether positive transfer of cognitive training, which so far has been observed for individual tests only, also generalizes to cognitive abilities, thereby carrying greater promise for improving everyday intellectual competence in adulthood and old age. In the COGITO Study, 101 younger and 103 older adults practiced six tests of perceptual speed (PS), three tests of working memory (WM), and three tests of episodic memory (EM) for over 100 daily 1-h sessions. Transfer assessment included multiple tests of PS, WM, EM, and reasoning. In both age groups, reliable positive transfer was found not only for individual tests but also for cognitive abilities, represented as latent factors. Furthermore, the pattern of correlations between latent change factors of practiced and latent change factors of transfer tasks indicates systematic relations at the level of broad abilities, making the interpretation of effects as resulting from unspecific increases in motivation or self-concept less likely. Keywords: cognitive training, cognitive abilities, transfer, latent factors, working memory
Disruptive behaviour disorders are reflected by a great variety of symptoms ranging from impulsive-hot tempered quarrels to purposeful and goal directed acts of cruelty. A growing body of data indicates that there are neurobiological factors that increase the risk for developing disruptive behaviour disorders. In this review, we give a broad overview of recent studies investigating physiological, neural, genetic factors, and specific neurotransmitter systems. We also discuss the impact of psychosocial risk and consider the effects of gene-environment interactions. Due to the heterogeneity of disruptive behaviour disorders, it is concluded that specific subtypes of disruptive behaviour should be considered both in terms their biological basis and in regard to specific treatment needs.
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 delta 13C values that decrease from the rim to the center from - 18.8‰ to - 25.7‰ (V-PDB), but normal marine delta 18 O 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 asTisoa 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.
Background: Abnormalities of 11q23 involving the MLL gene are found in approximately 10% of human leukemias. To date, nearly 100 different chromosome bands have been described in rearrangements involving 11q23 and 64 fusion genes have been cloned and characterized at the molecular level. In this work we present the identification of a novel MLL fusion partner in a pediatric patient with de novo biphenotypic acute leukemia. Methods: Cytogenetics, fluorescence in situ hybridization (FISH), molecular studies (RT-PCR and LDI-PCR), and bioinformatic sequence analysis were used to characterize the CT45A2 gene as novel MLL fusion partner in pediatric acute leukemia. Results: Fluorescence in situ hybridization of the patient G-banded metaphases demonstrated a cryptic insertion of 11q23 in Xq26.3 involving the MLL gene. Breakpoint fusion analysis revealed that a DNA fragment of 653 kb from 11q23, containing MLL exons 1-9 in addition to 16 other 11q23 genes, was inserted into the upstream region of the CT45A2 gene located at Xq26.3. In addition, a deletion at Xq26.3 encompassing the 3' region of the DDX26B gene (exons 9-16) and the entire CT45A1 gene was identified. RNA analysis revealed the presence of a novel MLL-CT45A2 fusion transcript in which the first 9 exons of the MLL gene were fused in-frame to exon 2 of the CT45A2 gene, resulting in a spliced MLL fusion transcript with an intact open reading frame. The resulting chimeric transcript predicts a fusion protein where the N-terminus of MLL is fused to the entire open reading frame of CT45A2. Finally, we demonstrate that all breakpoint regions are rich in long repetitive motifs, namely LINE/L1 and SINE/Alu sequences, but all breakpoints were exclusively identified outside these repetitive DNA sequences. Conclusion: We have identified CT45A2 as a novel spliced MLL fusion partner in a pediatric patient with de novo biphenotypic acute leukemia, as a result of a cryptic insertion of 11q23 in Xq26.3. Since CT45A2 is the first Cancer/Testis antigen family gene found fused with MLL in acute leukemia, future studies addressing its biologic relevance for leukemogenesis are warranted.
Background: The enhancer of zeste homolog 2 (EZH2) gene exerts oncogene-like activities and its (over)expression has been linked to several human malignancies. Here, we studied a possible association between EZH2 expression and prognosis in patients with renal cell carcinoma (RCC). Methods: EZH2 protein expression in RCC specimens was analyzed by immunohistochemistry using a tissue microarray (TMA) containing RCC tumor tissue and corresponding normal tissue samples of 520 patients. For immunohistochemical assessment of EZH2 expression, nuclear staining quantity was evaluated using a semiquantitative score. The effect of EZH2 expression on cancer specific survival (CSS) was assessed by univariate and multivariate Cox regression analyses. Results: During follow-up, 147 patients (28%) had died of their disease, median follow-up of patients still alive was 6.0 years (range 0 - 16.1 years). EZH2 nuclear staining was present in tumor cores of 411 (79%) patients. A multivariate Cox regression analysis revealed that high nuclear EZH2 expression was an independent predictor of poor CSS (>25-50% vs. 0%: HR 2.72, p = 0.025) in patients suffering from non-metastatic RCC. Apart from high nuclear EZH2 expression, tumor stage and Fuhrman's grading emerged as significant prognostic markers. In metastatic disease, nuclear EZH2 expression and histopathological subtype were independent predictive parameters of poor CSS (EZH2: 1-5%: HR 2.63, p = 0.043, >5-25%: HR 3.35, p = 0.013, >25%-50%: HR 4.92, p = 0.003, all compared to 0%: HR 0.36, p = 0.025, respectively). Conclusions: This study defines EZH2 as a powerful independent unfavourable prognostic marker of CSS in patients with metastatic and non-metastatic RCC.
The editorial board of Aging reviews research papers published in 2009,which they believe have or will have a significant impact on aging research.Among many others, the topics include genes that accelerate aging or incontrast promote longevity in model organisms, DNA damage responsesand telomeres, molecular mechanisms of life span extension by calorierestriction and pharmacologic interventions into aging. The emergingmessage in 2009 is that aging is not random but determined by agenetically-regulated longevity network and can be decelerated bothgenetically and pharmacologically.
Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30–90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in ~4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data can be used for comparative studies to address basic questions of fungal biology.
If insufficiently treated, Lyme borreliosis can evolve into an inflammatory disorder affecting skin, joints, and the CNS. Early innate immunity may determine host responses targeting infection. Thus, we sought to characterize the immediate cytokine storm associated with exposure of PBMC to moderate levels of live Borrelia burgdorferi. Since Th17 cytokines are connected to host defense against extracellular bacteria, we focused on interleukin (IL)-17 and IL-22. Here, we report that, despite induction of inflammatory cytokines including IL-23, IL-17 remained barely detectable in response to B. burgdorferi. In contrast, T cell-dependent expression of IL-22 became evident within 10 h of exposure to the spirochetes. This dichotomy was unrelated to interferon-gamma but to a large part dependent on caspase-1 and IL-1 bioactivity derived from monocytes. In fact, IL-1beta as a single stimulus induced IL-22 but not IL-17. Neutrophils display antibacterial activity against B. burgdorferi, particularly when opsonized by antibodies. Since neutrophilic inflammation, indicative of IL-17 bioactivity, is scarcely observed in Erythema migrans, a manifestation of skin inflammation after infection, protective and antibacterial properties of IL-22 may close this gap and serve essential functions in the initial phase of spirochete infection.
Background: Familial hemophagocytosis (FHL) is a rare disease associated with defects in proteins involved in CD8+ T-cell cytotoxicity. Hyperactivation of immune cells results in a perilous, Th1-driven cytokine storm. We set out to explore the regulation of cytokines in an FHL patient who was clinically stable on low-dose immunosuppressive therapy after bone marrow transplantation over a six-month period. During this period, chimerism analyses showed that the fraction of host cells was between 1 and 10%. Both parents of the patient as well as healthy volunteers were studied for comparison. Methods/Principal Findings: Using ELISA, quantitative real-time PCR, and clinical laboratory methods, we investigated constitutive and inducible cytokines, polymorphisms, and clinical parameters in whole blood and whole blood cultures. Although routine laboratory tests were within the normal range, the chemokines IP-10 and IL-8 as well as the cytokine IL-27p28 were increased up to 10-fold under constitutive and stimulated conditions compared to healthy controls. Moreover, high levels of IFNgamma and TNFalpha were produced upon stimulation. Unexpectedly, IFNgamma induction of IL-18 binding protein (IL-18BP) was markedly reduced (1.6-fold vs 5-fold in controls). The patient's mother featured intermediately increased cytokine levels, whereas levels in the father were similar to those in the controls. Conclusions/Significance: Since IL-18 plays a major role in perpetuating hemophagocytosis, the failure of IFNgamma to induce IL-18BP may constitute a fundamental pathogenetic mechanism. Furthermore, increased production of IL-8 and IL-27 appears to be associated with this disease. Such dysregulation of cytokines was also found in the heterozygous parents, providing a novel insight into genotype-phenotype correlation of FHL which may encourage future research of this rare disease.
We solved the crystal structure of a novel type of c-ring isolated from Bacillus pseudofirmus OF4 at 2.5 Å, revealing a cylinder with a tridecameric stoichiometry, a central pore, and an overall shape that is distinct from those reported thus far. Within the groove of two neighboring c-subunits, the conserved glutamate of the outer helix shares the proton with a bound water molecule which itself is coordinated by three other amino acids of outer helices. Although none of the inner helices contributes to ion binding and the glutamate has no other hydrogen bonding partner than the water oxygen, the site remains in a stable, ion-locked conformation that represents the functional state present at the c-ring/membrane interface during rotation. This structure reveals a new, third type of ion coordination in ATP synthases. It appears in the ion binding site of an alkaliphile in which it represents a finely tuned adaptation of the proton affinity during the reaction cycle. Formal Correction: This article has been formally corrected to address the following errors. 1. The images for Figures S2 and S3 were incorrectly switched. The image that appears as Figure S2 should be Figure S3, and the image that appears as Figure S3 should be Figure S2. The figure legends appear in the correct order. Please view the correct... (read formal correction) 2. The images for Figures S2 and S3 were incorrectly switched. The image that appears as Figure S2 should be Figure S3, and the image that appears as Figure S3 should be Figure S2. The figure legends appear in the correct order. Please view the correct... (read formal correction)
Background: Falciparum Malaria, an infectious disease caused by the apicomplexan parasite Plasmodium falciparum, is among the leading causes of death and morbidity attributable to infectious diseases worldwide. In Gabon, Central Africa, one out of four inpatients have severe malarial anemia (SMA), a life-threatening complication if left untreated. Emerging drug resistant parasites might aggravate the situation. This case control study investigates biomarkers of enhanced hemolysis in hospitalized children with either SMA or mild malaria (MM). Methods and Findings: Ninety-one children were included, thereof 39 SMA patients. Strict inclusion criteria were chosen to exclude other causes of anemia. At diagnosis, erythrophagocytosis (a direct marker for extravascular hemolysis, EVH) was enhanced in SMA compared to MM patients (5.0 arbitrary units (AU) (interquartile range (IR): 2.2–9.6) vs. 2.1 AU (IR: 1.3–3.9), p<0.01). Furthermore, indirect markers for EVH, (i.e. serum neopterin levels, spleen size enlargement and monocyte pigment) were significantly increased in SMA patients. Markers for erythrocyte ageing, such as CD35 (complement receptor 1), CD55 (decay acceleration factor) and phosphatidylserine exposure (annexin-V-binding) were investigated by flow cytometry. In SMA patients, levels of CD35 and CD55 on the red blood cell surface were decreased and erythrocyte removal markers were increased when compared to MM or reconvalescent patients. Additionally, intravascular hemolysis (IVH) was quantified using several indirect markers (LDH, alpha-HBDH, haptoglobin and hemopexin), which all showed elevated IVH in SMA. The presence of both IVH and EVH predicted the need for blood transfusion during antimalarial treatment (odds ratio 61.5, 95% confidence interval (CI): 8.9–427). Interestingly, this subpopulation is characterized by a significantly lowered reticulocyte production index (RPI, p<0.05). Conclusions: Our results show the multifactorial pathophysiology of SMA, whereby EVH and IVH play a particularly important role. We propose a model where removal of infected and non-infected erythrocytes of all ages (including reticulocytes) by EVH and IVH is a main mechanism of SMA. Further studies are underway to investigate the mechanism and extent of reticulocyte removal to identify possible interventions to reduce the risk of SMA development.
Proteins can be acetylated at the alpha-amino group of the N-terminal amino acid (methionine or the penultimate amino acid after methionine removal) or at the epsilon-amino group of internal lysines. In eukaryotes the majority of proteins are N-terminally acetylated, while this is extremely rare in bacteria. A variety of studies about N-terminal acetylation in archaea have been reported recently, and it was revealed that a considerable fraction of proteins is N-terminally acetylated in haloarchaea and Sulfolobus, while this does not seem to apply for methanogenic archaea. Many eukaryotic proteins are modified by differential internal acetylation, which is important for a variety of processes. Until very recently, only two bacterial proteins were known to be acetylation targets, but now 125 acetylation sites are known for E. coli. Knowledge about internal acetylation in archaea is extremely limited; only two target proteins are known, only one of which--Alba--was used to study differential acetylation. However, indications accumulate that the degree of internal acetylation of archaeal proteins might be underestimated, and differential acetylation has been shown to be essential for the viability of haloarchaea. Focused proteomic approaches are needed to get an overview of the extent of internal protein acetylation in archaea.
In this paper we discuss experimental evidence related to the structure and origin of the bosonic spectral function alpha 2F (omega) in high-temperature superconducting (HTSC) cuprates at and near optimal doping. Global properties of alpha 2F (omega), such as number and positions of peaks, are extracted by combining optics, neutron scattering, ARPES and tunnelling measurements. These methods give evidence for strong electron-phonon interaction (EPI) with 1<lambda ep <~ 3.5 in cuprates near optimal doping. We clarify how these results are in favor of the modified Migdal-Eliashberg (ME) theory for HTSC cuprates near optimal doping. In Section 2 we discuss theoretical ingredients—such as strong EPI, strong correlations—which are necessary to explain the mechanism of d-wave pairing in optimally doped cuprates. These comprise the ME theory for EPI in strongly correlated systems which give rise to the forward scattering peak. The latter is supported by the long-range part of EPI due to the weakly screened Madelung interaction in the ionic-metallic structure of layered HTSC cuprates. In this approach EPI is responsible for the strength of pairing while the residual Coulomb interaction and spin fluctuations trigger the d-wave pairing.
Background: Current conventional vaccination approaches do not induce potent CD8 T-cell responses for fighting mostly variable viral diseases such as influenza, avian influenza viruses or HIV. Following our recent study on vaccine penetration by targeting of vaccine to human hair follicular ducts surrounded by Langerhans cells, we tested in the first randomized Phase-Ia trial based on hair follicle penetration (namely transcutaneous route) the induction of virus-specific CD8 T cell responses. Methods and Findings: We chose the inactivated influenza vaccine – a conventional licensed tetanus/influenza (TETAGRIP®) vaccine – to compare the safety and immunogenicity of transcutaneous (TC) versus IM immunization in two randomized controlled, multi-center Phase I trials including 24 healthy-volunteers and 12 HIV-infected patients. Vaccination was performed by application of inactivated influenza vaccine according to a standard protocol allowing the opening of the hair duct for the TC route or needle-injection for the IM route. We demonstrated that the safety of the two routes was similar. We showed the superiority of TC application, but not the IM route, to induce a significant increase in influenza-specific CD8 cytokine-producing cells in healthy-volunteers and in HIV-infected patients. However, these routes did not differ significantly for the induction of influenza-specific CD4 responses, and neutralizing antibodies were induced only by the IM route. The CD8 cell response is thus the major immune response observed after TC vaccination. Conclusions: This Phase Ia clinical trial (Manon05) testing an anti-influenza vaccine demonstrated that vaccines designed for antibody induction by the IM route, generate vaccine-specific CD8 T cells when administered transcutaneously. These results underline the necessity of adapting vaccination strategies to control complex infectious diseases when CD8 cellular responses are crucial. Our work opens up a key area for the development of preventive and therapeutic vaccines for diseases in which CD8 cells play a crucial role.
Purpose. The aim of this prospective longitudinal clinical pilot study was the evaluation of the effect on the Oral Health Impact Profile (OHIP) and patient-centered results of the envelope technique for Connective Tissue Graft (CTG). Methods. Sixteen patients (11 females) 24 to 71 years of age (42.6±11.1) received CTG that had been harvested from the palate and grafted using the envelope technique. Prior to and 3 months after surgery, all patients were examined clinically, completed the OHIP-G49 questionnaire, and were asked to judge the results of surgery. Results. Mean baseline recession depth of 2.5±0.8 mm was reduced by 1.2±0.9 mm (P<.001). Root coverage amounted to 48±39%. In 5 of 16 defects complete root coverage was achieved. Pain at the donor site was more pronounced than at recipient site regarding prevalence (8/6; P=.007), intensity (2.1±2.3/1.1±1.9 [visual analogue scale]; P=.016), and duration (1.4±2.3/0.8±1.4 days; P=.042). Baseline OHIP (15.7±12.1) was decreased by 3.6±8.5 three months after surgery (P=.139). Thirteen patients (81%) would undergo CTG surgery for similar reasons again. Conclusions. Root coverage using CTG according to the envelope technique provided improvement of OHIP as early as 3 months after surgery. Over all, patients were reasonably satisfied with the surgical technique and its results.
In my dissertation I study the transmission of monetary and fiscal policy in New Keynesian DSGE models. In the first chapter we revisit the exchange rate channel in a two-country model of the U.S. and a panel of industrialized countries to analyse how monetary policy transmission in the U.S. changes if it becomes more trade integrated. We find that more openness lowers the sacrifice ratio, although the effect is quantitatively small and depends on the pricing of the firms. In the second chapter we simulate the impact of the U.S. fiscal stimulus package in 2009 on GDP. We find that the government spendingmultiplier is well below 1. The finding is robust to including rule-of-thumb consumers and simulating the stimulus in the recent recession. In the third chapter we collect the fiscal stimulus measures in the eleven biggest countries of the euro area. Then we do a robustness study by simulating the european package in five different models of the euro area. The macroeconomic models vary in terms of backward-looking decision making of the agents and openness. Our findings provide no support for a Keynesian multiplier. Instead they suggest that additional government spending will reduce private spending for consumption and investment purposes. If government spending faces an implementation lag, the initial effect on GDP may even be negative. In the fourth chapter I estimate a DSGE model for Germany and compute forecasts for the debt-to-GDP ratio. I find that the expected economic recovery will lead to a decrease in Germany’s indebtedness in the medium-term given that policy makers stick to the fiscal policy rules.
Lipid rafts are specialized plasma membrane micro-domains highly enriched in cholesterol, sphingolipids and glycosylphosphatidylinositol (GPI) anchored proteins. Lipid rafts are thought to be located in the exofacial leaflet of plasma membranes. Functionally, lipid rafts are involved in intracellular trafficking of proteins and lipids, secretory and endocytotic pathways, signal transduction, inflammation and in cell-surface proteolysis. There has been substantial interest in lipid rafts in brain, both with respect to normal functioning and with certain neurodegenerative diseases. Based on the impact of lipid rafts on multitude biochemical pathways, modulation of lipid rafts is used to study related disease pathways and probably offers a target for pharmacological intervention. Lipid rafts can be targeted by modulation of its main components, namely cholesterol and sphingolipids. Other approaches include the modulation of membrane dynamics and it has been reported that protein-lipid interactions can vary the occurrence and composition of these membrane micro-domains. The present review summarizes the possibilities to modulate lipid rafts with focus on neuronal cells. Keywords: Lipid raft, cholesterol, membrane fluidity, statin, cyclodextrine, docosahexaenoic acid.
Planning problems, like real-world planning and scheduling problems, are complex tasks. As an efficient strategy for handing such problems is the ‘divide and conquer’ strategy has been identified. Each sub problem is then solved independently. Typically the sub problems are solved in a linear way. This approach enables the generation of sub-optimal plans for a number of real world problems. Today, this approach is widely accepted and has been established e.g. in the organizational structure of companies. But existing interdependencies between the sub problems are not sufficiently regarded, as each problem are solved sequentially and no feedback information is given. The field of coordination has been covered by a number of academic fields, like the distributed artificial intelligence, economics or game theory. An important result is, that there exist no method that leads to optimal results in any given coordination problem. Consequently, a suitable coordination mechanism has to be identified for each single coordination problem. Up to now, there exists no process for the selection of a coordination mechanism, neither in the engineering of distributed systems nor in agent oriented software engineering. Within the scope of this work the ECo process is presented, that address exactly this selection problem. The Eco process contains the following five steps. • Modeling of the coordination problem • Defining the coordination requirements • Selection / Design of the coordination mechanism • Implementation • Evaluation Each of these steps is detailed in the thesis. The modeling has to be done to enable a systemic analysis of the coordination problem. Coordination mechanisms have to respect the given situation and the context in which the coordination has to be done. The requirements imposed by the context of the coordination problem are formalized in the coordination requirements. The selection process is driven by these coordination requirements. Using the requirements as a distinction for the selection of a coordination mechanism is a central aspect of this thesis. Additionally these requirements can be used for documentation of design decisions. Therefore, it is reasonable to annotate the coordination mechanisms with the coordination requirements they fulfill and fail to ease the selection process, for a given situation. For that reason we present a new classification scheme for coordination methods within this thesis that classifies existing coordination methods according to a set of criteria that has been identified as important for the distinction between different coordination methods. The implementation phase of the ECo process is supported by the CoPS process and CoPS framework that has been developed within this thesis, as well. The CoPS process structures the design making that has to be done during the implementation phase. The CoPS framework provides a set of basic features software agents need for realizing the selected coordination method. Within the CoPS process techniques are presented for the design and implementation of conversations between agents that can be applied not only within the context of the coordination of planning systems, but for multiagent systems in general. The ECo-CoPS approach has been successfully validated in two case studies from the logistic domain.
Therapy of hemorrhagic shock with following resuscitation-induced liver injury : in vivo study
(2010)
Shock resulting from life-threatening blood-loss (hemorrhagic shock) represents the most frequent injury pattern after a traumatic insult. Hemorrhagic shock induces inflammatory changes, characterized by highly complex pathophysiological pathways often resulting in death. In this study, we establish an experimental in vivo model of H/R in rats and study the mechanisms which determine the hepatic injury after H/R. Furthermore, we show that hemorrhagic shock with following resuscitation is accompanied with release of systemic and local pro-inflammatory mediators, increased infiltration of hepatic neutrophils in the liver, increased oxidative and nitrosative stress, enhanced cell death of both types, apoptosis and necrosis, conspicuous cytoskeletal rearrangements, loss of hepatic integrity and finally high general mortality rates, up to 80%. In addition, the effects of two potential therapeutic interventions to prevent the H/R induced liver injury are explored in a model of H/R in rats. First, the role of JNK and its inhibition by D-JNKI-1 in preservation of hepatic integrity following H/R was analyzed. Second, we investigated the potential of simvastatin to prevent the disturbed inflammatory response and hepatic injury after H/R. The effects of both therapeutic interventions were studied by looking at several inflammatory parameters, markers of oxidative and nitrosative stress, cytoskeleton integrity, microcirculatory parameters, underlying signaling cascades, liver damage and mortality. Highly specific blockade of JNK with the potent, inhibitory peptide D-JNKI-1 revealed the crucial role of the JNK signaling pathway in the H/R induced pathophysiology and strong protective effects of DJNKI- 1 in H/R induced liver injury, when the peptide was applied before and even after hemorrhagic shock. The other therapeutic intervention tested in this study was the use of simvastatin which also revealed protective effects after H/R and even a remarkable improvement in survival after H/R. We show that H/R induced release of pro-inflammatory cytokines, hepatic PMNL infiltration, increased oxidative and nitrosative stress, apoptosis and necrosis can be diminished by treatment with D-JNKI-1 but also with simvastatin in vivo. Furthermore, simvastatin reduces H/R induced cytoskelatal rearrangements, loss of liver integrity and the mortality rate after H/R. The key pathway which underlies these beneficial effects of simvastatin is the Rho kinase pathway. Identification of both mechanisms as well as the effectiveness of both substances provide new insights in the close interaction between hypoxia and the immune system and present a promising basis for the anti-inflammatory, hepatoprotective treatment after H/R.
One of the earliest and most striking observations made about HIV is the extensive genetic variation that the virus has within individual hosts, particularly in the hypervariable regions of the env gene which is divided into 5 variable regions (V1-V5) and 5 more constant (C1-C5) regions. HIV evolves at any time over the course of an individual’s infection and infected individuals harbours a population of genetically related but non-identical viruses that are under constant change and ready to adapt to changes in their environment. These genetically heterogeneous populations of closely related genomes are called quasispecies [65]. Tuberculosis or tubercle forming disease is an acute and/or chronic bacterial infection that primarily attacks the lungs, but which may also affect the kidneys, bones, lymph nodes, and brain. The disease is caused by Mycobacterium tuberculosis (MTB), a slow growing rod-shaped, acid fast bacterium. It is transmitted from person to person through inhalation of bacteria-carrying air droplets. Worldwide, one person out of three is infected with Mycobacterium tuberculosis – two billion people in total. TB currently holds the seventh place in the global ranking of causes of death [73]. In 2008, there were an estimated 9.4 (range, 8.9–9.9 million) million incident cases (equivalent to 139 cases per 100 000 population) of TB globally [75]. A complex biological interplay occurs between M. tuberculosis and HIV in coinfected host that results in the worsening of both pathologies. HIV promotes progression of M. tuberculosis either by endogenous reactivation or exogenous reinfection [77, 78] and, the course of HIV-1 infection is accelerated subsequent to the development of TB [80]. Active TB is associated with an increase in intra-patient HIV-1 diversity both systemically and at the infected lung sites [64,122]. The sustainability or reversal of the HIV-1 quasispecies heterogeneity after TB treatment is not known. Tetanus toxoid vaccinated HIV-1 infected patients developed a transient increase in HIV-1 heterogeneity which was reversed after few weeks [121]. Emergence of a heterogeneous HIV-1 population within a patient may be one of the mechanisms to escape strong immune or drug pressure [65,128]. The existence of better fitting and/or immune escape HIV-variants can lead to an increase in HIV-1 replication [129,130]. It might be that TB favourably selected HIV-1 variants which are sources for consistent HIV-1 replication. Understanding the mechanisms underlying the impacts of TB on HIV-1 is essential for the development of effective measures to reduce TB related morbidity and mortality in HIV-1 infected individuals. In the present study we studied whether the increase in HIV-1 quasispecies diversity during active TB is reversed or preserved throughout the course of antituberculous chemotherapy. For this purpose Two time point HIV-1 quasispecies were evaluated by comparing HIV-1 infected patients with active tuberculosis (HIV-1/TB) and HIV-1 infected patients without tuberculosis (HIV-1/non TB). Plasma samples were obtained from the Frankfurt HIV cohort and HIV-1 RNA was isolated. C2V5 env was amplified by PCR and molecular cloning was performed. Eight to twenty five clones were sequenced from each patient. Various phylogenetic analyses were performed including tree inferences, intra-patient viral diversity and divergence, selective pressure, co-receptor usage prediction and two time point identity of quasispecies comparison using Mantel’s test. We found out from this study that: 1) Active TB sustains HIV-1 quasispecies diversity for longer period 2. Active TB increases the rate of HIV-1 divergence 3) TB might slow down evolution of X4 variants And we concluded that active TB has an impact on HIV-1 viral diversity and divergence over time. The influence of active TB on longitudinal evolution of HIV- 1 may be predominant for R5 viruses. The use of CCR5-coreceptor inhibitors for HIV-1/TB patients as therapeutic approach needs further investigation.
Background: New drugs are constantly sought after to improve the survival of patients with malignant gliomas. The ideal substance would selectively target tumor cells without eliciting toxic side effects. Here, we report on the anti-proliferative, anti-migratory, and anti-invasive properties of the natural, nontoxic compound Curcumin observed in five human glioblastoma (GBM) cell lines in vitro. Methods: We used monolayer wound healing assays, modified Boyden chamber trans-well assays, and cell growth assays to quantify cell migration, invasion, and proliferation in the absence or presence of Curcumin at various concentrations. Levels of the transcription factor phospho-STAT3, a potential target of Curcumin, were determined by sandwich-ELISA. Subsequent effects on transcription of genes regulating the cell cycle were analyzed by quantitative real-time PCR. Effects on apoptosis were determined by caspase assays. Results: Curcumin potently inhibited GBM cell proliferation as well as migration and invasion in all cell lines contingent on dose. Simultaneously, levels of the biologically active phospho-STAT3 were decreased and correlated with reduced transcription of the cell cycle regulating gene c-Myc and proliferation marking Ki-67, pointing to a potential mechanism by which Curcumin slows tumor growth. Conclusions: Curcumin is part of the diet of millions of people every day and is without known toxic side effects. Our data show that Curcumin bears anti-proliferative, anti-migratory, and anti-invasive properties against GBM cells in vitro. These results warrant further in vivo analyses and indicate a potential role of Curcumin in the treatment of malignant gliomas.
This dissertation introduces in chapter 1 a new comparative approach to model-based research and policy analysis by constructing an archive of business cycle models. It includes many well-known models used in academia and at policy institutions. A computational platform is created that allows straightforward comparisons of models’ implications for monetary and fiscal stabilization policies. Chapter 2 applies business cycle models to forecasting. Several New Keynesian models are estimated on historical U.S. data vintages and forecasts are computed for the five most recent recessions. The extent of forecast heterogeneity for models and professional forecasts is analysed. Chapter 3 extends the forecasting analysis to a long sample and to the evaluation of density forecasts. Weighted forecasts are computed using a variety of weighting schemes. The accuracy of forecasts is evaluated and compared to professional forecasts and forecasts from nonstructural time series methods. Chapter 4 adds a new feature to existing business cycle models. Specifically, a medium-scale New Keynesian model is constructed that allows for strategic complementarities in price-setting. The role of trade integration for monetary policy transmission is explored. A new dimension of the exchange rate channel is highlighted by which monetary policy directly impacts domestic inflation. Chapter 5 tests whether simple symmetric monetary policy rules used in most business cycle models are a sufficient description of reality. I use quantile regressions to estimate policy parameters and find asymmetric reactions to inflation, the output gap and past interest rates.
In the following Magisterarbeit I am going to develop a Concept Empiricist model of conceptual thought, which is in its technical core primarily inspired and motivated by Larry Barsalou‘ s Perceptual Symbol Systems Theory (PSST) (1999, 2008a). But it is not a theory of concepts in the genuine sense only, but it also expands naturally on related topics like the ontology of mind and the problem of intentionality. This is not arbitrarily chosen, but a natural consequence of any contemporary Concept Empiricist theory, for those theories are in kind direct outgrowths of an embodied approach to cognition which yields these consequences – the natural extension to related topics – as will be shown. The roadmap for the Magisterarbeit is going to look like this: First I will delineate the embodied cognition framework. Within embodied cognition there is a plethora of differing attempts at explaining the diverse phenomena of higher and lower cognition which differ in the meanwhile tremendously from each other. Therefore it will be very useful to set clear boundaries between the differing approaches, which range from strong neural embodiment on the one side to a very promiscuous extended mind hypothesis on the other side, in order to make a clear case for Concept Empiricism. It will be also very helpful to set my favoured version of grounded cognition off against classical attempts at the phenomena which are to be explained. Following that I am going to present Larry Barsalou‘s Perceptual Symbol Systems Theory in more detail. I will do that to an extent which allows for an appropriate discussion of concept related phenomena, but which is not too lengthy. I will spare the reader with unnecessary psychological or neurobiological details as long as it is not really necessary for explaining or clarifying the phenomena with which I deal here. Having done this I will discuss at great length conceptual meaning. In doing so I will present a presentational theory of meaning which is anti-realist, internalist and imaginistic. In advertising for this theory I will recur to conceptual methods, intuition as well as to the empirical record. Next and related to this I will develop a resemblance based theory of intentionality which differs also widely from the already established theories of intentionality so far given. Indeed it possess a feature which makes it very distinct and this is, besides its reliance on pattern mapping, the statistical grounding of resemblance which allows a cognitive theory of resemblance which is definite and therefore not open to the counterarguments generally mashalled against related theories, which stress the importance of resemblance. A very distinctive feature of this theory of intentionality is additionally that intentionality is seen as a capacity which emerges naturally form the mental mechanism involved. As we will see, this is a distinctive advantage of it in comparison to other proposal in the field. A discussion of the ontology of mental states follows which is however primarily a discussion of mechanistic explanations and Bechtel‘s and McCauley‘s Heuristic Identity Theory (HIT). Those theories from philosophy of science and philosophy of cognitive science do not only deliver models for the ontology of mental states, but also epistemic criteria for evaluating a theory as superior or inferior. Especially the idea of productive continuity plays a role of pivotal importance in my Magisterarbeit. It might be a bit unfortunate that that an important consideration is discussed nearly at the end of the Magisterarbeit, since I refer to it very often, however, I considered it as equally unfortunate to delay the discussion of meaning and intentionality, which is already protruded by the overview chapter and the more technical parts, even more. Therefore I plead the reader to refer to later parts of the Magisterarbeit when it is necessary in order to understand earlier parts. In the course of writing I have gotten second thoughts regarding the adequacy of an ontology of mental states altogether, especially from the background of the theory of meaning and intentionality delivered here. Therefore I tried to accommodate for ontological concepts by means of a tentative phenomenological interpretation of them. Similar ideas influenced my deliberations regarding meaning too. I hope that this transition towards Phenomenology runs smoothly and that the high level of coherence which is my primary concern and something which I always strive for first is preserved. Further, I have dedicated a main chapter of the Magisterarbeit for possible and actual critics of the ideas brought forth by me. Besides the more classic standard objections there you can find a recent critique of the authors on which I refer most often. Naturally I try to refute any single criticism brought forth and I hope that the reader will approve my objection to the objections. I will round off the Magisterarbeit with some concluding remarks and prospects for future research.
Background: The faunal and floral relationship of northward-drifting India with its neighboring continents is of general biogeographic interest as an important driver of regional biodiversity. However, direct biogeographic connectivity of India and Southeast Asia during the Cenozoic remains largely unexplored. We investigate timing, direction and mechanisms of faunal exchange between India and Southeast Asia, based on a molecular phylogeny, molecular clock-derived time estimates and biogeographic reconstructions of the Asian freshwater crab family Gecarcinucidae. Results: Although the Gecarcinucidae are not an element of an ancient Gondwana fauna, their subfamily Gecarcinucinae, and probably also the Liotelphusinae, evolved on the Indian Subcontinent and subsequently dispersed to Southeast Asia. Estimated by a model testing approach, this dispersal event took place during the Middle Eocene, and thus before the final collision of India and the Tibet-part of Eurasia. Conclusions: We postulate that the India and Southeast Asia were close enough for exchange of freshwater organisms during the Middle Eocene, before the final Indian--Eurasian collision. Our data support geological models that assume the Indian plate having tracked along Southeast Asia during its move northwards.
Background: Complex care management is seen as an approach to face the challenges of an ageing society with increasing numbers of patients with complex care needs. The Medical Research Council in the United Kingdom has proposed a framework for the development and evaluation of complex interventions that will be used to develop and evaluate a primary care-based complex care management program for chronically ill patients at high risk for future hospitalization in Germany. Methods and design: We present a multi-method procedure to develop a complex care management program to implement interventions aimed at reducing potentially avoidable hospitalizations for primary care patients with type 2 diabetes mellitus, chronic obstructive pulmonary disease, or chronic heart failure and a high likelihood of hospitalization. The procedure will start with reflection about underlying precipitating factors of hospitalizations and how they may be targeted by the planned intervention (pre-clinical phase). An intervention model will then be developed (phase I) based on theory, literature, and exploratory studies (phase II). Exploratory studies are planned that entail the recruitment of 200 patients from 10 general practices. Eligible patients will be identified using two ways of 'case finding': software based predictive modelling and physicians' proposal of patients based on clinical experience. The resulting subpopulations will be compared regarding healthcare utilization, care needs and resources using insurance claims data, a patient survey, and chart review. Qualitative studies with healthcare professionals and patients will be undertaken to identify potential barriers and enablers for optimal performance of the complex care management program. Discussion: This multi-method procedure will support the development of a primary care-based care management program enabling the implementation of interventions that will potentially reduce avoidable hospitalizations.
The central difference between objectivist cognitivist semantics and embodied cognition consists in the fact that the latter is, in contrast to the former, mindful of binding meaning to context-sensitive mental systems. According to Lakoff/Johnson's experientialism, conceptual structures arise from preconceptual kinesthetic image-schematic and basic-level structures. Gallese and Lakoff introduced the notion of exploiting sensorimotor structures for higherlevel cognition. Three different types of X-schemas realise three types of environmentally embedded simulation: Areas that control movements in peri-personal space; canonical neurons of the ventral premotor cortex that fire when a graspable object is represented; the firing of mirror neurons while perceiving certain movements of conspecifics. ...
In the present work, the problem of protein folding is addressed from the point of view of equilibrium thermodynamics. The conformation of a globular protein in solution at common temperatures is quite complicated without any geometrical symmetry, but it is an ordered state in the sense of its biological activity. This complicated conformation of a single protein molecule is destroyed upon increasing the temperature or by the addition of appropriate chemical agents, as is revealed by the loss of its activity and change of the physical properties, and so on. Once the complicated native structures having biological activity are lost, it would be natural to suppose that the native structure could hardly be restored. Nevertheless, pioneers, such as Anson and Mirsky, recognized as early as in 1925 that this was not always the case. If one defines the folded and unfolded states of a protein as two distinct phases of a system, then under the variation of temperature the system is transformed from one phase state into another and vice versa. The process of protein folding is accompanied by the release or absorption of a certain amount of energy, corresponding to the first-oder-type phase transitions in the bulk. Knowing the partition function of the system one can evaluate its energy and heat capacity under different temperatures. This task was performed in this work. The results of the developed statistical mechanics model were compared with the results of molecular dynamic simulations of alanine poylpeptides. In particular, the dependencies on temperature of the total energy of the system and heat capacity were compared for alanine polypeptides consisting of 21, 30, 40, 50 and 100 amino acids. The good correspondence of the results of the theoretical model with the results of molecular dynamics simulations allowed to validate the assumptions made about the system and to establish the accuracy range of the theory. In order to perform the comparison of the results of theoretical model and the molecular dynamics simulations it is necessary to perform the efficient analysis of the results of molecular dynamics simulations. This task was also addressed in the present work. In particular, different ways to obtain dependence of the heat capacity on temperature from molecular dynamics simulations are discussed and the most efficient one is proposed. The present thesis reports the result of molecular dynamic simulations for not only alanine polypeptides by also for valine and leucine polypeptides. In valine and leucine polypeptides, it is also possible to observe the helix↔random coil transitions with the increase of temperature. The current thesis presents a work that starts with the investigation of the fundamental degrees of freedom in polypeptides that are responsible for the conformational transitions. Then this knowledge is applied for the statistical mechanics description of helix↔coil transitions in polypeptides. Finally, the theoretical formalism is generalized for the case of proteins in water environment and the comparison of the results of the statistical mechanics model with the experimental measurements of the heat capacity on temperature dependencies for two globular proteins is performed. The presented formalism is based on fundamental physical properties of the system and provides the possibility to describe the folding↔unfolding transitions quantitatively. The combination of these two facts is the major novelty of the presented approach in comparison to the existing ones. The “transparent” physical nature of the formalism provides a possibility to further apply it to a large variety of systems and processes. For instance, it can be used for investigation of the influence of the mutations in the proteins on their stability. This task is of primary importance for design of novel proteins and drug delivering molecules in medicine. It can provide further insights into the problem of protein aggregation and formation of amyloids. The problem of protein aggregation is closely associated with various illnesses such as Alzheimer and mad cow disease. With certain modifications, the presented theoretical method can be applied to the description of the protein crystallization process, which is important for the determination of the structure of proteins with X-Rays. There many other possible applications of the ideas described in the thesis. For instance, the similar formalism can be developed for the description of melting and unzipping of DNA, growth of nanotubes, formation of fullerenes, etc.
Functional and structural characterization of Aquifex aeolicus sulfide:quinone oxidoreductase
(2010)
This work presents the first complete structure of the membrane protein sulfide:quinone oxidoreductase (SQR), obtained by X-ray crystallography. Its description is complemented by the results of biochemical and functional experiments. SQRs are ubiquitous flavoprotein disulfide reductases (FDRs), present in all domains of life, including in humans. Their physiological role extends from sulfide detoxification to sulfide-dependent respiration and photosynthesis (in archaea and bacteria), to heavy metal tolerance (in yeast) and possibly to sulfide signalling (in higher eukaryotes). Until now understanding the function of SQRs was difficult because of the poor level of sequence conservation in this enzyme family, the limited functional characterization available and the absence of any structural data. SQR was identified in the native membranes of the hyperthermophilic bacterium Aquifex aeolicus by peptide mass fingerprinting (PMF) and by a spectrophotometric activity assay. The protein was solubilized in the detergent dodecyl-beta-D-maltoside (DDM) and purified to homogeneity in a functionally active state. It binds one FAD molecule per protein monomer and FAD is its only cofactor. Its structure was determined in the “as-purified”, substrate-bound and inhibitor-bound forms at resolutions of 2.3, 2.0 and 2.9 Å, respectively. It is composed of two Rossmann-fold domains and of one membrane-attachment region. Despite the overall monomeric architecture being similar to that of FDRs, the structure reveals properties that had not been observed in FDRs until now and that have strong implications for the SQR catalytic mechanism. Surprisingly, A. aeolicus SQR is trimeric in the crystal structure and in solution, as determined by density-matched analytical ultracentrifugation, cross-linking and single particle electron microscopy. The trimer creates an appropriate surface for binding lipids and thus ensures that SQR exclusively reduces hydrophobic quinones. SQR inserts to a depth of about 12 Å into the membrane as an integral monotopic membrane protein. The interaction is mediated by an amphipathic helix-turn-helix tripodal motif and two lipid clamps. A channel in the membrane-binding domain extends towards the si-side of FAD and represents the quinone-binding site. The quinone ring is sandwiched between the conserved amino acids Phe 385 and Ile 346 and is possibly protonated upon reduction via Glu 318, Lys 382 and/or neighboring solvent molecules. Sulfide polymerization occurs on the re-side of FAD, where the highly conserved Cys 156 and Cys 347 appear to be covalently bound to the putative product of the reaction, a polysulfur chain which takes the form of an S8 ring in some monomers. Finally, the structure shows that FAD is covalently connected to the protein in an unprecedented way, via a putative disulfide bridge between the 8-methyl group of the isoalloxazine moiety and Cys 124. The high resolution insight into the protein and all unexpected structural observations presented in this work suggest that the catalytic mechanism of SQRs is significantly different from that of FDRs. In agreement with the structural and functional data, two reaction schemes are proposed for A. aeolicus SQR. They both provide a detailed description of how sulfide and quinones reach and bind the active site, how electrons are transferred from sulfide to quinone via FAD and how the elongating polysulfur product is attached to the polypeptide and is finally released. The two hypotheses differ in defining the structure of the covalent protein-FAD intermediate that forms during the reaction cycle and whose identity still remains experimentally undetermined. Remarkably, the structure of the active site and the FAD-binding mode of A. aeolicus SQR are not conserved in another SQR structure which also became available recently, that of the archaeon Acidianus ambivalens. The variability in SQRs suggests that not all of these enzymes follow the same catalytic mechanism, despite having been considered homologous. Consequently, the currently available but contradictory sequence-based classifications of the SQR family were revised. A structure-based alignment calculated on the increasing number of available sequences allowed to define new SQR groups and their characteristic sequence fingerprints in agreement with the reported structural and functional data. In conclusion, the results obtained in this work offer for the first time a detailed look into the intriguing but complicated reactions catalysed by SQRs and provide a stimulus for further genetic, biochemical and structural investigation.
On the backdrop of the 2008 financial crisis this paper introduces an understanding of societal crises as a reduction in the meaning production of social entities, which can either be internally or externally provoked. The emergence of constitutions and, more generally, constitutional structures, can be understood as responses to both forms of crisis. This is the case because they are double-edged structures which are simultaneously oriented towards the maintenance of internal order and stability within a given social entity at the same time as they frame the transfer of the meaning components between the social entities and their environments. Thus, the 2008 financial crisis indicates a failure of constitutional bonding. When observed from an overall structural perspective, the reasons for this failure can be traced back to an increased discrepancy between the structural composition of world society and the constitutional structures in place. The crisis reflects a failure to respond to two simultaneous, inter-related and mutually re-inforcing structural transformations. First, there is the increased globalisation, which has led to massive dis-locations in the relative centrality of the different national configurations for the reproductive processes of functional systems. Second, there is a structural transformation of the transnational layer of world society through a reduced reliance on the centre/periphery differentiation and an increased reliance on functional differentiation. One of the many consequences of this development is the emergence of new forms of transnational law and politics. A new constitutional architecture which reflects these transformations is needed in order to ensure an adequate constitutional bonding of economic processes, as well as of other social processes.
Background: Prospective, observational studies that enroll large numbers of patients with few exclusion criteria may better reflect actual ongoing clinical experience than randomized clinical trials. Our purpose was to obtain efficacy and safety information from a cohort of subjects exposed to latanoprost/timolol fixed combination (FC) for [greater than or equal to]18 months using a prospective, observational design. Methods: In all, 577 office-based ophthalmologists in Germany switched 2339 patients with glaucoma or ocular hypertension to latanoprost/timolol FC for medical reasons. Follow-up visits were scheduled for every 6 months over 24 months; physicians followed usual care routines. Intraocular pressure (IOP), visual field status, optic nerve head findings, and adverse events were recorded. Efficacy parameters were evaluated for the per protocol (PP) population; the safety population included subjects receiving [greater than or equal to]1 drop of FC. Physicians rated efficacy, tolerability, and subject compliance at month 24. Results: Of the 2339 subjects switched to latanoprost/timolol FC (safety population), the primary reasons for switching were inadequate IOP reduction (78.2%) and desire to simplify treatment with once-daily dosing (29.4%; multiple reasons possible). In all, 1317 (56.3%) subjects completed the study, and 1028 (44.0%) were included in the PP population. Most discontinuations were due to loss to follow-up. Change in mean IOP from baseline to month 6 was -4.0 +/- 4.31 mmHg, a reduction that was maintained throughout (P<0.05 for change at all time points). By investigator assessments, optic disc parameters and visual field were stable over 24 months, and there was no relationship between IOP reduction over 24 months and development of a visual field defect. More than 90% of physicians rated latanoprost/timolol FC as "very good" or "good" for efficacy (PP population), tolerability, and compliance. The FC was safe and well tolerated. No change in iris color was reported by most subjects (83.1%) at month 24. Conclusions: Over 24 months, latanoprost/timolol FC effectively lowers IOP levels and is well tolerated in patients with glaucoma or ocular hypertension who change from their previous ocular hypotensive therapy for medical reasons. Investigator assessments found optic disc parameters and visual field to be stable throughout 24 months of follow-up.
Background: FibroTest (FT) is the most frequently used serum fibrosis marker and consists of an algorithm of five fibrosis markers (alfa2-macroglobulin, apolipoproteinA1, haptoglobin, GGT, bilirubin). The Enhanced Liver Fibrosis (ELF) test consists of an algorithm of three fibrosis markers (hyaluronic acid, amino-terminal propeptide-of-type-III-collagen, tissue-inhibitor of matrix-metaloproteinase-1). While a systematic review has shown comparable results for both individual markers, there has been no direct comparison of both markers. Methods: In the present study, the ELF-test was analyzed retrospectively in patients with chronic liver disease, who received a liver biopsy, transient elastography (TE) and the FibroTest using histology as the reference method. Histology was classified according to METAVIR and the Ludwig's classification (F0-F4) for patients with chronic hepatitis C and B virus (HCV, HBV) infection and primary biliary cirrhosis (PBC), respectively. Results: Seventy-four patients were analysed: 36 with HCV, 10 with HBV, and 28 with PBC. The accuracy (AUROC) for the diagnosis of significant fibrosis (F[greater than or equal to]2) for ELF and FibroTest was 0.78 (95%CI:0.67-0.89) and 0.69 (95%-CI:0.57-0.82), respectively (difference not statistically significant, n.s.). The AUROC for the diagnosis of liver cirrhosis was 0.92 (95%CI:0.83-1,00), and 0.91 (95%CI:0.83-0.99), respectively (n.s.). For 66 patients with reliable TE measurements the AUROC for the diagnosis of significant fibrosis (cirrhosis) for TE, ELF and FT were 0.80 (0.94), 0.76 (0.92), and 0.67 (0.91), respectively (n.s.). Conclusion: FibroTest and ELF can be performed with comparable diagnostic accuracy for the non-invasive staging of liver fibrosis. Serum tests are informative in a higher proportion of patients than transient elastography.
Active chlorine species play a dominant role in the catalytic destruction of stratospheric ozone in the polar vortices during the late winter and early spring seasons. Recently, the correct understanding of the ClO dimer cycle was challenged by the release of new laboratory absorption cross sections (Pope et al., 2007) yielding significant model underestimates of observed ClO and ozone loss (von Hobe et al., 2007). Under this aspect, nocturnal Arctic stratospheric limb emission measurements carried out by the balloon version of the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS-B) from Kiruna (Sweden) on 11 January 2001 and 20/21 March 2003 have been reanalyzed with regard to the chlorine reservoir species ClONO2 and the active species, ClO and ClOOCl (Cl2O2). New laboratory measurements of IR absorption cross sections of ClOOCl for various temperatures and pressures allowed for the first time the retrieval of ClOOCl mixing ratios from remote sensing measurements. High values of active chlorine (ClOx) of roughly 2.3 ppbv at 20 km were observed by MIPAS-B in the cold mid-winter Arctic vortex on 11 January 2001. While nighttime ClOOCl shows enhanced values of nearly 1.1 ppbv at 20 km, ClONO2 mixing ratios are less than 0.1 ppbv at this altitude. In contrast, high ClONO2 mixing ratios of nearly 2.4 ppbv at 20 km have been observed in the late winter Arctic vortex on 20 March 2003. No significant ClOx amounts are detectable on this date since most of the active chlorine has already recovered to its main reservoir species ClONO2. The observed values of ClOx and ClONO2 are in line with the established polar chlorine chemistry. The thermal equilibrium constants between the dimer formation and its dissociation, as derived from the balloon measurements, are on the lower side of reported data and in good agreement with values recommended by von Hobe et al. (2007). Calculations with the ECHAM/MESSy Atmospheric Chemistry model (EMAC) using established kinetics show similar chlorine activation and deactivation, compared to the measurements in January 2001 and March 2003, respectively.
Emissions of sulphur hexafluoride (SF6), one of the strongest greenhouse gases on a per molecule basis, are targeted to be collectively reduced under the Kyoto Protocol. Because of its long atmospheric lifetime (estimated as 800 to 3200 years), the accumulation of SF6 in the atmosphere is a direct measure of its global emissions. Examination of our extended data set of globally distributed high-precision SF6 observations shows an increase in SF6 abundance from near zero in the 1970s to a global mean of 6.7 ppt by the end of 2008. In-depth evaluation of our long-term data records shows that the global source of SF6 decreased after 1995, most likely due to SF6 emission reductions in industrialised countries, but increased again after 1998. By subtracting those emissions reported by Annex I countries to the United Nations Framework Convention of Climatic Change (UNFCCC) from our observation-inferred SF6 source leaves a surprisingly large gap of more than 70–80% of non-reported SF6 emissions in the last decade. This suggests a strong under-estimation of emissions in Annex I countries and underlines the urgent need for independent atmospheric verification of greenhouse gases emissions accounting.
Epoxyeicotrienoic acids (EETs) are cytochrome P450-dependent anti-hypertensive and anti-inflammatory derivatives of arachidonic acid, which are highly abundant in the kidney and considered reno-protective. EETs are degraded by the enzyme soluble epoxide hydrolase (sEH) and sEH inhibitors are considered treatment for chronic renal failure (CRF). We determined whether sEH inhibition attenuates the progression of CRF in the 5/6-nephrectomy model (5/6-Nx) in mice. 5/6-Nx mice were treated with a placebo, an ACE-inhibitor (Ramipril, 40 mg/kg), the sEH-inhibitor cAUCB or the CYP-inhibitor fenbendazole for 8 weeks. 5/6-Nx induced hypertension, albuminuria, glomerulosclerosis and tubulo-interstitial damage and these effects were attenuated by Ramipril. In contrast, cAUCB failed to lower the blood pressure and albuminuria was more severe as compared to placebo. Plasma EET-levels were doubled in 5/6 Nx-mice as compared to sham mice receiving placebo. Renal sEH expression was attenuated in 5/6-Nx mice but cAUCB in these animals still further increased the EET-level. cAUCB also increased 5-HETE and 15-HETE, which derive from peroxidation or lipoxygenases. Similar to cAUCB, CYP450 inhibition increased HETEs and promoted albuminuria. Thus, sEH-inhibition failed to elicit protective effects in the 5/6-Nx model and showed a tendency to aggravate the disease. These effects might be consequence of a shift of arachidonic acid metabolism into the lipoxygenase pathway.
Sacoglossan sea slugs are unique in the animal kingdom in that they sequester and maintain active plastids that they acquire from the siphonaceous algae upon which they feed, making the animals photosynthetic. While most sacoglossan species digest their freshly ingested plastids within hours, four species from the family Plakobranchidae retain their stolen plastids (kleptoplasts) in a photosynthetically active state on time scales of weeks to months. The molecular basis of plastid maintenance within the cytosol of digestive gland cells in these photosynthetic metazoans is yet unknown, but is widely thought to involve gene transfer from the algal food source to the slugs based upon previous investigations of single genes. Indeed, normal plastid development requires hundreds of nuclear-encoded proteins, with protein turnover in photosystem II in particular known to be rapid under various conditions. Moreover, only algal plastids, not the algal nuclei, are sequestered by the animals during feeding. If algal nuclear genes are transferred to the animal either during feeding or in the germ line, and if they are expressed, then they should be readily detectable with deep-sequencing methods. We have sequenced expressed mRNAs from actively photosynthesizing, starved individuals of two photosynthetic sea slug species, Plakobranchus ocellatus Van Hasselt, 1824 and Elysia timida Risso, 1818. We find that nuclear-encoded, algal-derived genes specific to photosynthetic function are expressed neither in P. ocellatus nor in E. timida. Despite their dramatic plastid longevity, these photosynthetic sacoglossan slugs do not express genes acquired from algal nuclei in order to maintain plastid function.
Methanogenic archaea are a group of strictly anaerobic microorganisms characterized by their strict dependence on the process of methanogenesis for energy conservation. Among the archaea, they are also the only known group synthesizing proteins containing selenocysteine or pyrrolysine. All but one of the known archaeal pyrrolysine-containing and all but two of the confirmed archaeal selenocysteine-containing protein are involved in methanogenesis. Synthesis of these proteins proceeds through suppression of translational stop codons but otherwise the two systems are fundamentally different. This paper highlights these differences and summarizes the recent developments in selenocysteine- and pyrrolysine-related research on archaea and aims to put this knowledge into the context of their unique energy metabolism.
The magnetic field sensors enabling birds to extract orientational information from the Earth’s magnetic field have remained enigmatic. Our previously published results from homing pigeons have made us suggest that the iron containing sensory dendrites in the inner dermal lining of the upper beak are a candidate structure for such an avian magnetometer system. Here we show that similar structures occur in two species of migratory birds (garden warbler, Sylvia borin and European robin, Erithacus rubecula) and a non-migratory bird, the domestic chicken (Gallus gallus). In all these bird species, histological data have revealed dendrites of similar shape and size, all containing iron minerals within distinct subcellular compartments of nervous terminals of the median branch of the Nervus ophthalmicus. We also used microscopic X-ray absorption spectroscopy analyses to identify the involved iron minerals to be almost completely Fe III-oxides. Magnetite (Fe II/III) may also occur in these structures, but not as a major Fe constituent. Our data suggest that this complex dendritic system in the beak is a common feature of birds, and that it may form an essential sensory basis for the evolution of at least certain types of magnetic field guided behavior.
Experimental results are presented for 180 in silico designed octapeptide sequences and their stabilizing effects on the major histocompatibility class I molecule H-2Kb. Peptide sequence design was accomplished by a combination of an ant colony optimization algorithm with artificial neural network classifiers. Experimental tests yielded nine H-2Kb stabilizing and 171 nonstabilizing peptides. 28 among the nonstabilizing octapeptides contain canonical motif residues known to be favorable for MHC I stabilization. For characterization of the area covered by stabilizing and non-stabilizing octapeptides in sequence space, we visualized the distribution of 100,603 octapeptides using a self-organizing map. The experimental results present evidence that the canonical sequence motives of the SYFPEITHI database on their own are insufficient for predicting MHC I protein stabilization.
Introduction: Purpura fulminans (PF) is a devastating complication of uncontrolled systemic inflammation, associated with high incidence of amputations, skin grafts and death. In this study, we aimed to clarify the clinical profile of pediatric patients with PF who improved with protein C (PC) treatment, explore treatment effects and safety, and to refine the prognostic significance of protein C plasma levels. Methods: In Germany, patients receiving protein C concentrate (Ceprotin(R), Baxter AG, Vienna, Austria) are registered. The database was used to locate all pediatric patients with PF treated with PC from 2002 to 2005 for this National, retrospective, multi-centered study. Results: Complete datasets were acquired in 94 patients, treated in 46 centers with human, non-activated protein C concentrate for purpura fulminans. PC was given for 2 days (median, range 1-24 days) with a median daily dose of 100 IU/kg. Plasma protein C levels increased from a median of 27% to a median of 71% under treatment. 22.3% of patients died, 77.7% survived to discharge. Skin grafts were required in 9.6%, amputations in 5.3%. PF recovered or improved in 79.8%, remained unchanged in 13.8% and deteriorated in 6.4%. Four adverse events occurred in 3 patients, none classified as severe. Non-survivors had lower protein C plasma levels (P < 0.05) and higher prevalence of coagulopathy at admission (P < 0.01). Time between admission and start of PC substitution was longer in patients who died compared to survivors (P = 0.03). Conclusions: This retrospective dataset shows that, compared to historic controls, only few pediatric patients with PF under PC substitution needed dermatoplasty and/or amputations. Apart from epistaxis, no bleeding was observed. Although the data comes from a retrospective study, the evidence we present suggests that PC had a beneficial impact on the need for dermatoplasty and amputations, pointing to the potential value of carrying out a prospective randomised controlled trial.
Nep1 (Emg1) is a highly conserved nucleolar protein with an essential function in ribosome biogenesis. A mutation in the human Nep1 homolog causes Bowen–Conradi syndrome—a severe developmental disorder. Structures of Nep1 revealed a dimer with a fold similar to the SPOUT-class of RNA-methyltransferases suggesting that Nep1 acts as a methyltransferase in ribosome biogenesis. The target for this putative methyltransferase activity has not been identified yet. We characterized the RNA-binding specificity of Methanocaldococcus jannaschii Nep1 by fluorescence- and NMR-spectroscopy as well as by yeast three-hybrid screening. Nep1 binds with high affinity to short RNA oligonucleotides corresponding to nt 910–921 of M. jannaschii 16S rRNA through a highly conserved basic surface cleft along the dimer interface. Nep1 only methylates RNAs containing a pseudouridine at a position corresponding to a previously identified hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) in eukaryotic 18S rRNAs. Analysis of the methylated nucleoside by MALDI-mass spectrometry, HPLC and NMR shows that the methyl group is transferred to the N1 of the pseudouridine. Thus, Nep1 is the first identified example of an N1-specific pseudouridine methyltransferase. This enzymatic activity is also conserved in human Nep1 suggesting that Nep1 is the methyltransferase in the biosynthesis of m1acp3-Psi in eukaryotic 18S rRNAs.