Characterization of CDK5RAP2 as a novel regulator in the Hippo signaling pathway

CEP161 is a novel component of the Dictyostelium discoideum centrosome and is the ortholog of mammalian CDK5RAP2. Mutations in CDK5RAP2 are associated with autosomal recessive primary microcephaly (MCPH), a neurodevelopmental disorder characterized by reduced head circumference, a reduction in the size of the cerebral cortex and a mild to moderate mental retardation. Here we show that the amino acids 1-763 of the 1381 amino acids of CEP161 protein are sufficient for centrosomal targeting and centrosome association. AX2 cells over-expressing truncated and full length CEP161 proteins have defects in growth and development. Furthermore, we identified the kinase SvkA (severinkinase A) as its interaction partner which is the D. discoideum Hippo related kinase designated here as Hrk-svk. Hrk-svk is the direct homolog of human MST1. Both proteins co-localize at the centrosome. We further demonstrate that this interaction is also conserved in mammals. We were able to show that CDK5RAP2 interacts with MST1 and TAZ and it also down-regulates the transcript levels of TAZ in HEK293T cells. Taken together, our data on Dictyostelium CEP161 and human CDK5RAP2 supports the hypothesis that CDK5RAP2 as a novel regulator of Hippo signaling pathway. We propose that CDK5RAP2 mutations may lead to a decrease in the number of neurons and the subsequent reduction of brain size by regulating the hippo signaling pathway.

Varianzanalysen - Prüfen der Voraussetzungen und nichtparametrische Methoden sowie praktische Anwendungen mit R und SPSS. Version 1.1 (2.3.2015)

Die Voraussetzunen der parametrischen 1- und mehrfaktoriellen Varianzanalyse, mit und ohne Messwiederholungen, werden besprochen. Ferner werden eine Reihe von alternativen Verfahren vorgestellt, insbesondere einige nichtparametrische, darunter RT (rank transform), INT (inverse normal transform), ART (aligned rank transform), Puri & Sen (L statistic), van der Waerden und Akritas & Brunner (ATS anova type statistic), die sich auf die parametrische Varianzanalyse zurückführen lassen, sowie dichotome und ordinale logistische Regression. Hierzu werden Lösungen mit R und SPSS ausführlich gezeigt.

Concepts of the Global South

Where and what is the Global South? If you ask people on the street, many would probably not have the faintest idea. In everyday parlance and mass media, Global South has hardly become a household term. In academic and (global) policy circles, though, the term is used with much more gusto. Politicians refer to it. The United Nations organize their statistical data in accordance with the term. Academics write books about it - or, as in our case, explicitly include the term in the name of a research center: Global South Studies Center (GSSC). But what does the term entail? Who uses it and why? And what are the implications of marking distinctions between the Global South and the Global North? We thought it relevant to address these questions in more detail – after all, we work for a recently established research institute featuring the term in its name. Accordingly, we asked a number of academics, journals and academic institutions to reflect on the term. In this online issue, we share their various perspectives and critical reflections on the notion of the Global South – see also a short discussion on a number of YouTube videos we have included.

Reflections on migration in the global south

How can we achieve a better understanding of the variations in international migration to, from, and within the Global South? To facilitate a dia-logue about this topic, we asked a number of contributors to write or to provide a video statement about their region of expertise. To some we explicitly posed the following question: Is it possible to distinguish current or historical experiences or patterns of migration in the Global South that differ from patterns in the Global North?

Micro-Foundations of Financialization. Status Anxiety and the Market for Consumer Credit in Chile

This project investigates why people in Chile acquired so much consumer debt in contexts of material prosperity, and asks what the role of inequality and commodification is in this process. The case raises an important challenge to the literature. Insofar as existing accounts assume that the financialization of consumption occurs in contexts marked by wage stagnation and a general deterioration of the middle classes, they engender two contradictory explanations: while political economists argue that people use credit in order to smooth their consumption in the face of market volatility, economists maintain that concentration of wealth at the top pushes middle income consumers to emulate the expenditures of the rich and consume beyond their means. These explanations do not necessarily fit the reality of developing countries. Triangulating in-depth interviews with middle class families, multivariate statistical analysis and secondary literature, the project shows that consumers in Chile use credit to finance “ordinary” forms of consumption that do not aim either at coping with market instability or emulating and signaling status to others. Rather, Chileans use department store credit cards in order to acquire a standard package of “inconspicuous” goods that they feel entitled to have. From this point of view, the systematic indebtedness of consumers originates in a major concern with “rank”, “achievement” and "security" that – following De Botton -- I call “status anxiety”. Status anxiety does not stem from the desire to emulate rich consumers, but from the impossibility of complying with normative expectations about what a middle class family should be (and have) that outweigh wage improvements. The project thus investigates the way in which “status anxiety” is systematically reproduced by means of two broad mechanisms that prompt people to acquire consumer debt. The first mechanism generating debt stems from an increase of real wages and high levels of inequality. It is explained by a general sociological principle known as relative deprivation, which points to the fact that general satisfaction with one´s income, possessions or status, is assessed not in absolute terms such as total income, but in relation with reference groups. In this sense, I explore the mechanisms that operate as catalyzers of relative deprivation, by making explicit social inequalities and distorting the perception of others´ wealth. Despite upward mobility and economic improvement, Chileans share the perception of “falling behind,” which materializes in an “imaginary middle class” against which people compare their status, possessions and economic independence. Finally, I show that the commodification of education, health and pension funds does not directly prompt people to acquire consumer debt, but operate as “income draining” mechanisms that demand higher shares of middle class families’ “discretionary income.” In combination with “relative deprivation,” these “income draining” mechanisms leave families with few options to perform their desired class identities, other than learning how to bring resources from the future into the present with the help of department store credit cards.

Repeated evolution of heat responsiveness among Brassicaceae COPIA transposable elements

Eukaryotic genomes contain repetitive DNA sequences. This includes simple repeats and more complex transposable elements (TEs). Many TEs reach high copy numbers in the host genome, owing to their amplification abilities by specific mechanisms. There is growing evidence that TEs contribute to gene transcriptional regulation. However, excess of TE activity may lead to reduced genome stability. Therefore, TEs are suppressed by the transcriptional gene silencing machinery via specific chromatin modifications. In contrary, effectiveness of the epigenetic silencing mechanisms imposes risk for TE survival in the host genome. Therefore, TEs may have evolved specific strategies for bypassing epigenetic control and allowing the emergence of new TE copies. Recent studies suggested that the epigenetic silencing can be, at least transiently, attenuated by heat stress in A. thaliana. Heat stress induced strong transcriptional activation of COPIA78 family LTR-retrotransposons named ONSEN, and even their transposition in mutants deficient in siRNA-biogenesis. ONSEN transcriptional activation was facilitated by the presence of heat responsive elements (HREs) within the long terminal repeats, which serve as a binding platform for the HEAT SHOCK FACTORs (HSFs). This thesis focused on the evolution of ONSEN heat responsiveness in Brassicaceae. By using whole-transcriptome sequencing approach, multiple Arabidopsis lyrata ONSENs with conserved heat response were found and together with ONSENs from other Brassicaceae were used to reconstruct the evolution of ONSEN HREs. This indicated ancestral situation with two, in palindrome organized, HSF binding motifs. In the genera Arabidopsis and Ballantinia, a local duplication of this locus increased number of HSF binding motifs to four, forming a high-efficiency HRE. In addition, whole transcriptome analysis revealed novel heat-responsive TE families COPIA20, COPIA37 and HATE. Notably, HATE represents so far unknown COPIA family which occurs in several Brassicaceae species but is absent in A. thaliana. Putative HREs were identified within the LTRs of COPIA20, COPIA37 and HATE of A. lyrata, and could be preliminarily validated by transcriptional analysis upon heat induction in subsequent survey of Brassicaeae species. Subsequent phylogenetic analysis indicated a repeated evolution of heat responsiveness within Brassicaceae COPIA LTR-retrotransposons. This indicates that acquisition of heat responsiveness may represent a successful strategy for survival of TEs within the host genome.

Ein Programm für die Parallelisierung dynamisch adaptiver Mehrgitterverfahren

In dieser Arbeit werden dynamisch adaptive Mehrgitterverfahren parallelisiert. Bei dynamisch adaptiven Mehrgitterverfahren wird ein Gebiet mit einem Gitter überdeckt, und auf diesem Gitter wird gerechnet, indem Gitterpunkte in der Umgebung herangezogen werden, um den Wert des nächsten Zeitpunktes zu bestimmen. Dann werden gröbere und feinere Gitter erzeugt und verwendet, wobei die feineren Gitter sich auf Teilgebiete konzentrieren. Diese Teilgebiete ändern sich im Verlauf der Zeit. Durch die Verwendung der zusätzlichen Gitter werden die numerischen Eigenschaften verbessert. Die Parallelisierung solcher Verfahren geschieht in der Regel durch Bisektion. In der vorliegenden Arbeit wird die Umverteilung der Gebiete realisiert, indem Mengen von einzelnen Gitterpunkten verschickt werden. Das ist ein Scheduling-Verfahren. Die Mehrgitterstrukturen sind so aufgebaut, dass fast beliebige Gitterpunktverteilungen auf den Gitterebenen vorliegen können. Die Strukturen werden einmal erzeugt, und nur bei Bedarf geändert, sodass keine Speicherallokationen während der Iterationen nötig sind. Neben dem Gitter sind zusätzliche Strukturen, wie zum Beispiel die Randstrukturen, erforderlich. Eine Struktur Farbenfeld verzeichnet, auf welchem Kern sich ein Außenrandpunkt befindet. In der parallelen adaptiven Verfeinerung werden für einzelne durch ein Entscheidungskriterium ausgewählte Gitterpunkte 5 x 5 Punktüberdeckungen vorgenommen. Dazu werden die verfügbaren Entscheidungsinformationen zur Bestimmung von komplexeren Strukturen herangezogen. Damit muss das Verfeinerungsgitter nicht komplett abgebaut und dann wieder aufgebaut werden, sondern nur die Änderungen am Gitter sind vorzunehmen. Das spart viel Berechnungszeit. Der letzte Schritt besteht darin, den Lastausgleich durchzuführen. Zunächst werden die Lasttransferwerte bestimmt, die angeben, wie viele Gitterpunkte von wo nach wo zu verschicken sind. Das geschieht mit Hilfe einer PLB genannten Methode bzw. einer Variante. PLB wurde bisher vor allem für kombinatorische Probleme eingesetzt. Dann erfolgt eine Auswahl der zu verschickenden Gitterpunkte mit einer Strategie, welche Punkte eines Kerns zu welchen Nachbarkernen transferiert werden sollen. Im letzten Schritt werden schließlich die ausgewählten Punkte migriert, wobei alle Gitterpunktstrukturen umgebaut werden und solche Informationen gepackt werden müssen, sodass ein Umbau seiner Gitterpunktstrukturen bei dem Empfänger möglich wird. Neben den Gitterpunktstrukturen müssen auch Strukturen für die parallele adaptive Verfeinerung verändert werden. Es muss ein Weiterverschicken von Gitterpunkten möglich sein, wenn über die Lastkanten in mehreren Runden Last verschickt wird. Während des Lastausgleichs wird noch Arbeit durch eine Struktur Zwischenkorrektur durchgeführt, die es ermöglicht, das Farbenfeld intakt zu halten, wenn benachbarte Gitterpunkte gleichzeitig verschickt werden.

Nuclei of Nearby Active Galaxies: NIR and Sub-mm Views and Finalizing the LINC-NIRVANA Fringe and Flexure Tracking System: Flexure and Temperature Behavior

The work presented in my thesis addresses the two cornerstones of modern astronomy: Observation and Instrumentation. Part I deals with the observation of two nearby active galaxies, the Seyfert 2 galaxy NGC 1433 and the Seyfert 1 galaxy NGC 1566, both at a distance of $\sim10$ Mpc, which are part of the Nuclei of Galaxies (NUGA) sample. It is well established that every galaxy harbors a super massive black hole (SMBH) at its center. Furthermore, there seems to be a fundamental correlation between the stellar bulge and SMBH masses. Simulations show that massive feedback, e.g., powerful outflows, in Quasi Stellar Objects (QSOs) has an impact on the mutual growth of bulge and SMBH. Nearby galaxies follow this relation but accrete mass at much lower rates. This gives rise to the following questions: Which mechanisms allow feeding of nearby Active Galactic Nuclei (AGN)? Is this feeding triggered by events, e.g., star formation, nuclear spirals, outflows, on $\sim500$ pc scales around the AGN? Does feedback on these scales play a role in quenching the feeding process? Does it have an effect on the star formation close to the nucleus? To answer these questions I have carried out observations with the Spectrograph for INtegral Field Observation in the Near Infrared (SINFONI) at the Very Large Telescope (VLT) situated on Cerro Paranal in Chile. I have reduced and analyzed the recorded data, which contain spatial and spectral information in the H-band ($1.45 \mic-1.85 \mic$) and K-band ($1.95 \mic-2.45 \mic$) on the central $10\arcsec\times10\arcsec$ of the observed galaxies. Additionally, Atacama Large Millimeter/Sub-millimeter Array (ALMA) data at $350$ GHz ($\sim0.87$ mm) as well as optical high resolution Hubble Space Telescope (HST) images are used for the analysis. For NGC 1433 I deduce from comparison of the distributions of gas, dust, and intensity of highly ionized emission lines that the galaxy center lies $\sim70$ pc north-northwest of the prior estimate. A velocity gradient is observed at the new center, which I interpret as a bipolar outflow, a circum nuclear disk, or a combination of both. At least one dust and gas arm leads from a $r\sim200$ pc ring towards the nucleus and might feed the SMBH. Two bright warm H$_2$ gas spots are detected that indicate hidden star formation or a spiral arm-arm interaction. From the stellar velocity dispersion (SVD) I estimate a SMBH mass of $\sim1.74\times10^7$ \msol. For NGC 1566 I observe a nuclear gas disk of $\sim150$ pc in radius with a spiral structure. I estimate the total mass of this disk to be $\sim5.4\times10^7$ \msol. What mechanisms excite the gas in the disk is not clear. Neither can the existence of outflows be proven nor is star formation detected over the whole disk. On one side of the spiral structure I detect a star forming region with an estimated star formation rate of $\sim2.6\times10^{-3}$ \msol\ yr$^{-1}$. From broad Br$\gamma$ emission and SVD I estimate a mean SMBH mass of $\sim5.3\times10^6$ \msol\ with an Eddington ratio of $\sim2\times10^{-3}$. Part II deals with the final tests of the Fringe and Flexure Tracker (FFTS) for LBT INterferometric Camera and the NIR/Visible Adaptive iNterferometer for Astronomy (LINC-NIRVANA) at the Large Binocular Telescope (LBT) in Arizona, USA, which I conducted. The FFTS is the subsystem that combines the two separate beams of the LBT and enables near-infrared interferometry with a significantly large field of view. The FFTS has a cryogenic system and an ambient temperature system which are separated by the baffle system. I redesigned this baffle to guarantee the functionality of the system after the final tests in the Cologne cryostat. The redesign did not affect any scientific performance of LINC-NIRVANA. I show in the final cooldown tests that the baffle fulfills the temperature requirement and stays $<110$ K whereas the moving stages in the ambient system stay $>273$ K, which was not given for the old baffle design. Additionally, I test the tilting flexure of the whole FFTS and show that accurate positioning of the detector and the tracking during observation can be guaranteed.

A Game of Horns: Transnational Flows of Rhino Horn

A multi-sectorial regime of protection including international treaties, conservation and security measures, demand reduction campaigns and quasi-military interventions has been established to protect rhinos. Despite these efforts, the poaching of rhinos and trafficking of rhino horn continue unabated. This dissertation asks why the illegal market in rhinoceros horn is so resilient in spite of the myriad measures employed to disrupt it. A theoretical approach grounded in the sociology of markets is applied to explain the structure and functioning of the illegal market. The project follows flows of rhino horn from the source in southern Africa to illegal markets in Southeast Asia. The multi-sited ethnography included participant observations, interviews and focus groups with 416 informants during fourteen months of fieldwork. The sample comprised of, amongst others, convicted and active rhino poachers, smugglers and kingpins, private rhino breeders and hunting outfitters, African and Asian law enforcement officials, as well as affected local communities and Asian consumers. Court files, CITES trade data, archival materials, newspaper reports and social media posts were also analysed to supplement findings and to verify and triangulate data from interviews, focus groups and observations. Central to the analysis is the concept of “contested illegality”, a legitimization mechanism employed by market participants along the different segments of the horn supply chain. These actors' implicit or explicit contestation of the state-sponsored label of illegality serves as a legitimising and enabling mechanism, facilitating participation in gray or illegal markets for rhino horn. The research identified fluid interfaces between legal, illegal and gray markets, with recurring actors who have access to transnational trade structures, and who also possess market and product knowledge, as well as information about the regulatory regime and its loopholes. It is against the background of colonial, apartheid and neoliberal exploitation and marginalization of local communities that a second argument is introduced: the path dependency of conservation paradigms. Underpinning rhino conservation and regulation are archaic and elitist conservation regimes that discount the potential for harmonious relationships between local communities and wildlife. The increasing militarization of anti-poaching measures and green land grabs are exacerbating the rhino problem by alienating communities further from conservation areas and wild animals. The third argument looks at how actors deal with coordination problems in transnational illegal markets. Resolving the coordination problems of cooperation, value and competition are considered essential to the operation of formal markets. It is argued that the problem of security provides an additional and crucial obstacle to actors transacting in markets. The systematic analysis of flows between the researched sites of production, distribution and consumption of rhino horn shows that the social embeddedness of actors facilitates the flourishing of illegal markets in ways that escape an effective enforcement of CITES regulations.

Post-translational lysine-acetylation of Ran and its regulation by Sirtuin deacetylases

Through recent advances in high-throughput mass spectrometry it has become evident that post-translational N-(epsilon)-lysine-acetylation is a modification found on thousands of proteins of all cellular compartments and all essential physiological processes. Many aspects in the biology of lysine-acetylation are poorly understood, including its regulation by lysine-acetyltransferases and lysine-deacetylases (KDACs). Here, the role of this modification was investigated for the small GTP-binding protein Ran, which, inter alia, is essential for the regulation of nucleocytoplasmic transport. To this end, site-specifically acetylated Ran was produced in E. coli by genetic code expansion. For five previously identified sites, Ran acetylation was tested regarding its impact on the intrinsic GTP hydrolysis rate, the assembly of export complexes (modeled in vitro with the export receptor CRM1 and the export substrate Spn1) and the interaction of Ran with its GTPase activation protein RanGAP and RanBP1. Overall, mild effects of Ran acetylation were observed for intrinsic and RanGAP-stimulated GTP hydrolysis rates. The interaction of active Ran with RanBP1 was negatively influenced by Ran acetylation at K159. Moreover, CRM1 bound to Ran acetylated at K37, K99 or K159 interacted more strongly with Spn1. Thus, lysine-acetylation interferes with essential aspects of Ran function. An in vitro screen was performed to identify potential Ran KDACs. The NAD+-dependent KDACs of the Sirtuin class showed activity towards two acetylation sites of Ran, K37 and K71. The specificity of Sirtuins was further analyzed based on an additional Ran acetylation site, K38. Since deacetylation of RanAcK38 was much slower compared to RanAcK37, di-acetylated RanAcK37/38 was tested next. The deacetylation rate of di-acetylated Ran was comparable to that of RanAcK37. Deacetylation experiments under single turnover conditions revealed that deacetylation occurs first at the K38 site in the di-acetylated RanAcK37/38 background. The ability of Sirtuins to deacetylate two adjacent AcKs was further investigated based on two proteins, which had previously been found to be di-acetylated and targeted by Sirtuins, namely the tumor suppressor protein p53 and phosphoenolpyruvate carboxykinase 1 (PEPCK1). p53 was readily deacetylated at two di-acetylation sites (K372/372 and K381/382), whereas PEPCK1 was not deacetylated in vitro. Taken together, these results have important implications for the substrate specificity of Sirtuins.