OPUS 4 | Universitätspublikationen

Latitudinal differences in the amplitude of the OAE-2 carbon isotopic excursion: pCO2 and paleoproductivity (2011)

Elisabeth C. van Bentum Gert-Jan Reichart Astrid Forster Jacobus S. Sinninghe Damsté

A complete, well-preserved record of the Cenomanian/Turonian (C/T) Oceanic Anoxic Event 2 (OAE-2) was recovered from Demerara Rise in the southern North Atlantic Ocean (ODP site 1260). Across this interval, we determined changes in the stable carbon isotopic composition of sulfur-bound phytane (δ13Cphytane, a biomarker for photosynthetic algae. The δ13Cphytane record shows a positive excursion at the onset of the OAE-2 interval, with an unusually large amplitude (~7 ‰) compared to existing C/T proto-North Atlantic δ13Cphytane records (3–6 ‰). Overall, the amplitude of the excursion of δ13Cphytane decreases with latitude. Using reconstructed sea surface temperature (SST) gradients for the proto-North Atlantic, we investigated environmental factors influencing the latitudinal δ13Cphytane gradient. The observed gradient is best explained by high productivity at DSDP Site 367 and Tarfaya basin before OAE-2, which changed in overall high productivity throughout the proto-North Atlantic during OAE-2. During OAE-2, productivity at site 1260 and 603B was thus more comparable to the mid-latitude sites. Using these constraints as well as the SST and δ13Cphytane-records from Site 1260, we subsequently reconstructed pCO2 levels across the OAE-2 interval. Accordingly, pCO2 decreased from ca. 1750 to 900 ppm during OAE-2, consistent with enhanced organic matter burial resulting in lowering pCO2. Whereas the onset of OAE-2 coincided with increased pCO2, in line with a volcanic trigger for this event, the observed cooling within OAE-2 probably resulted from CO2 sequestration in black shales outcompeting CO2 input into the atmosphere. Together these results show that the ice-free Cretaceous world was sensitive to changes in pCO2 related to perturbations of the global carbon cycle.

Structural characterization and interaction studies of ubiquitin-like proteins (2011)

Alexis Rozenknop

Ubiquitin is a highly conserved protein involved in several cellular processes like protein degradation, endocytosis, signal transduction and DNA repair. The discovery of ubiquitin-like proteins (UBL) and ubiquitin-like domains (ULD) increases the number of regulation pathways where the property of the ubiquitin-fold is profitable. Autophagy is the catabolic pathway used in cells to deliver cytosolic components and dysfunctional organelles to the lysosome for degradation. MAP1LC3 proteins are ubiquitin-like proteins involved in one hand for the expansion of the autophagosome, which sequesters cytosolic substrates. In the other hand, these proteins (LC3- and GABARAP- subfamilies) bind to autophagic receptors linked to polyubiquitinated proteins aggregates. For this project, the 3D structure of the GABARAPL-1/NBR1-LIR complex was determined and confirmed that GABARAPL-1 belongs to the MAP1LC3 proteins family, structurally characterized by an ubiquitin-fold, consisting of a central beta-sheet formed by four beta-strands and two alpha-helices on one side of the beta-sheet, preceded N terminally by two alpha-helices, resulting in the formation of two hydrophobic pockets, hp1 and hp2. The autophagic receptor NBR1 interacts with GABARAPL-1 through the hp1 and hp2 with its LIR motif taking an extended beta conformation upon binding, forming an intermolecular beta-sheet with the second beta-strand of GABARAPL 1. This LC3- interacting region (LIR) consists of an Theta XX Gamma sequence preceded by acidic amino acids, with Theta and Gamma represented by any aromatic and hydrophobic residues, respectively. Interaction studies of the LIR domains of p62, Nix and NBR1 with different members of the MAP1LC3 proteins family indicate that the presence of a tryptophan in the LIR motif increases the binding affinity. Substitution to other aromatic amino acids or increasing the number of negatively charged residues at the N-terminus of the LIR motif, however, has little effect on the binding affinity due to enthalpy-entropy compensation, suggesting that effector proteins can interact with a wide variety of different sequences with similar and moderate binding affinities. Additionally to be present in proteins dealing with protein folding and degradation, ubiquitin-like domain were found protein involved in the regulation of signal transduction like TBK1, a serine/threonine kinase responsible for induction of immune response. In this second project, based on the NMR chemical shifts of the TBK1 domain contained between amino acids 302 and 383, secondary structure prediction programs (TALOS and CSI) confirmed the presence of an Ubiquitin-like domain in TBK1 by identifying one alpha-helix and four beta-strands sequentially aligned like following beta-beta-alpha-beta-beta. This alignment corresponds perfectly with the secondary structure elements of Ubiquitin and proved that TBK1_ULD belongs to the UBL protein superfamily. The similarity to ubiquitin was even bigger by the presence in addition of a small beta-strand and a short helix, which are observed as the beta 5-strand and a 310-helix in Ubiquitin, respectively. The first attempts on the 3D structure determination confirmed the Ub-fold but due to the lack of assignment in TBK1_ULD, only a structure based on ubiquitin as a model was determined. Interaction studies of TBK1_ULD with the IAD-SRR domain of IRF3 showed that both side of the molecule seems involved and that the TBK1/IRF3 interaction is more complex than a one to one binding process. Unfortunately, the instability of TBK1_ULD associated to the difficulty in the purification of IAD-SRR did not allow to further study this interaction more precisely. Finally, to overcome the difficulty encountered in NMR experiments because of low expression and/or poor solubility, an expression vector using the intrinsic property of ubiquitin was designed. Fused to proteins or peptides targets, this construct produced proteins and peptides in a larger amount than with traditional expression vectors and also with a less cost than chemical synthesis for pure labeled peptides for NMR structural studies. The presence of a hexa histidine tag was useful for the isolation and the purification of the constructs. The existence of a TEV cleavage site was created to keep the possibility of releasing the ubiquitin moiety from the expressed protein or peptide. Moreover, the ubiquitin-tag could also still be attached to the protein/peptide of interest when biophysical methods like NMR, ITC or CD spectroscopy are applied, providing the same results than for the protein/peptide moiety alone.

De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology (2012)

Jurgen F. Nijkamp Marcel van den Broek Erwin Datema Stefan de Kok Lizanne Bosman M. Luttik Pascale Daran-Lapujade Wanwipa Vongsangnak Jens Nielsen Wilbert HM Heijne Paul Klaassen Chris J. Paddon Darren Platt Peter Kötter Roeland C. van Ham Marcel JT Reinders Jack T. Pronk Dick de Ridder Jean-Marc Daran

Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization compared to the reference strain S. cerevisiae S288C were analyzed. In addition to a few large deletions and duplications, nearly 3000 indels were identified in the CEN.PK113-7D genome relative to S288C. These differences were overrepresented in genes whose functions are related to transcriptional regulation and chromatin remodelling. Some of these variations were caused by unstable tandem repeats, suggesting an innate evolvability of the corresponding genes. Besides a previously characterized mutation in adenylate cyclase, the CEN.PK113-7D genome sequence revealed a significant enrichment of non-synonymous mutations in genes encoding for components of the cAMP signalling pathway. Some phenotypic characteristics of the CEN.PK113-7D strains were explained by the presence of additional specific metabolic genes relative to S288C. In particular, the presence of the BIO1 and BIO6 genes correlated with a biotin prototrophy of CEN.PK113-7D. Furthermore, the copy number, chromosomal location and sequences of the MAL loci were resolved. The assembled sequence reveals that CEN.PK113-7D has a mosaic genome that combines characteristics of laboratory strains and wild-industrial strains.

Chemical composition of modern and fossil Hippopotamid teeth and implications for paleoenvironmental reconstructions and enamel formation: 1. major and minor element variation (2011)

Gerhard Brügmann Joachim Krause Thomas C. Brachert Ottmar Kullmer Friedemann Schrenk Immaculate Ssemmanda Dieter F. Mertz

Bioapatite in mammalian teeth is readily preserved in continental sediments and represents a very important archive for reconstructions of environment and climate evolution. This project intends to provide a detailed data base of major, minor and trace element and isotope tracers for tooth apatite using a variety of microanalytical techniques. The aim is to identify specific sedimentary environments and to improve our understanding on the interaction between internal metabolic processes during tooth formation and external nutritional control and secondary alteration effects. Here, we use the electron microprobe, to determine the major and minor element contents of fossil and modern molar enamel, cement and dentin from hippopotamids. Most of the studied specimens are from different ecosystems in Eastern Africa, representing modern and fossil lakustrine (Lake Kikorongo, Lake Albert, and Lake Malawi) and modern fluvial environments of the Nile River system. Secondary alteration effects in particular FeO, MnO, SO3 and F concentrations, which are 2 to 10 times higher in fossil than in modern enamel; secondary enrichments in fossil dentin and cement are even higher. In modern and fossil enamel, along sections perpendicular to the enamel-dentin junction (EDJ) or along cervix-apex profiles, P2O5 and CaO contents and the CaO/P2O5 ratios are very constant (StdDev ~1 %). Linear regression analysis reveals very tight control of the MgO (R2∼0.6), Na2O and Cl variation (for both R2>0.84) along EDJ-outer enamel rim profiles, despite large concentration variations (40 % to 300 %) across the enamel. These minor elements show well defined distribution patterns in enamel, similar in all specimens regardless of their age and origin, as the concentration of MgO and Na2O decrease from the enamel-dentin junction (EDJ) towards the outer rim, whereas Cl displays the opposite variation. Fossil enamel from hippopotamids which lived in the saline Lake Kikorongo have a much higher MgO/Na2O ratio (∼1.11) than those from the Neogene fossils of Lake Albert (MgO/Na2O∼0.4), which was a large fresh water lake like those in the western Branch of the East African Rift System today. Similarly, the MgO/Na2O ratio in modern enamel from the White Nile River (∼0.36), which has a Precambrian catchment of dominantly granite and gneisses and passes through several saline zones, is higher than that from the Blue Nile River, whose catchment is the Neogene volcanic Ethiopian Highland (MgO/Na2O∼0.22). Thus, particularly MgO/Na2O might be a sensitive fingerprint for environments where river and lake water have suffered strong evaporation. Enamel formation in mammals takes place at successive mineralization fronts within a confined chamber where ion and molecule transport is controlled by the surrounding enamel organ. During the secretion and maturation phases the epithelium generates different fluid composition, which in principle, should determine the final composition of enamel apatite. This is supported by co-linear relationships between MgO, Cl and Na2O which can be interpreted as binary mixing lines. However, if maturation starts after secretion is completed the observed element distribution can only be explained by recrystallization of existing and addition of new apatite during maturation. Perhaps the initial enamel crystallites precipitating during secretion and the newly formed bioapatite crystals during maturation equilibrate with a continuously evolving fluid. During crystallization of bioapatite the enamel fluid becomes continuously depleted in MgO and Na2O, but enriched in Cl which results in the formation of MgO, and Na2O-rich, but Cl-poor bioapatite near the EDJ and MgO- and Na2O-poor, but Cl-rich bioapatite at the outer enamel rim. The linkage between lake and river water composition, bioavailability of elements for plants, animal nutrition and tooth formation is complex and multifaceted. The quality and limits of the MgO/Na2O and other proxies have to be established with systematic investigations relating chemical distribution patterns to sedimentary environment and to growth structures developing as secretion and maturation proceed during tooth formation.

Goethe-Spektrum : das Mitarbeitermagazin der Goethe-Universität Frankfurt ; 4/11 (2011)

Residual circulation trajectories and transit times into the extratropical lowermost stratosphere (2010)

Thomas Birner Harald Bönisch

Transport into the extratropical lowermost stratosphere (LMS) can be divided into a slow part (time-scale of several months to years) associated with the global-scale stratospheric residual circulation and a fast part (time-scale of days to a few months) associated with (mostly quasi-horizontal) mixing (i.e. two-way irreversible transport, including stratosphere-troposphere exchange). The stratospheric residual circulation can be considered to consist of two branches: a deep branch more strongly associated with planetary waves breaking in the middle to upper stratosphere, and a shallow branch more strongly associated with synoptic-scale waves breaking in the subtropical lower stratosphere. In this study the contribution due to the stratospheric residual circulation alone to transport into the LMS is quantified using residual circulation trajectories, i.e. trajectories driven by the (time-dependent) residual mean meridional and vertical velocities. This contribution represents the advective part of the overall transport into the LMS and can be viewed as providing a background onto which the effect of mixing has to be added. Residual mean velocities are obtained from a comprehensive chemistry-climate model as well as from reanalysis data. Transit times of air traveling from the tropical tropopause to the LMS along the residual circulation streamfunction are evaluated and compared to recent mean age of air estimates. A clear time-scale separation with much smaller transit times into the mid-latitudinal LMS than into polar LMS is found that is indicative of a clear separation of the shallow from the deep branch of the residual circulation. This separation between the shallow and the deep circulation branch is further manifested in a clear distinction in the aspect ratio of the vertical to meridional extent of the trajectories as well as the integrated mass flux along the residual circulation trajectories. The residual transit time distribution reproduces qualitatively the observed seasonal cycle of youngest air in the extratropical LMS in fall and oldest air in spring.

Die Förderung kognitiver Prozesse beim Schreiben mit Prompts (2011)

Christin Picard

Im Mittelpunkt der Arbeit steht das Schreiben als Lerninstrument im Rahmen von Lernjournalen. Ausgehend von der Annahme, dass durch Schreiben höherrangige kognitive Prozesse angeregt werden können, ist das Ziel der vorliegenden Arbeit die Untersuchung der Effekte von Schreibinstruktionen (Prompts) auf die Qualität kognitiver Prozesse bei der Textproduktion. Im Rahmen zweier Untersuchungen werden dazu Studierende angeleitet, mit den Aufgaben Texte zu verschiedenen Themengebieten zu verfassen. Die Texte werden mithilfe einer Taxonomie, mit der die Komplexität von Lernergebnissen abgebildet wird, analysiert und ausgewertet. Im Zentrum der ersten Untersuchung steht die Frage, inwiefern sich verschiedene Anforderungsspeziﬁka der Prompts auf die Komplexität der produzierten Texte auswirken. Die zweite Untersuchung geht der Frage nach, wie Schreibprozesse durch verschiedene Formen von Feedback beeinﬂusst werden und befasst sich mit den Wechselwirkungen des Feedbacks,der Motivation der Lerner und der aus den Texten erkennbaren Verarbeitungstiefe. Die Ergebnisse zeigen zum einen, dass Lerner mit Prompts bereits zu Beginn eines Lernzyklus dazu angeregt werden können, Elaborationsstrategien einzusetzen und komplexe Wissensstrukturen beim Schreiben aufzubauen. Zum anderen deuten sich Effekte des Feedbacks auf die Motivation der Lerner an, da sich in Abhängigkeit der Feedbackform unterschiedliche Motivationsverläufe nachweisen ließen. Die Befunde weisen also darauf hin, dass Feedback den Lernprozess auf der motivationalen Ebene beeinﬂusst. Insgesamt werden in der Arbeit Faktoren untersucht, die bei der Gestaltung einer Lernumgebung mit Lernjournalen zu beachten sind. Die Befunde geben Hinweise darauf, wie Lernjournale in eine Seminarstruktur eingebettet werden können, um die Komplexität der Schreibprozesse erwachsener Lerner zu erhöhen.

Uni-Report : Jg. 44 Nr. 6 vom 06.12.2011 (2011)

A close eye on the eagle-eyed visual acuity hypothesis of autism (2011)

Sven Bölte Sabine Schlitt Volker Gapp Daniela Hainz Shella Schirman Fritz Poustka Bernhard Weber Christine M. Freitag Angela Ciaramidaro Henrik Walter

Autism spectrum disorders (ASD) have been associated with sensory hypersensitivity. A recent study reported visual acuity (VA) in ASD in the region reported for birds of prey. The validity of the results was subsequently doubted. This study examined VA in 34 individuals with ASD, 16 with schizophrenia (SCH), and 26 typically developing (TYP). Participants with ASD did not show higher VA than those with SCH and TYP. There were no substantial correlations of VA with clinical severity in ASD or SCH. This study could not confirm the eagle-eyed acuity hypothesis of ASD, or find evidence for a connection of VA and clinical phenotypes. Research needs to further address the origins and circumstances associated with altered sensory or perceptual processing in ASD.

Ships, ports and particulate air pollution - an analysis of recent studies (2011)

Daniel Müller Stefanie Uibel Masaya Takemura Doris Klingelhöfer Jan David Alexander Groneberg

The duration of use is usually significantly longer for marine vessels than for roadside vehicles. Therefore, these vessels are often powered by relatively old engines which may propagate air pollution. Also, the quality of fuel used for marine vessels is usually not comparable to the quality of fuels used in the automotive sector and therefore, port areas may exhibit a high degree of air pollution. In contrast to the multitude of studies that addressed outdoor air pollution due to road traffic, only little is known about ship-related air pollution. Therefore the present article aims to summarize recent studies that address air pollution, i.e. particulate matter exposure, due to marine vessels. It can be stated that the data in this area of research is still largely limited. Especially, knowledge on the different air pollutions in different sea areas is needed.

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