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Zwischen Aufbruch und Wanderlust : eine Reise durch die Romantikausstellung des Museums Giersch
(2015)
Reading is an essential ability to master everyday life in our society. The ability to read is based on specific connections between brain regions involved in the reading process – so-called cortical networks for reading. These cortical networks for reading allow us to learn the correct identification of visual words. The use of visual words is based on knowledge about the orthography (lexical) and the meaning of words (semantic). This knowledge must be acquired by beginning readers (first grader), i.e. beginning readers learn in a first step to link letters to a whole word and in a second step associate this whole word with meaning. To retrieve this knowledge during visual word recognition (VWR) a cortical network for lexical-semantic process must be activated. However, it is currently unclear whether beginning readers and reading experts activate the same neuronal network during VWR. Therefore, the aim of this thesis was to investigate the question whether beginning readers (first grader, children) and reading experts (adults) use different cortical networks for the lexical-semantic processing in VWR.
To address this question we recorded electroencephalographic (EEG) activity during VWR in children and adults. Children and adults were instructed to read a visualizable word to compare this word with a following picture stimulus. The first part of this thesis is concerned with the analysis of ERPs for visual word recognition in children and adults at sensor level. For both groups we observed the typical ERP components P100 and N170 for visual word recognition. These components differed in amplitude and time course between both groups. The second part of this thesis investigated the neuronal generators (brain areas) of ERPs during VWR and possible differences between children and adults at source level. We observed a high overlap in brain areas involved during VWR in children and adults. However, the brain areas differed in activation and time course between children and adults. Finally, the third and most important part of the thesis investigated the question whether children and adults use different cortical networks for the lexical-semantic processing in VWR over time. To address this question Dynamic Causal Modeling (DCM) and Bayesian model comparison were used. We compared nine biologically plausible cortical network models underlying the ventral lexical-semantic path in VWR. In addition, increasing time intervals were used to consider possible changes of network structure during VWR. The network models included eight brain regions (four bilateral pairs) involved in the lexical-semantic processing in VWR: occipital cortex (OC), temporo-occipital part of inferior temporal gyrus (ITG), temporal pole (TP), and inferior frontal gyrus (IFG). In almost all time intervals we found evidence that children and adults use the same cortical networks for the lexical-semantic processing in VWR. However, we found differences between adults and children in the connection strengths of the favoured model. Interestingly, we found a stronger direct connection from OC to IFG in adults compared to children.
In conclusion, our results suggest that children and adults activate largely the same lexical-semantic networks during VWR over time. This supports the notion that children and adults use the same biological fiber connections for VWR. However in contrast to children, adults showed increased use of the shortcut pathway from OC to IFG. The increased use of the shortcut pathway from OC to IFG in adults can be interpreted as consequence of learning. Learning causes in accordance with the Hebbian learning rule (“neurons that fire together, wire together” (Hebb, 1949)) synaptic change. Consequently the frequent coactivation of the input and output stage of OC and IFG during the lexical-semantic process facilitates the stronger direct connection between both brain areas. The stronger direct connection from OC to IFG most likely allows adult reading experts to speed up the lexical-semantic process during VWR. Accordingly, we conclude that the stronger direct connections from OC to IFG in adults compared to children underlay the different reading capabilities in both groups.
Membrane proteins are biological macromolecules that are located in a cell’s membrane and are responsible for essential functions within an organism, which makes them to prominent drug targets. The extraction of membrane proteins from the hydrophobic membrane bilayer to determine high-resolution crystal structures is a difficult task and only 2% of all solved proteins structures are membrane proteins. Computational methods may help to gain deeper insights into membrane protein structures and their functions. This study will give an overview of such computational methods on a representative set of membrane proteins and will provide ideas for future computational and experimental research on membrane proteins.
In a first step (chapter 2), I updated an earlier, manually-curated data set of homologous membrane proteins (HOMEP) to more recent versions in 2010 (HOMEP2) and 2013 (HOMEP3) using an automated clustering approach. High-resolution structures of membrane proteins listed in the PDB_TM database were structurally aligned and subsequently clustered using structural similarity scores. Both data sets were used as a standard gold reference set for subsequent work.
Subsequently, I have updated and applied the sequence alignment program AlignMe to determine protein descriptors that are suitable for detecting evolutionary relationship between homologous a-helical membrane proteins. Single input descriptors were tested alone and in combination with each other in different modes of AlignMe by optimizing gap penalties on the HOMEP2 data set. Most accurate alignments and homology models on the HOMEP2 data set were observed when using position-specific substitution information (P), secondary structure propensities (S) and transmembrane propensities (T) in the AlignMe PST mode. An evaluation on an independent reference set of membrane protein sequence alignments from the BAliBASE collection showed that different modes of AlignMe are suitable for different sequence similarity levels. The AlignMe PST mode improved the alignment accuracy significantly for distantly related proteins, whereas for closely-related proteins from the BAliBASE set the AlignMe PS mode was more suitable. This work was published in March 2013 in PLOS ONE. In order to allow also an easier usage of the AlignMe program, I have implemented a web server of AlignMe (chapter 4) that provides the optimized settings and gap penalties for the AlignMe P, PS and PST modes. A comparison to other recent alignment web server shows that the alignments of AlignMe are similar or even more accurate than those of other methods, especially for very distantly related proteins for which the inclusion of membrane protein information has been shown to be suitable. This work was published in the NAR web server issue in July 2014.
Although membrane-specific information has been shown to be suitable for aligning distantly related membrane proteins on a sequence level, such information was not incorporated into structural alignment programs making it unclear which method is the most suitable for aligning membrane proteins. Thus, I compared 13 widely-used pairwise structural alignment methods on an updated reference set of homologous membrane protein structures (HOMEP3) and evaluated their accuracy by building models based on the underlying sequence alignments and used scoring functions (e.g., AL4 or CAD-score) to rate the model accuracy (chapter 5). The analysis showed that fragment-based approaches such as FR-TM-align are the most useful for aligning structures of membrane proteins that have undergone large conformational changes whereas rigid approaches were more suitable for proteins that were solved in the same or a similar state. However, no method showed a significant higher accuracy than any other. Additionally, all methods lack a measure to rate the reliability of the accuracy for a specific position within a structure alignment. In order to solve these problems, I propose a consensus-type approach that combines alignments from four different methods, namely FR-TM-align, DaliLite, MATT and FATCAT and assigns a confidence value to each position of the alignment that describes the agreement between the methods. This work has been published 2015 in the journal “PROTEINS: structure, function and bioinformatics”.
Consensus alignments were then generated for each pair of proteins of the HOMEP3 data set and subsequently analyzed for single evolutionary events within membrane spanning segments and for irregular structures (e.g., 310- and p-helices) (chapter 6). Interestingly, single insertions and deletions could be observed with the help of consensus alignments in the conserved membrane-spanning segments of membrane proteins in four protein families. The detection of such single InDels might help to identify crucial residues for a proteins function.
Acinetobacter baumannii virulence is mediated by the concerted action of three phospholipases D
(2015)
Acinetobacter baumannii causes a broad range of opportunistic infections in humans. Its success as an emerging pathogen is due to a combination of increasing antibiotic resistance, environmental persistence and adaptation to the human host. To date very little is known about the molecular basis of the latter. Here we demonstrate that A. baumannii can use phosphatidylcholine, an integral part of human cell membranes, as sole carbon and energy source. We report on the identification of three phospholipases belonging to the PLD superfamily. PLD1 and PLD2 appear restricted to the bacteria and display the general features of bacterial phospholipases D. They possess two PLDc_2 PFAM domains each encompassing the HxKx4Dx6GS/GGxN (HKD) motif necessary for forming the catalytic core. The third candidate, PLD3, is found in bacteria as well as in eukaryotes and harbours only one PLDc_2 PFAM domain and one conserved HKD motif, which however do not overlap. Employing a markerless mutagenesis system for A. baumannii ATCC 19606T, we generated a full set of PLD knock-out mutants. Galleria mellonella infection studies as well as invasion experiments using A549 human lung epithelial cells revealed that the three PLDs act in a concerted manner as virulence factors and are playing an important role in host cell invasion.
Tectonin β-propeller containing protein 2 (TECPR2) was first identified in a mass- spectrometric approach as an interactor of GABARAP, an ATG8-family protein playing a role in autophagy. The mammalian ATG8 protein family consists of seven members, namely MAP1LC3A (LC3A), MAP1LC3B (LC3B), MAP1LC3C (LC3C), GABARAP, GABARAPL1 and GABARAPL2. All share an ubiquitin-like core and possess two additional N-terminal α-helices, which are important for the distinct functions of the proteins. First determined in various organelles the ATG8 proteins are shown to be involved in autophagy, supporting the formation and cargo recruitment of autophagosomes, the vesicles transporting cargo for autophagic degradation.
Autophagy is the process of recycling cytoplasmic contents by degradation of misfolded proteins or damaged organelles in order to supply nutrients. Also clearance of pathogens can be achieved via autophagy. Importantly, LC3B is incorporated into the autophagosomal membrane and is therefore used as the main marker for autophagosomes. Previous studies exhibited that depletion of TECPR2 leads to a loss of LC3B-positive structures in cells, which suggests TECPR2 to positively regulate autophagic processes.
A frame shift deletion in the gene encoding for TECPR2 causes the generation of a premature stop codon and subsequent an unstable version of the protein, which is then degraded. Mutation in the TECPR2 gene triggers a neurodegenerative disorder termed hereditary spastic paraparesis (HSP). HSPs are a diverse group of neurodegenerative diseases that are characterized by spasticity in prevalent lower extremities and were mediated by a loss of axonal integrity of the corticospinal motor neurons. In the context of HSP more than 50 gene loci were identified by now. While TECPR2 is a human ATG8 binding protein and positive regulator of autophagy causing a form of HSP, the exact function of TECPR2 is unknown.
This study primarily focused on the determination of TECPR2’s binding mode to ATG8 proteins in vitro and in cells. The association of TECPR2 to all ATG8-family proteins was confirmed in in vitro pulldown experiments. Following fragment-based binding and peptide array experiments, the LC3-interacting region (LIR) of TECPR2 could be verified with mutants of TECPR2 lacking the LIR motif. Nuclear magnetic resonance (NMR) and isothermal titration calorimetry (ITC) were conducted to gain deeper insights into the binding preference to the different ATG8-family members. Moreover, the crystal structure of TECPR2-LIR was solved. In cells colocalization studies with overexpressed ATG8 proteins unraveled a preferential binding to the LC3-subfamily.
Further, mass spectrometric analysis revealed novel association partners of TECPR2: SEC24D, HOPS and BLOC-1, all of those participating in different endomembrane trafficking pathways. Interaction and colocalization of TECPR2 with these components was validated with several immunoprecipitation experiments and the N-terminal part of the protein comprising the WD40-domain could be defined as the binding site for all three of the association partners. In further approaches, the requirement of the LIR-motif and the necessity of the availability of LC3 protein for the particular interactions were determined. Interestingly, in the absence of LC3C the binding of TECPR2 to SEC24D was completely disrupted whereas a loss of LC3B only resulted in a decreased association. Notably, the binding proteins were not subjected to autophagosomal degradation, indicating that TECPR2 may operate as a multifunctional scaffold protein. While depletion of TECPR2 destabilized HOPS and BLOC-1, the autophagy defect observed in TECRP2-deficient cells could not be attributed to functional impairment of these two complexes.
Moreover, loss of TECPR2 led to a decline in protein levels of SEC24D and of its heterodimer partner SEC23A. Thus, TECPR2 is required to regulate the protein levels of SEC23A and SEC24D and subsequently the formation of the heterodimers. Together, SEC24D and SEC23A form the inner coat of COPII vesicles. These vesicles are responsible for the anterograde transport of cargo from the ER toward the Golgi compartment. COPII-coated vesicles are secreted form ER at distinct sites, termed ER exit sites (ERES). The small GTPase SAR1A maintains the vesicle budding, coating and secretion at the ERES. Together with SEC13, SEC31 forms the outer coat of the COPII vesicles and therefore serves as a general ERES marker.
Consistent with a defect in COPII coat assembly, the number of ERES diminished in the absence of TECPR2. These phenotypes could be rescued by the wildtype TECPR2 protein but not by the LIR-mutant. Intriguingly, these results were mimicked by depletion of LC3C, which localized to ERES. By monitoring the release of various cargos from ER in dependency of TECPR2 or LC3C, a role of both proteins in ER export was determined. These facts indicated that TECPR2 cooperates with LC3C to facilitate COPII assembly, ERES maintenance and ER export. Notably, fibroblast derived from a HSP patient carrying mutated TECPR2 showed diminished SEC24D protein levels and delayed ER export.
Concurrent with emerging evidence for a role of ERES in autophagosome formation, depletion of TECPR2 or LC3C or overexpression of a constitutive inactive SAR1 mutant reduced puncta formation of the early autophagosomal protein WIPI2.
In summary, this study uncovered a role for TECPR2 in ER export at ERES through interaction and stabilization of SEC24D, a COPII coat protein. This process also depended on ATG8-family protein LC3C, which is localized at ERES. Both proteins are required for correct COPII-mediated secretion. Moreover, the presence of TECPR2 and LC3C on ER allows development of omegasomes, membranous structures budding ER to form autophagosomes, by stabilization of WIPI2 and therefore contribute to autophagosome formation.
Part VI of our series on ISIS : "Blogforum 'Kalifat des Terrors: Interdisziplinäre Perspektiven auf den Islamischen Staat".
In 2014, two insurgency organisations stood out by their expansion, success and brutality: The Islamic State (IS) and Boko Haram (BH). The former emerged from the conflicts in Syria and Iraq and became a major actor in the Middle East, its influence reaching beyond the borders of its self-proclaimed “caliphate”, while the latter spread its violence throughout north-eastern Nigeria, spilling over into Cameroon, Chad and Niger. Because of their still growing success, many wonder about a possible partnership between IS and BH. To this I answer that there is a connection, but no partnership. Currently, any evidence suggesting a partnership is circumstantial at best...
Be it in the case of opening a website, sending an email, or high-frequency trading, bits and bytes of information have to cross numerous nodes at which micro-decisions are made. These decisions concern the most efficient path through the network, the processing speed, or the priority of incoming data packets.
Despite their multifaceted nature, micro-decisions are a dimension of control and surveillance in the twenty-first century that has received little critical attention. They represent the smallest unit and the technical precondition of a contemporary network politics – and of our potential opposition to it. The current debates regarding net neutrality and Edward Snowden’s revelation of NSA surveillance are only the tip of the iceberg. What is at stake is nothing less than the future of the Internet as we know it.
Background aims: Immunomagnetic enrichment of CD34+ hematopoietic “stem” cells (HSCs) using paramagnetic nanobead coupled CD34 antibody and immunomagnetic extraction with the CliniMACS plus system is the standard approach to generating T-cell-depleted stem cell grafts. Their clinical beneficence in selected indications is established. Even though CD34+ selected grafts are typically given in the context of a severely immunosuppressive conditioning with anti-thymocyte globulin or similar, the degree of T-cell depletion appears to affect clinical outcomes and thus in addition to CD34 cell recovery, the degree of T-cell depletion critically describes process quality. An automatic immunomagnetic cell processing system, CliniMACS Prodigy, including a protocol for fully automatic CD34+ cell selection from apheresis products, was recently developed. We performed a formal process validation to support submission of the protocol for CE release, a prerequisite for clinical use of Prodigy CD34+ products.
Methods: Granulocyte-colony stimulating factor–mobilized healthy-donor apheresis products were subjected to CD34+ cell selection using Prodigy with clinical reagents and consumables and advanced beta versions of the CD34 selection software. Target and non-target cells were enumerated using sensitive flow cytometry platforms.
Results: Nine successful clinical-scale CD34+ cell selections were performed. Beyond setup, no operator intervention was required. Prodigy recovered 74 ± 13% of target cells with a viability of 99.9 ± 0.05%. Per 5 × 10E6 CD34+ cells, which we consider a per-kilogram dose of HSCs, products contained 17 ± 3 × 10E3 T cells and 78 ± 22 × 10E3 B cells.
Conclusions: The process for CD34 selection with Prodigy is robust and labor-saving but not time-saving. Compared with clinical CD34+ selected products concurrently generated with the predecessor technology, product properties, importantly including CD34+ cell recovery and T-cell contents, were not significantly different. The automatic system is suitable for routine clinical application.
Allergy against birch pollen is among the most common causes of spring pollinosis in Europe and is diagnosed and treated using extracts from natural sources. Quality control is crucial for safe and effective diagnosis and treatment. However, current methods are very difficult to standardize and do not address individual allergen or isoallergen composition. MS provides information regarding selected proteins or the entire proteome and could overcome the aforementioned limitations. We studied the proteome of birch pollen, focusing on allergens and isoallergens, to clarify which of the 93 published sequence variants of the major allergen, Bet v 1, are expressed as proteins within one source material in parallel. The unexpectedly complex Bet v 1 isoallergen composition required manual data interpretation and a specific design of databases, as current database search engines fail to unambiguously assign spectra to highly homologous, partially identical proteins. We identified 47 non-allergenic proteins and all 5 known birch pollen allergens, and unambiguously proved the existence of 18 Bet v 1 isoallergens and variants by manual data analysis. This highly complex isoallergen composition raises questions whether isoallergens can be ignored or must be included for the quality control of allergen products, and which data analysis strategies are to be applied.
We present an extensive experimental study of the recently predicted pygmy quadrupole resonance (PQR) in Sn isotopes, where complementary probes were used. In this study, (α,α' γ ) and (γ , γ') experiments were performed on 124Sn. In both reactions, Jπ = 2+ states below an excitation energy of 5 MeV were populated. The E2 strength integrated over the full transition densities could be extracted from the (γ , γ') experiment, while the (α,α'γ ) experiment at the chosen kinematics strongly favors the excitation of surface modes because of the strong α-particle absorption in the nuclear interior. The excitation of such modes is in accordance with the quadrupole-type oscillation of the neutron skin predicted by a microscopic approach based on self-consistent density functional theory and the quasiparticle-phonon model (QPM). The newly determined γ -decay branching ratios hint at a non-statistical character of the E2 strength, as it has also been recently pointed out for the case of the pygmy dipole resonance (PDR). This allows us to distinguish between PQR-type and multiphonon excitations and, consequently, supports the recent first experimental indications of a PQR in 124Sn.
2004 erschütterten Terroranschläge in London und Madrid die Welt. Die Reaktion der EU/EG im seinerzeit schnellsten Gesetzgebungsverfahren seit Bestehen: Verabschiedung der Vorratsdatenspeicherungsrichtlinie. 2009 sah der EuGH die Richtlinie trotzdem als Binnenmarktregelung an, mit der Harmonisierung auf dem Informationsmarkt herbeigeführt werden sollte. Äußerungen zum Inhalt – quasi als obiter dictum möglich gewesen – versagte er sich. 2010 beurteilte dann das BVerfG die bundesdeutsche Umsetzung, aber – ganz dem Verhältnis von EuGH und BVerfG entsprechend – nur den die europäischen Mindestvorgaben überschießenden Teil. Dieses Gesetz hatte national schon für reichlich Sprengstoff im Rechtsstaat gesorgt und u.a. den Rücktritt der beharrlich widersetzlichen Justizministerin bewirkt. ...
Im Wirtschaftsregulierungsrecht treten immer häufiger Mehrpersonenverhältnisse auf: Die Regulierungsentscheidung der Regulierungsbehörde betrifft nicht nur den Adressaten, sondern hat mittelbar auch Wirkungen auf die Ausgestaltung der Wettbewerbsfreiheit der Konkurrenten. Materielles und Verfahrensrecht erlauben aber bisher kaum eine Beteiligung der Interessen des Dritten. Verwaltungsrecht und Verwaltungswissenschaft sind aufgefordert, hierfür Problemkonstellationen zu identifizieren und Lösungsvor-schläge zu unterbreiten.
Der Beitrag analysiert zunächst Dreiecksverhältnisse mit besonderem Blick auf das Wirtschaftsverwaltungsrecht und schlägt als einen möglichen Weg zur Bewältigung daraus resultierender Probleme in Instrumenten der Kooperation vor, wie sie etwa im Gesundheitsrecht mit dem Gemeinsamen Bundesausschuss (GBA) existieren, auch wenn dieses Rechtsgebiet (zu Unrecht) als wenig als wegweisend wahrgenommen wird.
Sowohl bezüglich der Modellierung der Sprachkompetenz bei mehrsprachigen Kindern als auch hinsichtlich der Bestimmung der hierfür notwendigen Indikatoren herrscht nach wie vor Forschungsbedarf. Die entsprechenden Erkenntnisse sind aber für eine valide Sprachstandsdiagnostik, auf Basis welcher auch eine Sprachförderung stattfinden kann, unerlässlich. In der vorliegenden Dissertation werden daher mit Hilfe von Verteilungsstatistiken, konfirmatorischen Faktoranalysen und Strukturgleichungsmodellen zunächst ausgewählte Sprachstandsindikatoren sowie das Konstrukt Sprachkompetenz von Kindern mit Deutsch als Zweitsprache zu Beginn der 1. Klasse modelliert und im Anschluss ihr Einfluss auf die Orthographiekompetenz dieser Schülerinnen und Schüler am Ende der 2. Klasse untersucht. Zusätzlich wird das phonologische Arbeitsgedächtnis als ein weiterer Prädiktor in das Modell eingebunden. Es wird der Fragestellung nachgegangen, ob die für die Modellierung der Sprachkompetenz verwendeten Indikatoren, wie bspw. Bildbenennung, Kasus, Syntaxerwerbsstufen und die mittlere Äußerungslänge (MLU) für die Gruppe der mehrsprachigen Kinder in der Schuleingangsphase geeignet bzw. valide sind. Dabei werden die jeweiligen Streuungen, die Korrelationen untereinander (konvergente Validität) sowie die Leistung der Indikatoren für die jeweiligen sprachlichen Kompetenzbereiche anhand der Höhe der Faktorladungen betrachtet. Ebenfalls wird die prognostische Validität der Indikatoren hinsichtlich der Rechtschreibkompetenz beleuchtet. Des Weiteren wird geprüft, ob sich die Sprachkompetenz bei DaZ-Kindern in eine semantische, eine morphologische und eine syntaktische Fähigkeit unterteilen lässt und ob die Sprachkompetenz als Faktor zweiter Ordnung modelliert werden kann. Weitere Fragestellungen betreffen die Modellierung der Rechtschreibkompetenz, also die Anzahl und Art der latenten Variablen, die dieses Konstrukt abbilden, sowie den Einfluss des phonologischen Arbeitsgedächtnisses und der einzelnen sprachlichen auf die orthographischen Teilkompetenzen.
The subject matter of this article is Axel Honneth’s theory of recognition as it has been exposed in his more recent book, Das Recht der Freiheit. Throughout the paper his attempts to describe injustices within modern capitalist societies using the notions of pathologies and anomie will be analyzed and criticized, especially from the viewpoint of their inability to deal with processes and contexts of disrecognition (Aberkennung). With help of this category, Honneth’s diagnosis regarding the moral progress in modern societies, as well as his notion of second order disorders, as injustices will be confronted and, hopefully, complemented.
Die Substitution von klassischen, mit der Nahrungsmittelproduktion in Konkurrenz stehenden, Substraten wie Glukose durch alternative Kohlenstoffquellen in der Biotechnologie ist sowohl aus ethischer, als auch aus ökonomischer Sicht erstrebenswert. Diese Arbeit beschreibt die Synthese von Bulkchemikalien in Form zweier Dicarboxylsäuren und einer Feinchemikalie in Form eines Sesquiterpens aus dem alternativen Substrat Methanol mit Hilfe genetisch veränderter Stämme des methylotrophen α-Proteobakteriums Methylobacterium extorquens.
Mesacon- und (2S)-Methylsuccinsäure sind Dicarboxylsäurederivate der CoA-Ester Mesaconyl- und (2S)-Methylsuccinyl-CoA, die als Intermediate im Ethylmalonyl-CoA- Weg (EMCP) vorkommen. M. extorquens nutzt den EMCP für die Regeneration von Glyoxylat, das für das Wachstum auf C1-Substraten wie Methanol obligatorisch ist. In dieser Arbeit konnte erstmals Mesacon- und (2S)-Methylsuccinsäure de novo durch die Expression einer für die Vorstufen Mesaconyl- und (2S)-Methylsuccinyl-CoA aktiven Thioesterase produziert werden. Ein kobaltlimitiertes Wachstum von M. extorquens führte aufgrund mangelnder Cofaktorversorgung zweier Vitamin-B12-abhäniger Mutasen im EMCP zu einer Akkumulation der beiden CoA-Ester-Vorstufen, womit eine Produktion von 0.65 g/l Mesacon- und (2S)-Methylsuccinsäure erreicht wurde. Weitergehende Untersuchungen belegten außerdem einen positiven Effekt eines ausgeschalteten PHB-Zyklusses auf die Produktion der beiden EMCP- Dicarboxylsäurederivate.
Diese Arbeit beinhaltet zusätzlich grundlagenwissenschaftliche Untersuchungen zur Substitution der EMCP-katalysierten Glyoxylatregeneration durch einen heterologen Glyoxylatzyklus in EMCP-negativen M. extorquens-Stämmen. Dabei konnte erstmals ein methanolverwertendes, methylotrophes Bakterium identifiziert werden, das einen Serin-Zyklus in Kombination mit dem Glyoxylat-Zyklus zur Kohlenstoffassimilation verwendet, ohne dabei zusätzliche Stoffwechselwege zur CO2-Fixierung wie den EMCP, RuMP oder CBB-Zyklus zu verwenden.
Die Präsenz einer nativen C30-Carotinoidbiosynthese, ausgehend von der Vorstufe Farnesylpyrophosphat (FPP), empfiehlt M. extorquens als Produktionsorganismus für (Sesqui-)Terpene. In dieser Arbeit wurde mit Hilfe einer induzierbar gesteuerten Expression einer Terpensynthase in Form einer α-Humulen-Synthase, einer FPP-Synthase und eines prokaryontischen Mevalonatweges, erstmals die de novo Synthese eines Terpens aus Methanol am Beispiel des α-Humulens etabliert. Durch optimierte Expressionen der Terpensynthase, FPPS und einzelner MVA-Gene mit Hilfe angepasster Translationsinitiationsraten der jeweiligen ribosomalen Bindestellen und der Verwendung eines in der nativen Carotinoidbiosynthese inhibierten M. extorquens-Stammes wurden finale Produkttiter von bis zu 1.65 g/l α-Humulen in Fed-Batch-Fermentationen erreicht.
Diese kumulative Dissertation beinhaltet außerdem einen Reviewartikel, in dem der verwendete Mikroorganismus M. extorquens in mikrobiologischer, genetischer, biochemischer und auch biotechnologischer Hinsicht ausführlich beschrieben wird. Zudem gibt ein Buchkapitel eine Übersicht über die Verwendung von Methanol in der Biotechnologie.
We describe a new large-sized species of hypercarnivorous hyainailourine–Kerberos langebadreae gen. & sp. nov.–from the Bartonian (MP16) locality of Montespieu (Tarn, France). These specimens consist of a skull, two hemimandibles and several hind limb elements (fibula, astragalus, calcaneum, metatarsals, and phalanges). Size estimates suggest K. langebadreae may have weighed up to 140 kg, revealing this species as the largest carnivorous mammal in Europe at that time. Besides its very large size, K. langebadreae possesses an interesting combination of primitive and derived features. The distinctive skull morphology of K. langebadreae reflects a powerful bite force. The postcranial elements, which are rarely associated with hyainailourine specimens, indicate an animal capable of a plantigrade stance and adapted for terrestrial locomotion. We performed the first phylogenetic analysis of hyainailourines to determine the systematic position of K. langebadreae and to understand the evolution of the group that includes other massive carnivores. The analysis demonstrates that Hemipsalodon, a North American taxon, is a hyainailourine and is closely related to European Paroxyaena. Based on this analysis we hypothesize the biogeographic history of the Hyainailourinae. The group appeared in Africa with a first migration to Europe during the Bartonian that likely included the ancestors of Kerberos, Paroxyaena and Hemipsalodon, which further dispersed into North America at this time. We propose that the hyainailourines dispersed into Europe also during the Priabonian. These migrants have no ecological equivalent in Europe during these intervals and likely did not conflict with the endemic hyaenodont proviverrines. The discovery of K. langebadreae shows that large body size appears early in the evolution of hyainailourines. Surprisingly, the late Miocene Hyainailouros shares a more recent common ancestor with small-bodied hyainailourines (below 15 kg). Finally, our study supports a close relationship between the Hyainailourinae and Apterodontinae and we propose the new clade: Hyainailouridae.
Background & Aims: Hepatitis C virus (HCV) cell entry is mediated by several cell surface receptors, including scavenger receptor class B type I (SR-BI). Oxidized low density lipoprotein (oxLDL) inhibits the interaction between HCV and SR-BI in a noncompetitive manner. We tested whether serum oxLDL levels correlate with sustained virologic response (SVR) rates after interferon-based treatment of chronic hepatitis C.
Methods: Baseline oxLDL was determined in 379 participants with chronic HCV genotype 1 infection from the INDIV-2 study using a commercial enzyme-linked immunosorbent assay. The mechanistic in vitro studies used full-length and subgenomic HCV genomes replicating in hepatoma cells.
Results: In the multivariate analysis, oxLDL was found to be an independent predictor of SVR. Oxidized LDL did not correlate with markers of inflammation (alanine transaminase, ferritin), nor was serum oxLDL affected by exogenous interferon administration. Also, oxLDL did not alter the sensitivity of HCV replication to interferon. However, oxLDL was found to be a potent inhibitor of cell-to-cell spread of HCV between adjacent cells in vitro. It could thus reduce the rate at which new cells are infected by HCV through either the cell-free or cell-to-cell route. Finally, serum oxLDL was significantly associated with the estimated infected cell loss rate under treatment.
Conclusions: Oxidized LDL is a novel predictor of SVR after interferon-based therapy and may explain the previously observed association of LDL with SVR. Rather than being a marker of activated antiviral defenses it may improve chances of SVR by limiting spread of infection to naive cells through the cell-to-cell route.
Hypoxia potentiates palmitate-induced pro-inflammatory activation of primary human macrophages
(2015)
Pro-inflammatory cytokines secreted by adipose tissue macrophages (ATMs) contribute to chronic low-grade inflammation and obesity-induced insulin resistance. Recent studies have shown that adipose tissue hypoxia promotes an inflammatory phenotype in ATMs. However, our understanding of how hypoxia modulates the response of ATMs to free fatty acids within obese adipose tissue is limited. We examined the effects of hypoxia (1% O2) on the pro-inflammatory responses of human monocyte-derived macrophages to the saturated fatty acid palmitate. Compared with normoxia, hypoxia significantly increased palmitate-induced mRNA expression and protein secretion of IL-6 and IL-1β. Although palmitate-induced endoplasmic reticulum stress and nuclear factor κB pathway activation were not enhanced by hypoxia, hypoxia increased the activation of JNK and p38 mitogen-activated protein kinase signaling in palmitate-treated cells. Inhibition of JNK blocked the hypoxic induction of pro-inflammatory cytokine expression, whereas knockdown of hypoxia-induced transcription factors HIF-1α and HIF-2α alone or in combination failed to reduce IL-6 and only modestly reduced IL-1β gene expression in palmitate-treated hypoxic macrophages. Enhanced pro-inflammatory cytokine production and JNK activity under hypoxia were prevented by inhibiting reactive oxygen species generation. In addition, silencing of dual-specificity phosphatase 16 increased normoxic levels of IL-6 and IL-1β and reduced the hypoxic potentiation in palmitate-treated macrophages. The secretome of hypoxic palmitate-treated macrophages promoted IL-6 and macrophage chemoattractant protein 1 expression in primary human adipocytes, which was sensitive to macrophage JNK inhibition. Our results reveal that the coexistence of hypoxia along with free fatty acids exacerbates macrophage-mediated inflammation.
"Mehr Licht!" – so lauteten, glaubt man seinem Arzt Carl Vogel, die letzten Worte des größten deutschen Dichters und Denkers Johann Wolfgang Goethe. Aus der Sicht der Fluoreszenzmikroskopie ist das kein guter Grundsatz. Die Kernidee der Lichtscheiben-Fluoreszenzmikroskopie (LSFM) liegt in der Macht der dunklen Seite. Anders gesagt: Sie folgt dem Prinzip, dass weniger manchmal viel mehr sein kann. Die schonende Beleuchtung empfindlicher Proben bei der LSFM birgt großes Potenzial für die moderne Zell- und Entwicklungsbiologie.
Background Reaching the therapeutic target of remission or low-disease activity has improved outcomes in patients with rheumatoid arthritis (RA) significantly. The treat-to-target recommendations, formulated in 2010, have provided a basis for implementation of a strategic approach towards this therapeutic goal in routine clinical practice, but these recommendations need to be re-evaluated for appropriateness and practicability in the light of new insights.
Objective To update the 2010 treat-to-target recommendations based on systematic literature reviews (SLR) and expert opinion.
Methods A task force of rheumatologists, patients and a nurse specialist assessed the SLR results and evaluated the individual items of the 2010 recommendations accordingly, reformulating many of the items. These were subsequently discussed, amended and voted upon by >40 experts, including 5 patients, from various regions of the world. Levels of evidence, strengths of recommendations and levels of agreement were derived.
Results The update resulted in 4 overarching principles and 10 recommendations. The previous recommendations were partly adapted and their order changed as deemed appropriate in terms of importance in the view of the experts. The SLR had now provided also data for the effectiveness of targeting low-disease activity or remission in established rather than only early disease. The role of comorbidities, including their potential to preclude treatment intensification, was highlighted more strongly than before. The treatment aim was again defined as remission with low-disease activity being an alternative goal especially in patients with long-standing disease. Regular follow-up (every 1–3 months during active disease) with according therapeutic adaptations to reach the desired state was recommended. Follow-up examinations ought to employ composite measures of disease activity that include joint counts. Additional items provide further details for particular aspects of the disease, especially comorbidity and shared decision-making with the patient. Levels of evidence had increased for many items compared with the 2010 recommendations, and levels of agreement were very high for most of the individual recommendations (≥9/10).
Conclusions The 4 overarching principles and 10 recommendations are based on stronger evidence than before and are supposed to inform patients, rheumatologists and other stakeholders about strategies to reach optimal outcomes of RA.
This paper empirically investigates how organizational hierarchy affects the allocation of credit within a bank. Using an exogenous variation in organizational design, induced by a reorganization plan implemented in roughly 2,000 bank branches in India during 1999-2006, and employing a difference-in-differences research strategy, we find that increased hierarchization of a branch decreases its ability to produce "soft" information on loans, leads to increased standardization of loans and rationing of "soft information" loans. Furthermore, this loss of information brings about a reduction in performance on loans: delinquency rates and returns on similar loans are worse in more hierarchical branches. We also document how hierarchical structures perform better in environments that are characterized by a high degree of corruption, thus highlighting the benefits of hierarchical decision making in restraining rent seeking activities. Finally, we document a channel - managerial interference - through which hierarchy affects loan outcomes.
Written during the fin de siècle, a period known as one of “sexual anarchy,” Ménie Muriel Dowie’s feminist Gallia (1895) joins the literary works of famous writers like Mona Caird or Sarah Grand. Wells. But although her novel covers the most explosive topics of the nineteenth century, namely degeneration and the female pursuit of emancipation, Dowie does not achieve great distinction as the limited se-lection of secondary literature on Gallia confirms. From my point of view, this has mostly to do with Dowie’s radical ideas on maintaining Britain’s health and su-premacy, as well as with the novel’s unconventional structure according that makes it hard to say what Dowie actually drives at. Superficially, Gallia might look like a conventional, but failed love-story with a strong and feminist heroine. But on sec-ond glance, one realises that some more important structure underlies this stereo-type-looking plot. Dowie’s creed is not that man is the measure – although the pub-licly powerful positions in this novel are all held by male characters – but that women set the new benchmarks for Britain’s society by secretly pulling the strings in order to disengage from male dominance.
Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal -arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods – BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence.
Amines are potentially important for atmospheric new particle formation, but their concentrations are usually low with typical mixing ratios in the pptv range or even smaller. Therefore, the demand for highly sensitive gas-phase amine measurements has emerged in the last several years. Nitrate chemical ionization mass spectrometry (CIMS) is routinely used for the measurement of gas-phase sulfuric acid in the sub-pptv range. Furthermore, extremely low volatile organic compounds (ELVOCs) can be detected with a nitrate CIMS. In this study we demonstrate that a nitrate CIMS can also be used for the sensitive measurement of dimethylamine (DMA, (CH3)2NH) using the NO3−•(HNO3)1 − 2• (DMA) cluster ion signal. Calibration measurements were made at the CLOUD chamber during two different measurement campaigns. Good linearity between 0 and ∼ 120 pptv of DMA as well as a sub-pptv detection limit of 0.7 pptv for a 10 min integration time are demonstrated at 278 K and 38 % RH.
Dass die in den letzten Jahren stattfindende Ausweitung der Rechtsgeschichte(n) durch globale und transnationale Perspektiven gerade in der Völkerrechtsgeschichte auf besonders fruchtbaren Boden fällt, liegt auf der Hand. Denn Regulierung, Normierung und Legitimation überregionaler Beziehungen bieten sich wie kaum ein anderes Themenfeld für eine Horizonterweiterung über den Nationalstaat hinaus an. Aus einer vornehmlich europäischen Völkerrechtsgeschichte werden damit Völkerrechtsgeschichten in der Dialektik von lokalen und globalen Bezugspunkten. ...
We examine the inter-linkages between financial factors and real economic activity. We review the main theoretical approaches that allow financial frictions to be embedded into general equilibrium models. We outline, from a policy perspective, the most recent empirical papers focusing on the propagation of exogenous shocks to the economy, with a particular emphasis on works dealing with time variation of parameters and other types of nonlinearities. We then present an application to the analysis of the changing transmission of financial shocks in the euro area. Results show that the effects of a financial shock are time-varying and contingent on the state of the economy. They are of negligible importance in normal times but they greatly matter in conditions of stress.
Este artigo analisa a crítica de Adorno à ontologia de Heidegger. Para tal, utiliza como leitmotiv a interpretação heideggeriana de Kant. Procuraremos mostrar que para Adorno a edificação da ontologia fundamental a partir da filosofia de Kant é uma interpretação indevida desta. Por fim, procura apontar uma possível saída na filosofia de Adorno para o problema da necessidade de fundamentação do discurso filosófico. Tal saída passa pela constatação da importância da arte para a construção da universalidade na filosofia.
O presente artigo visa a fazer algumas anotações sobre educação, emancipação e crítica social no pensamento de Theodor W. Adorno. Esses temas se relacionam direta e indiretamente nos escritos de Adorno e assinalam a coerência epistemológica da sua teoria crítica em relação a ambos. Desse modo, a questão que colocamos é a seguinte: como compreender a tensão presente entre as necessidades de uma educação para a emancipação e as condições para efetivá-la? Essa questão nos encaminha para outra: é possível relacionar, nos textos adornianos, uma perspectiva de se pensar a educação para a emancipação, articulada a uma crítica social no contexto atual? Primeiramente, fazemos uma breve incursão no que consiste o pensamento contra a barbárie em Adorno, sobretudo, a partir do sentido de Auschwitz como símbolo da relação entre civilização e barbárie que o autor faz. Num segundo momento, nos confrontamos com a questão da formação cultural na Teoria da Semiformação, cujo escopo do texto é apontar os limites da formação cultural e consequentemente os limites da educação no âmbito do capitalismo avançado. Por fim, pretendemos discutir a ideia de "crítica social" em Adorno, articulada aos temas anteriores, isto é, apontar algumas ponderações para uma educação contra a barbárie e a semiformação frentes aos desafios impostos pela sociedade atual.
The Treaty of Maastricht imposed the strict obligation on the European Union (EU) to establish an economic and monetary union, now Article 3(4) TEU. This economic and monetary union is, however, not designed as a separate entity but as an integral part of the EU. The single currency was to become the currency of the EU and to be the legal tender in all Member States unless an exemption was explicitly granted in the primary law of the EU, as in the case of the UK and Denmark. The newly admitted Member States are obliged to introduce the euro as their currency as soon as they fulfil the admission criteria. Technically, this has been achieved by transferring the exclusive competence for the monetary policy of the Member States whose currency is the euro on the EU, Article 3(1)(c) TFEU and by bestowing the euro with the quality of legal tender, the only legal tender in the EU, Article 128(1) sentence 3 TFEU.
The paper traces the developments from the formation of the European Economic and Monetary Union to this date. It discusses the fact that the primary mandate of the European System of Central Banks (ESCB) is confined to safeguarding price stability and does not include general economic policy. Finally, the paper contributes to the discussion on whether the primary law of the European Union would support a eurozone exit. The Treaty of Maastricht imposed the strict obligation on the European Union (EU) to establish an economic and monetary union, now Article 3(4) TEU. This economic and monetary union is, however, not designed as a separate entity but as an integral part of the EU. The single currency was to become the currency of the EU and to be the legal tender in all Member States unless an exemption was explicitly granted in the primary law of the EU, as in the case of the UK and Denmark. The newly admitted Member States are obliged to introduce the euro as their currency as soon as they fulfil the admission criteria. Technically, this has been achieved by transferring the exclusive competence for the monetary policy of the Member States whose currency is the euro on the EU, Article 3(1)(c) TFEU and by bestowing the euro with the quality of legal tender, the only legal tender in the EU, Article 128(1) sentence 3 TFEU.
In its meeting on 6 September 2012, the Governing Council of the ECB took decisions on a number of technical features regarding the Eurosystem’s outright transactions in secondary sovereign bond markets (OMT). This decision was challenged in the German Federal Constitutional Court (GFCC) by a number of constitutional complaints and other petitions. In its seminal judgment of 14 January 2014, the German court expressed serious doubts on the compatibility of the ECB’s decision with the European Union law.
It admitted the complaints and petitions even though actual purchases had not been executed and the control of acts of an organ of the EU in principle is not the task of the GFCC. As justification for this procedure the court resorted to its judicature on a reserved “ultra vires” control and the defense of the “constitutional identiy” of Germany. In the end, however, the court referred the case pursuant to Article 267 TFEU to the European Court of Justice (ECJ) for preliminary rulings on several questions of EU law. In substance, the German court assessed OMT as an act of economic policy which is not covered by the competences of the ECB. Furthermore, it judged OMT as a – by EU primary law – prohibited monetary financing of sovereign debt. The defense of the ECB (disruption of monetary policy transmission mechanism) was dismissed without closer scrutiny as being “irrelevant”. Finally the court opened, however, a way for a compromise by an interpretation of OMT in conformity with EU law under preconditions, specified in detail.
Procedure and findings of this judgment were harshly criticized by many economists but also by the majority of legal scholars. This criticism is largely convincing in view of the admissibility of the complaints. Even if the “ultra vires” control is in conformity with prior decisions of court it is in this judgment expanded further without compelling reasons. It is also questionable whether the standing of the complaining parties had to be accepted and whether the referral to the ECJ was indicated. The arguments of the court are, however, conclusive in respect of the transgression of competences by the ECB and – to somewhat lesser extent – in respect of the monetary debt financing. The dismissal of the defense as “irrelevant” is absolutey persuasive.
Irrigation intensifies land use by increasing crop yield but also impacts water resources. It affects water and energy balances and consequently the microclimate in irrigated regions. Therefore, knowledge of the extent of irrigated land is important for hydrological and crop modelling, global change research, and assessments of resource use and management. Information on the historical evolution of irrigated lands is limited. The new global historical irrigation data set (HID) provides estimates of the temporal development of the area equipped for irrigation (AEI) between 1900 and 2005 at 5 arcmin resolution. We collected sub-national irrigation statistics from various sources and found that the global extent of AEI increased from 63 million ha (Mha) in 1900 to 111 Mha in 1950 and 306 Mha in 2005. We developed eight gridded versions of time series of AEI by combining sub-national irrigation statistics with different data sets on the historical extent of cropland and pasture. Different rules were applied to maximize consistency of the gridded products to sub-national irrigation statistics or to historical cropland and pasture data sets. The HID reflects very well the spatial patterns of irrigated land as shown on historical maps for the western United States (around year 1900) and on a global map (around year 1960). Mean aridity on irrigated land increased and mean natural river discharge on irrigated land decreased from 1900 to 1950 whereas aridity decreased and river discharge remained approximately constant from 1950 to 2005. The data set and its documentation are made available in an open-data repository at https://mygeohub.org/publications/8 (doi:10.13019/M20599).
Background: Although the risk of developing colorectal cancer (CRC) is 2-4 times higher in case of a positive family history, risk-adapted screening programs for family members related to CRC- patients do not exist in the German health care system. CRC screening recommendations for persons under 55 years of age that have a family predisposition have been published in several guidelines.
The primary aim of this study is to determine the frequency of positive family history of CRC (1st degree relatives with CRC) among 40–54 year old persons in a general practitioner (GP) setting in Germany. Secondary aims are to detect the frequency of occurrence of colorectal neoplasms (CRC and advanced adenomas) in 1st degree relatives of CRC patients and to identify the variables (e.g. demographic, genetic, epigenetic and proteomic characteristics) that are associated with it. This study also explores whether evidence-based information contributes to informed decisions and how screening participation correlates with anxiety and (anticipated) regret.
Methods/Design: Prior to the beginning of the study, the GP team (GP and one health care assistant) in around 50 practices will be trained, and about 8,750 persons that are registered with them will be asked to complete the “Network against colorectal cancer” questionnaire. The 10 % who are expected to have a positive family history will then be invited to give their informed consent to participate in the study. All individuals with positive family history will be provided with evidence-based information and prevention strategies. We plan to examine each participant’s family history of CRC in detail and to collect information on further variables (e.g. demographics) associated with increased risk. Additional stool and blood samples will be collected from study-participants who decide to undergo a colonoscopy (n ~ 350) and then analyzed at the German Cancer Research Center (DKFZ) Heidelberg to see whether further relevant variables are associated with an increased risk of CRC. One screening list and four questionnaires will be used to collect the data, and a detailed statistical analysis plan will be provided before the database is closed (expected to be June 30, 2015).
Discussion: It is anticipated that when persons with a family history of colorectal cancer have been provided with professional advice by the practice team, there will be an increase in the availability of valid information on the frequency of affected individuals and an increase in the number of persons making informed decisions. We also expect to identify further variables that are associated with colorectal cancer. This study therefore has translational relevance from lab to practice.
Trial registration: German Clinical Trials Register DRKS00006277
In cases in which there is the possibility of massive human losses, the threshold likelihood of their occurrence, and the non-excessive costs of their prevention, we ought to act now. This is all the more definitely the case because it may well be that this is the time-of-last-opportunity to head off one or more potential disasters, all of which may still be preventable by sufficiently rapid reductions in carbon emissions from the combustion of fossil fuel. It is unfair that the present generation should incur as heavy a burden as it does of seizing the last opportunity for prevention of disasters like large sea-level rises, but the unfairness is not sufficient to make the burden unreasonable to bear, especially since it is not in fact as heavy as often believed.
Sparse coding is a popular approach to model natural images but has faced two main challenges: modelling low-level image components (such as edge-like structures and their occlusions) and modelling varying pixel intensities. Traditionally, images are modelled as a sparse linear superposition of dictionary elements, where the probabilistic view of this problem is that the coefficients follow a Laplace or Cauchy prior distribution. We propose a novel model that instead uses a spike-and-slab prior and nonlinear combination of components. With the prior, our model can easily represent exact zeros for e.g. the absence of an image component, such as an edge, and a distribution over non-zero pixel intensities. With the nonlinearity (the nonlinear max combination rule), the idea is to target occlusions; dictionary elements correspond to image components that can occlude each other. There are major consequences of the model assumptions made by both (non)linear approaches, thus the main goal of this paper is to isolate and highlight differences between them. Parameter optimization is analytically and computationally intractable in our model, thus as a main contribution we design an exact Gibbs sampler for efficient inference which we can apply to higher dimensional data using latent variable preselection. Results on natural and artificial occlusion-rich data with controlled forms of sparse structure show that our model can extract a sparse set of edge-like components that closely match the generating process, which we refer to as interpretable components. Furthermore, the sparseness of the solution closely follows the ground-truth number of components/edges in the images. The linear model did not learn such edge-like components with any level of sparsity. This suggests that our model can adaptively well-approximate and characterize the meaningful generation process.
Ceraceosorus bombacis is an early-diverging lineage of smut fungi and a pathogen of cotton trees (Bombax ceiba). To study the evolutionary genomics of smut fungi in comparison with other fungal and oomycete pathogens, the genome of C. bombacis was sequenced and comparative genomic analyses were performed. The genome of 26.09 Mb encodes for 8,024 proteins, of which 576 are putative-secreted effector proteins (PSEPs). Orthology analysis revealed 30 ortholog PSEPs among six Ustilaginomycotina genomes, the largest groups of which are lytic enzymes, such as aspartic peptidase and glycoside hydrolase. Positive selection analyses revealed the highest percentage of positively selected PSEPs in C. bombacis compared with other Ustilaginomycotina genomes. Metabolic pathway analyses revealed the absence of genes encoding for nitrite and nitrate reductase in the genome of the human skin pathogen Malassezia globosa, but these enzymes are present in the sequenced plant pathogens in smut fungi. Interestingly, these genes are also absent in cultivable oomycete animal pathogens, while nitrate reductase has been lost in cultivable oomycete plant pathogens. Similar patterns were also observed for obligate biotrophic and hemi-biotrophic fungal and oomycete pathogens. Furthermore, it was found that both fungal and oomycete animal pathogen genomes are lacking cutinases and pectinesterases. Overall, these findings highlight the parallel evolution of certain genomic traits, revealing potential common evolutionary trajectories among fungal and oomycete pathogens, shaping the pathogen genomes according to their lifestyle.
Background: Xanthophyllomyces dendrorhous is a basal agaricomycete with uncertain taxonomic placement, known for its unique ability to produce astaxanthin, a carotenoid with antioxidant properties. It was the aim of this study to elucidate the organization of its CoA-derived pathways and to use the genomic information of X. dendrorhous for a phylogenomic investigation of the Basidiomycota.
Results: The genome assembly of a haploid strain of Xanthophyllomyces dendrorhous revealed a genome of 19.50 Megabases with 6385 protein coding genes. Phylogenetic analyses were conducted including 48 fungal genomes. These revealed Ustilaginomycotina and Agaricomycotina as sister groups. In the latter a well-supported sister-group relationship of two major orders, Polyporales and Russulales, was inferred. Wallemia occupies a basal position within the Agaricomycotina and X. dendrorhous represents the basal lineage of the Tremellomycetes, highlighting that the typical tremelloid parenthesomes have either convergently evolved in Wallemia and the Tremellomycetes, or were lost in the Cystofilobasidiales lineage. A detailed characterization of the CoA-related pathways was done and all genes for fatty acid, sterol and carotenoid synthesis have been assigned.
Conclusions: The current study ascertains that Wallemia with tremelloid parenthesomes is the most basal agaricomycotinous lineage and that Cystofilobasidiales without tremelloid parenthesomes are deeply rooted within Tremellomycetes, suggesting that parenthesomes at septal pores might be the core synapomorphy for the Agaricomycotina. Apart from evolutionary insights the genome sequence of X. dendrorhous will facilitate genetic pathway engineering for optimized astaxanthin or oxidative alcohol production.
Background: Astrocytomas are the most common primary brain tumors distinguished into four histological grades. Molecular analyses of individual astrocytoma grades have revealed detailed insights into genetic, transcriptomic andepigenetic alterations. This provides an excellent basis to identify similarities and differences between astrocytoma grades. Methods: We utilized public omics data of all four astrocytoma grades focusing on pilocytic astrocytomas (PA I), diffuse astrocytomas (AS II), anaplastic astrocytomas (AS III) and glioblastomas (GBM IV) to identify similarities and differences using well-established bioinformatics and systems biology approaches. We further validated the expression and localization of Ang2 involved in angiogenesis using immunohistochemistry. Results: Our analyses show similarities and differences between astrocytoma grades at the level of individual genes, signaling pathways and regulatory networks. We identified many differentially expressed genes that were either exclusively observed in a specific astrocytoma grade or commonly affected in specific subsets of astrocytoma grades in comparison to normal brain. Further, the number of differentially expressed genes generally increased with the astrocytoma grade with one major exception. The cytokine receptor pathway showed nearly the same number of differentially expressed genes in PA I and GBM IV and was further characterized by a significant overlap of commonly altered genes and an exclusive enrichment of overexpressed cancer genes in GBM IV. Additional analyses revealed a strong exclusive overexpression of CX3CL1 (fractalkine) and its receptor CX3CR1 in PA I possibly contributing to the absence of invasive growth. We further found that PA I was significantly associated with the mesenchymal subtype typically observed for very aggressive GBM IV. Expression of endothelial and mesenchymal markers (ANGPT2, CHI3L1) indicated a stronger contribution of the micro-environment to the manifestation of the mesenchymal subtype than the tumor biology itself. We further inferred a transcriptional regulatory network associated with specific expression differences distinguishing PA I from AS II, AS III and GBM IV. Major central transcriptional regulators were involved in brain development, cell cycle control, proliferation, apoptosis, chromatin remodeling or DNA methylation. Many of these regulators showed directly underlying DNA methylation changes in PA I or gene copy number mutations in AS II, AS III and GBM IV. Conclusions: This computational study characterizes similarities and differences between all four astrocytoma grades confirming known and revealing novel insights into astrocytoma biology. Our findings represent a valuable resource for future computational and experimental studies.
During CNS development and adult neurogenesis, immature neurons travel from the germinal zones towards their final destination using cellular substrates for their migration. Classically, radial glia and neuronal axons have been shown to act as physical scaffolds to support neuroblast locomotion in processes known as gliophilic and neurophilic migration, respectively (Hatten, 1999; Marin and Rubenstein, 2003; Rakic, 2003). In adulthood, long distance neuronal migration occurs in a glial-independent manner since radial glia cells differentiate into astrocytes after birth. A series of studies highlight a novel mode of neuronal migration that uses blood vessels as scaffolds, the so-called vasophilic migration. This migration mode allows neuroblast navigation in physiological and also pathological conditions, such as neuronal precursor migration after ischemic stroke or cerebral invasion of glioma tumor cells. Here we review the current knowledge about how vessels pave the path for migrating neurons and how trophic factors derived by glio-vascular structures guide neuronal migration both during physiological as well as pathological processes
‘Being with oneself in the other’ is a well-known formula that Hegel uses to characterize the basic relation of subjective freedom. This phrase points to the fact that subjects can only come to themselves if they remain capable of going beyond themselves. This motif also plays a significant role in Hegel’s philosophy of art. The article further develops this motif by exploring the extent to which this polarity of selfhood and otherhood is also characteristic of states of aesthetic freedom. It does not offer an exegesis of Hegel’s writings, but attempts to remain as close as possible to the spirit of Hegel’s philosophy – with some help from Kant and Adorno. The argument begins with some key terms on the general state of subjective freedom in order to distinguish it from the particular role of aesthetic freedom and then, finally, drawing again on Hegel, works out the sense in which aesthetic freedom represents an important variant of freedom.
Diffusion tensor imaging (DTI) is amongst the simplest mathematical models available for diffusion magnetic resonance imaging, yet still by far the most used one. Despite the success of DTI as an imaging tool for white matter fibers, its anatomical underpinnings on a microstructural basis remain unclear. In this study, we used 65 myelin-stained sections of human premotor cortex to validate modeled fiber orientations and oft used microstructure-sensitive scalar measures of DTI on the level of individual voxels. We performed this validation on high spatial resolution diffusion MRI acquisitions investigating both white and gray matter. We found a very good agreement between DTI and myelin orientations with the majority of voxels showing angular differences less than 10°. The agreement was strongest in white matter, particularly in unidirectional fiber pathways. In gray matter, the agreement was good in the deeper layers highlighting radial fiber directions even at lower fractional anisotropy (FA) compared to white matter. This result has potentially important implications for tractography algorithms applied to high resolution diffusion MRI data if the aim is to move across the gray/white matter boundary. We found strong relationships between myelin microstructure and DTI-based microstructure-sensitive measures. High FA values were linked to high myelin density and a sharply tuned histological orientation profile. Conversely, high values of mean diffusivity (MD) were linked to bimodal or diffuse orientation distributions and low myelin density. At high spatial resolution, DTI-based measures can be highly sensitive to white and gray matter microstructure despite being relatively unspecific to concrete microarchitectural aspects.
Background: Hundreds of West African healthcare workers (HCW) have become ill with Ebola virus disease (EVD) and died during the recent outbreak. The occurrence of occupational infections in laboratories could be due to the lack of use of personal protective equipment, the failure to implement specific regulations about the use of equipment and how to work with hazardous materials. Our study attempted to assess the information as well as training level of HCW of a German high level isolation unit and their concern over an occupationally acquired EVD.
Methods: During the recent Ebola virus outbreak a survey was conducted among HCWs, using an anonymous questionnaire.
Results: Although 70% of our total study population stated that they have all the information needed to care for Ebola patients, only 18.2% of laboratory workers and 29.4% of the HCW of the virology department felt sufficiently trained. The HCW rated the Internet (64.3%) and the daily press (54.3%) as the most important sources of information. Medical literature (45.7%) and official institutions (40.4%) were rated less often.
Conclusions: Formulated pointedly, the HCW turned to popular science to get the information they need to feel safe. Further in house training regarding practical skills and reference to scientific literature would be a better solution to ensure workplace safety.
Background: The pathomechanisms of atherosclerosis and vascular remodelling are under intense research. Only a few in vivo tools to study these processes longitudinally in animal experiments are available. Here, we evaluated the potential of micro-CT technology.
Methods: Lumen areas of the common carotid arteries (CCA) in the ApoE-/- partial carotid artery ligation mouse model were compared between in vivo and ex vivo micro-CT technique and serial histology in a total of 28 animals. AuroVist-15 nm nanoparticles were used as in vivo blood pool contrast agent in a Skyscan 1176 micro-CT at resolution of 18 μmeter voxel size and a mean x-ray dose of 0.5 Gy. For ex vivo imaging, animals were perfused with MicroFil and imaged at 9 μmeter voxel size. Lumen area was evaluated at postoperative days 7, 14, and 28 first by micro-CT followed by histology.
Results: In vivo micro-CT and histology revealed lumen loss starting at day 14. The lumen profile highly correlated (r = 0.79, P<0.0001) between this two methods but absolute lumen values obtained by histology were lower than those obtained by micro-CT. Comparison of in vivo and ex vivo micro-CT imaging revealed excellent correlation (r = 0.83, P<0.01). Post mortem micro-CT yielded a higher resolution than in vivo micro-CT but there was no statistical difference of lumen measurements in the partial carotid artery ligation model.
Conclusion: These data demonstrate that in vivo micro-CT is a feasible and accurate technique with low animal stress to image remodeling processes in the murine carotid artery.