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Proliferation and apoptosis are fundamental cellular processes that are important for the development and homeostasis of multi-cellular organisms. Deregulation of these processes plays an important role in tumor formation. Often, genes that control homeostasis by regulating proliferation and apoptosis are mutated or improperly expressed in tumors. In this project, the physiological and pathological functions of FUSE Binding Protein 1 (FBP1) were studied to elucidate the involvement of this gene in the context of embryonic development and tumorigenesis. Two reasons led to the hypothesis that FBP1 might be relevant in this context. FBP1 was isolated in the group of PD Dr. Martin Zörnig using a functional yeast survival screen for the identification of anti-apoptotic genes involved in tumorigenesis, and the anti-apoptotic function of FBP1 was confirmed in the human colon carcinoma cell line RKO. In addition, FBP1 had been published to function as a transcriptional regulator that activates expression of the proto-oncogene c-myc. This gene stimulates cell proliferation and is overexpressed in many tumors. Analysis of FBP1 expression by immunhistochemistry in normal and tumor tissue samples revealed frequent and significant overexpression of FBP1 in Hepatocellular Carcinoma (HCC). To study the functional relevance of FBP1 activity for this tumor type, apoptosis and proliferation of the HCC cell line Hep3B were studied in dependence of FBP1 expression. Downregulation of FBP1 by lentiviral expression of FBP1-specific short hairpin RNA (shRNA) reduced proliferation and increased sensitivity to apoptosis. Subcutaneous injection of FBP1-deficient Hep3B cells into immunodeficient NOD/SCID mice demonstrated that tumor growth was strongly decreased in comparison to control cells. mRNA expression studies by quantitative real time PCR showed reduced mRNA levels of the pro-apoptotic genes Bik, Noxa, TRAIL and TNF-􀀁 in the absence of FBP1. In addition, the cell cycle inhibitors p21 and p15 were repressed by FBP1 while Cyclin D2 expression was decreased in the absence of FBP1. Surprisingly, expression of c-myc was not altered by FBP1 downregulation, indicating a different mechanism of c-myc regulation in HCC cells. These results demonstrate that overexpression of FBP1 inhibits apoptosis and stimulates proliferation in HCC cells by regulating the transcription of relevant target genes. Therefore, FBP1 might represent a promising therapeutic target for the treatment of HCC. For analysis of the physiological function of FBP1, a gene trap mouse model was established. In these mice, the gene trap vector pT1􀀂geo is inserted in intron 19 of the FBP1 locus, leading to the expression of a fusion protein consisting of a truncated FBP1 (lacking the last 62 amino acids), 􀀁-Galactosidase and Neomycin Phosphotransferase. Luciferase reporter assays demonstrated that the fusion protein was not capable of activating the c-myc promoter and even showed a dominant negative effect. Thus, this gene trap mouse serves as a functional FBP1 knockout model. Phenotyping of the FBP1 gene trap mice showed that homozygous mutation of FBP1 resulted in embryonic lethality at late stages of embryonic development (E15.5-E16.5). Heterozygous mice were viable, but born at lower frequencies, indicating a gene dosage- or a dominant negative effect of the FBP1 fusion protein. The cellular effects of FBP1 inactivation were tested in mouse embryonic fibroblasts isolated from FBP1 gene trap mice. While proliferation was reduced in the absence of wildtype FBP1, apoptosis was not affected. Expression analysis showed that in homozygous MEFs p15 and p21 transcripts were upregulated, while decreased cmyc mRNA levels were measured. Closer inspection of homozygous gene trap embryos revealed an anemic phenotype that appeared most pronounced around embryonic day 15.5. Analysis of fetal livers, the main site of hematopoiesis at this stage of development, showed a strongly reduced total cell number in homozygous embryos. Evaluation of the different hematopoietic cell lineages did not reveal significant changes in particular differentiated cell types. Instead, all cell lineages seemed to be affected equally by FBP1 inactivation. In contrast, analysis of hematopoietic progenitor cell populations showed an increased percentage of multipotent progenitor cells (MPPs) and a strongly reduced number of long-term hematopoietic stem cells (LT-HSCs). Functional analysis of MPPs by in vitro colony formation assays demonstrated that the FBP1-mutant cells possess a normal colony formation potential while their expansion capacity was reduced. Competitive transplantation of lineage negative fetal liver cells into irradiated recipient mice resulted in reduced engraftment of liverderived progenitor cells from homozygous FBP1 gene trap mice. However, stable engraftment was observed over a period of 12 weeks, demonstrating that the FBP1-deficient LT-HSCs are in principle capable of long-term repopulation. These results demonstrate that FBP1 exerts an essential function during definitive hematopoiesis. It can be speculated that FBP1 influences proliferation, apoptosis and possibly also stem cell self-renewal through the regulation of specific target genes within the hematopoietic progenitor cells. Alternatively, extrinsic effects caused by the absence of FBP1 activity could impair the function of the progenitor cells.
Background: FTY720, an immunomodulator derived from a fungal metabolite which reduces circulating lymphocyte counts by increasing the homing of lymphocytes to the lymph nodes has recently gained interest in stroke research. The aim of this study was to evaluate the protective efficacy of FTY720 in cerebral ischemia in two different application paradigms and to gather first data on the effect of FTY720 on the rate of spontaneous bacterial infections in experimental stroke. Methods: Middle cerebral artery occlusion (MCAO) in C57BL/6 mice (strain J, groups of 10 animals) was performed with two different durations of ischemia (90 min and 3 h) and FTY720 was applied 2 h after vessel occlusion to study the impact of reperfusion on the protective potency of FTY720. Lesion size was determined by TTC staining. Mice treated with FTY720 or vehicle were sacrificed 48 h after 90 min MCAO to determine the bacterial burden in lung and blood. Results: FTY720 1 mg/kg significantly reduced ischemic lesion size when administered 2 h after the onset of MCAO for 3 h (45.4 +/- 22.7 mm3 vs. 84.7 +/- 23.6 mm3 in control mice, p = 0.001) and also when administered after reperfusion, 2 h after the onset of MCAO for 90 min (31.1 +/- 28.49 mm3 vs. 69.6 +/- 27.2 mm3 in control mice, p = 0.013). Bacterial burden of lung homogenates 48 h after stroke did not increase in the group treated with the immunomodulator FTY720 while there was no spontaneous bacteremia 48 h after MCAO in treated and untreated animals. Conclusions: Our results corroborate the experimental evidence of the protective effect of FTY720 seen in different rodent stroke models. Interestingly, we found no increase in bacterial lung infections even though FTY720 strongly reduces the number of circulating leukocytes.
Background: Studies on allele length polymorphism designate several glacial refugia for Norway spruce (Picea abies) in the South Carpathian Mountains, but infer only limited expansion from these refugia after the last glaciation. To better understand the genetic dynamics of a South Carpathian spruce lineage, we compared ancient DNA from 10,700 and 11,000-year-old spruce pollen and macrofossils retrieved from Holocene lake sediment in the Retezat Mountains with DNA extracted from extant material from the same site. We used eight primer pairs that amplified short and variable regions of the spruce cpDNA. In addition, from the same lake sediment we obtained a 15,000-years-long pollen accumulation rate (PAR) record for spruce that helped us to infer changes in population size at this site. Results: We obtained successful amplifications for Norway spruce from 17 out of 462 pollen grains tested, while the macrofossil material provided 22 DNA sequences. Two fossil sequences were found to be unique to the ancient material. Population genetic statistics showed higher genetic diversity in the ancient individuals compared to the extant ones. Similarly, statistically significant Ks and Kst values showed a considerable level of differentiation between extant and ancient populations at the same loci. Lateglacial and Holocene PAR values suggested that population size of the ancient population was small, in the range of 1/10 or 1/5 of the extant population. PAR analysis also detected two periods of rapid population growths (from ca. 11,100 and 3900 calibrated years before present (cal yr BP)) and three bottlenecks (around 9180, 7200 and 2200 cal yr BP), likely triggered by climatic change and human impact. Conclusion: Our results suggest that the paternal lineages observed today in the Retezat Mountains persisted at this site at least since the early Holocene. Combination of the results from the genetic and the PAR analyses furthermore suggests that the higher level of genetic variation found in the ancient populations and the loss of ancient allele types detected in the extant individuals were likely due to the repeated bottlenecks during the Holocene. This study demonstrates how past population size changes inferred from PAR records can be efficiently used in combination with ancient DNA studies. The joint application of palaeoecological and population genetic analyses proved to be a powerful tool to understand the influence of past population demographic changes on the haplotype diversity and genetic composition of forest tree species.
The power to dissociate : molecular function of the twin-ATPase ABCE1 in archaeal ribosome recycling
(2010)
In this thesis, the structure of the C-terminal domain of presenilin-1, the catalytic component of the y-secretase complex, is investigated by NMR spectroscopy. The ysecretase complex has a definitive role in the pathogenic development of Alzheimer's disease, in that it mediates the cleavage of aprecursor to create the amyloid ß peptide. Aggregates of amyloid ß which form amyloid plaques are the most overt clinieal feature observed in the post-mortem brains of Alzheimer's patient. In addition, many of the mutations found in the aggressive early onset familial Alzheimer's disease have been linked to presenilin-1, highlighting its importance in disease progression and deeming it an important target for investigation. One of the greatest challenges for the structural investigation of the y-secretase components is their low expression yields in cell-based systems. We therefore applied continuous-exchange cell-free expression to obtain sufficient amounts of protein for our structural studies. An added benefit of the cell-free expression system is the freedom to incorporate any desired combination of stable-isotope labels directly into sampies. We were therefore able to develop a labeling scheme which targets the amino acid composition of transmembrane a-helices, allowing us to simplify an assignment procedure whieh tends to be cumbersome and diffieult for most a-helical transmembrane proteins. The y-secretase complex is a member of the intramembrane cleaving proteases which, as their name implies, cleave their transmembrane substrates within the bilayer. Single particle analysis of the y-secretase (1) as weil as crystal structures of rhomboid (2) and S2P (3) have revealed the presence of hydrophilie po res within the membrane where catalysis occurs. In light of evidence that certain elements of CTF reside in close proximity or even contribute to the formation of the hydrophilic pore, we chose to study the structure of CTF in mieelles, whieh may be better suited to accommodate CTF in isolation as compared with solid membranes in the absence of the other y-secretase components. The structure of CTF was solved to 1.7 A (backbone r.m.s.d) and revealed the presence of unusual features, including a partially membrane-spanning helix which situates the catalytic asparte at its N-terminus in what would be the center of the membrane where catalysis is proposed to occur, as weil as a severely kinked helix which is partially embedded beneath the surface of the membrane (P6). Interestingly, similar features have been observed in the crystal structure of the GlpG rhomboid. In addition, a soluble helix was found in the long N-terminal loop of CTF which until now has been described as unstructured. The first part of the thesis is designed to provide an introduction to Alzheimer's disease, the role of y-secretase and its presenilin-l catalytic component in disease progression, as weil as cell-free expression and liquid-state NMR techniques involved in the structural investigation of membrane proteins. In chapter 2, the reader is familiarized with the history, the clinical manifestation, and biochemical features of Alzheimer's disease. The chapter goes further to describe the role of the y-secretase complex and its individual components in disease progression and substrate processing. Chapter 3 focuses more specifically on presenilin-l in the context of the newly emerging class of intramembrane proteases. In chapter 4, attention is shifted to the cell-free expression system with special focus on the expression of membrane proteins, and chapter 5 explores the various liquid-state NMR techniques that were required for the characterization of CTF. The second part of the thesis is cumulative and contains original research, method, and review articles that were produced during the course of study. Chapter 6 explores the various techniques and innovations used to study membrane proteins using continuous exchange cell-free expression coupled with NMR spectroscopy. In chapter 7, a new technique, transmembrane segment targeted labeling, is described as a tool that facilitates the backbone assignment of transmembrane proteins which display severe overlap in NMR spectra. Chapter 8 presents the novel NMR structure of the C-terminal fragment of presenilin-l solved in SOS micelles.
The single unit doctrine proposes that each one of our percepts and sensations is represented by the activity of specialized high-level cells in the brain. A common criticism applied to this proposal is the one referred to as the "combinatorial problem". We are constantly confronted with unlimited combinations of elements and features, and yet we face no problem in recognizing patterns and objects present in visual scenes. Are there enough neurons in the brain to singly code for each one of our percepts? Or is it the case that perceptions are represented by the distributed activity of different neuronal ensembles? We lack a general theory capable of explaining how distributed information can be efficiently integrated into single percepts. The working hypothesis here is that distributed neuronal ensembles signal relations present in the stimulus by selectively synchronizing their spiking responses. Synchronization is generally associated with oscillatory activity in the brain. Gamma oscillations in particular have been linked to various integrative processes in the visual system. Studies in anesthetized animals have shown a conspicuous increase in power for the gamma frequency band (30 to 60 Hz) in response to visual stimuli. Recently, these observations have been extended to behavioral studies which addressed the role of gamma activity in cognitive processes demanding selective attention. The initial motivation for carrying out this work was to test if the binding-by-synchronization (BBS) hypothesis serves as a neuronal mechanism for perceptual grouping in the visual system. To this aim we used single and superimposed grating stimuli. Superimposed gratings (plaids) are bi-stable stimuli capable of eliciting different percepts depending on their physical characteristics. In this way, plaids can be perceived either as a single moving surface (pattern plaids), or as two segregated surfaces drifting in different directions (component plaids). While testing the BBS hypothesis, we performed various experiments which addressed the role of both stimulus and cortical architecture on the properties of gamma oscillations in the primary visual cortex (V1) of monkeys. Additionally, we investigated whether gamma activity could also be modulated by allocating attention in time. Finally, we report on gamma-phase shifts in area V1, and how they depend on the level of neuronal activation. ...
This work deals with the use of dielectrics with high permeability, so-called high-k dielectrics in organic thin-film field-effect transistors (FETs). The central part was the preparation of the high-k dielectric and its implementation in transistors, in which organic semiconductors were used as active layer. A field-effect transistor can be used to measure the charge carrier mobility. Employing high-k dielectrics the carrier concentration in the active layer can be greatly increased. In this way, high charge carrier concentrations in organic layers can be achieved without chemical doping. As high-k dielectric strontium titanate (STO) was selected. It is also available as a niobium-doped and therefore conducting substrate material. Thus, one has an ideal substrate for the growth of the dielectric layer in conjunction with a substrate which acts as gate electrode. As the organic semiconductor the small molecules pentacene and copper phthalocyanine (CuPc) were sublimated, as electrical contacts gold was used. As a key part of this work an ultra high vacuum chamber system was constructed for in situ preparation of field effect transistors. For the deposition of the organic thin films a molecular beam deposition chamber was built, including a manipulator and effusion cells as evaporation sources. For the preparation of the dielectric a sputtering chamber was set-up. Another chamber was used in conjunction with an effusion cell for the deposition of the gold contacts. For the structured deposition of the different layers in the devices a shadow mask system was implemented. Movable masks could be positioned by means of a wobble stick onto the sample carriers. The system thus allowed for the use of masks in all chambers. The different thin films required in the transistor structure were first individually prepared and characterized. For the characterization primarily X-ray diffraction and optical microscopy were used. The growth of pentacene was analyzed on aplha-AlO substrates. With X-ray diffraction the (00l) reflections of the thin film phase were observed. In growth studies of CuPc aplha-AlO and STO substrates were used. With X-ray diffraction the aplha-phase was detected. With increasing substrate temperature an increase in crystallinity, but also an increase in surface roughness was observed. The sputtering of STO as a high-k dielectric was studied and optimized. Simultaneously, a high deposition rate, a smooth film surface and good crystallinity of the layer were required. As the most important parameters the substrate temperature, pressure and sputtering power were identified. Argon and oxygen were employed as sputtering gases, as substrate MgO was used. The films showed in comparison to crystalline STO a distortion to larger lattice constants. The degree of distortion decreased with increasing chamber pressure, on the other hand, deposition rate decreased with increasing chamber pressure as well. By combining the individual deposition processes FETs in bottom-gate geometry were prepared. The first step was always sputtering of the STO dielectric on niobium-doped STO substrates. Subsequently, the electrodes and the organic layer were deposited. For comparison transistors on silicon substrates with silicon dioxide (SiO2) as the dielectric were prepared. To study the transistor properties a measurement setup was build. A dielectric constant of about 190 for the STO in the transistors was achieved. The transistors with CuPc as active layer showed p-type conduction behavior. The transistors with STO as dielectric had a much stronger response than those with SiO2. They reached mobilities of 2E-4 cm2/Vs at very low applied voltages of 3V. It could thus be demonstrated that STO is suitable as a dielectric for organic FETs, and that through the use of high-k dielectrics high charge carrier densities can be achieved.
NK cells are part of the innate immune system, and are important players in the body’s first defence line against virus-infected and malignantly transformed cells. While T cells recognize neoplastic cells in an MHC-restricted fashion, NK cells do not require prior sensitization and education about the target. In leukemia and lymphoma patients undergoing allogeneic hematopoietic stem cell transplantation not only T cells but also NK cells have been found to mediate potent graft-versus-tumor effects. Hence, autologous or donor-derived NK cells hold great promise for cancer immunotherapy. Since the generation of highly purified NK cell products for clinical applications is labor-intensive and time consuming, established human NK cell lines such as NK-92 are also being considered for clinical protocols. NK-92 cells display phenotypic and functional characteristics similar to activated primary NK cells. While NK-92 cells are highly cytotoxic towards malignant cells of hematologic origin, they do not affect healthy human tissues. NK-92 cells can be expanded under GMP-compliant conditions, and can therefore be provided in sufficient numbers with defined phenotypic characteristics for clinical applications. Safety of NK-92 cells for adoptive immunotherapy was already shown in two phase I/II clinical trials...
In der folgenden Arbeit werden Eigenschaften von Verzweigungsprozessen in zufälliger Umgebung (engl. branching processes in random environment, kurz BPREs) untersucht. Das Modell geht auf Smith (1969) und Athreya (1971) zurück. Ein BPRE ist ein einfaches mathematisches Modell für die Entwicklung einer Population von apomiktischen (d.h. sich ungeschlechtlich fortpflanzenden) Individuen in diskreter Zeit, wobei die Umgebungsbedingungen einen Einfluß auf den Fortpflanzungserfolg der Individuen haben. Dabei wird angenommen, dass die Umgebungsbedingungen in den einzelnen Generationen zufällig sind, und zwar unabhängig und identisch verteilt von Generation zu Generation. Man denke z.B. an eine Population von Pflanzen mit einem einjährigen Zyklus, die in jedem Jahr anderen Witterungsbedingungen ausgesetzt sind, wobei angenommen wird, dass diese sich unabhängig und identisch verteilt ändern. In Kapitel 1 wird eines der wichtigsten Hilfsmittel zur Beschreibung von BPREs, die sogenannte zugehörige Irrfahrt, eingeführt und die Klassifizierung von BPREs beschrieben. In Kapitel 2 werden bekannte Resultate, insbesondere zu kritischen, schwach subkritischen und stark subkritischen Verzweigungsprozessen, wiederholt. In Kapitel 3 wird der sogenannte intermediär subkritische Fall behandelt. Mithilfe von funktionalen Grenzwertsätzen für bedingte Irrfahrten wird die genaue Asymptotik der Überlebenswahrscheinlichkeit des Prozesses, die bereits in Vatutin (2004) bewiesen wurde, unter etwas allgemeineren Voraussetzungen gezeigt. Anschließend wird untersucht, wie häufig der Prozess, bedingt auf Überleben, nur noch aus einem Individuum besteht. Im letzten Teil des Kapitels wird ein funktionaler Grenzwertsatz für die zugehörige Irrfahrt, bedingt aufs Überleben des Prozesses, gezeigt. Diese konvergiert, richtig skaliert, gegen einen Levy-Prozess, der darauf bedingt ist, sein Minimum am Ende anzunehmen. In Kapitel 4 werden große Abweichungen von BPREs untersucht. Die Ratenfunktion des BPRE wird sowohl für den Fall mindestens geometrisch schnell abfallender Tails, als auch für den Fall von Nachkommenverteilungen mit schweren Tails bestimmt. Wie sich herausstellt, hängt die Ratenfunktion von der Ratenfunktion der zugehörigen Irrfahrt, der exponentiellen Abfallrate der Überlebenswahrscheinlichkeit sowie, bei Nachkommenverteilungen mit schweren Tails, auch von den Tails derselben ab. In der Ratenfunktion spiegeln sich die wahrscheinlichsten Wege, um Ereignisse der großen Abweichungen zu realisieren, wider, was in Kapitel 4.3 beschrieben wird. In Kapitel 4.4 wird im speziellen Fall von Nachkommenverteilungen mit gebrochen-linearer Erzeugendenfunktion die Ratenfunktion für Ereignisse bestimmt, bei denen ein superkritischer BPRE überlebt, aber klein im Vergleich zum Erwartungswert bleibt. In Kapitel 4.5 werden die großen Abweichungen, bedingt auf die Umgebung untersucht (engl. quenched). In diesem Fall können unwahrscheinliche Ereignisse nur über den Verzweigungsmechanismus und nicht mehr über eine außergewöhnliche Umgebung realisiert werden. Zum Abschluss der Dissertation werden Verzweigungsprozesse in zufälliger Umgebung, bedingt auf Überle-ben, simuliert. Dazu wird eine Konstruktion nach Geiger (1999) angewendet. Diese erlaubt es, Galton-Watson Bäume in variierender Umgebung, bedingt auf Überleben, entlang einer Ahnenlinie zu konstruieren. Der Fall geometrischer Nachkommenverteilungen, auf den wir uns in Kapitel 5 beschränken, erlaubt die explizite Berechnung der benötigten Verteilungen. Als Anwendung des Grenzwertsatzes aus Kapitel 3.1 können nun intermediär subkritische Verzweigungsprozesse, bedingt auf Überleben, wie folgt simuliert werden: Zunächst wird die Umgebung zufällig bestimmt, und zwar als Irrfahrt, bedingt darauf ihr Minimum am Ende anzunehmen. Anschließend wird, der Geiger-Konstruktion folgend, ein Verzweigungsprozess in dieser Umgebung, bedingt auf Überleben, simuliert. Zum Abschluss wird in einem kurzen Ausblick auf aktuelle Forschung verwiesen. Im Anhang befinden sich einige technische Resultate.
Der Neocortex der Säugetiere weist charakteristische Schichtungen auf, und jede dieser Schichten enthält verschiedene Typen von Neuronen, die in stereotypen Mustern angeordnet sind. Die Ausbildung dieser geschichteten Struktur ist nur dann möglich, wenn korrekte Migration von Neuronen von proliferativen Zonen zu deren Endpositionen stattfindet. Die exakte Migration und Schichtung wird von Mutationen beeinflusst, die entweder die migratorische Fähigkeit der Neuronen beeinträchtigen, oder deren Fähigkeit, die Position zu erkennen, an der sie die Wanderung beenden sollten (Gupta et al., 2002, Rice et al., 2001, Walsh et al., 2000). In den letzten Jahren wurde das extrazelluläre Protein Reelin als wichtiger Faktor bekannt, der sich auf mehrere Schritte der neuronalen Migration und Schichtung in der Großhirnrinde auswirkt (zusammengefasst in (Tissir et al., 2003). Das sekretierte Glykoprotein Reelin kontrolliert die Migration der Neuronen durch die Bindung an zwei Lipoproteinrezeptoren, den Very-low-density lipoprotein Rezeptor (VLDLR) und den Apolipoprotein E Rezeptor 2 (ApoER2) (D'Arcangelo et al., 1999). Die Bindung von Reelin an ApoER2 und VLDLR ruft die Phosphorylierung von Disabled-1 (Dab1) (D'Arcangelo et al., 1999, Howell et al., 1997), einem Adapterprotein, das an die intrazelluläre Domäne der Rezeptoren bindet, hervor, indem sie Kinasen der Src-Familie (SFKs) aktiviert (Arnaud et al., 2003, Bock et al., 2003a). Außer der Bedeutung des Reelin-Signalwegs für die korrekte Entwicklung des Nervensystems und dem Wissen, dass die Unterbrechung dieses Signalwegs zu verschiedenen neurologischen Krankheiten wie Epilepsie, Schizophrenie und der Alzheimerkrankheit führt (Costa et al., 2002, Botella-Lopez et al., 2006, Herz et al., 2006), ist die molekulare Grundlage der Aktivierung dieses Signalwegs an der Zellmembran noch kaum charakterisiert. Da VLDLR und ApoER2 keine intrinsische Kinaseaktivität besitzen, wurde die Existenz eines Korezeptors für mindestens eine Dekade vermutet, und die genaue Natur dieses Korezeptors ist unbekannt. EphrinBs, Transmembranliganden für Eph-Rezeptoren, besitzen die Fähigkeit zur Signalgebung, die für synaptische Plastizität und Angiogenese durch Sprossung erforderlich ist, indem sie die Aktivität anderer Transmembranrezeptoren wie AMPAR beziehungsweise VEGFR2 beeinflussen (Sawamiphak et al., 2010b, Segura et al., 2007, Essmann et al., 2008). Darüber hinaus führt die Stimulation von cortikalen Neuronen in Kultur mit löslichen EphB-Rezeptoren zur Rekrutierung und Aktivierung von SFKs in Membranpatches, in denen sich ephrinB-Liganden befinden (Palmer et al., 2002). Deshalb nehmen wir an, dass ephrinB in vivo funktionell mit dem Reelin-Signalweg verbunden sein könnte. Der Fokus dieser Arbeit liegt darin, zu zeigen, dass das neuronale Wegweisermolekül ephrinB einen entscheidenden Korezeptor für die Reelin-Signalgebung während der Entwicklung geschichteter Strukturen im Gehirn darstellt. Um zu erforschen, ob ephrinB und die Reelin-Signalgebung in vivo genetisch interagieren, wurden zuerst Mäuse mit Compound-Mutationen hergestellt, die eine Nullmutation im Gen für ephrinB3 tragen und heterozygot für Reelin sind (rl/+; b3-/-). Reeler ist eine autosomal rezessive Mutation der Maus, die, wenn sie heterozygot auftritt, keinen offenkundigen Phänotyp aufweist (Caviness et al., 1972, Caviness et al., 1978). Wir zeigen, dass ephrinBs genetisch mit Reelin interagieren, da Mäuse mit Compound-Mutationen (rl/+; b3 -/-) und ephrinB1-, B2- und B3-Dreifach-Knockouts die verschiedenen Defekte in der Entwicklung phänokopieren, die im Neocortex, Hippocampus und Cerebellum der reeler-Mäuse beobachtet wurden. Eines der Kennzeichen des reeler-Phänotyps ist die gestörte Schichtung der Großhirnrinde mit einer Marginalzone (MZ), die eine äußerst große Zahl an Zellen enthält (Caviness, 1982). Sowohl die Compound-Mäuse als auch die Triple-ephrinB1B2B3-knockouts zeigten eine Zunahme der Zellzahl in der MZ. Um die cortikalen Defekte detailliert zu charakterisieren, wurde die Verteilung von postmitotischen migrierenden Neuronen im Cortex von rl/+; b3-/- Compound-Mäusen mit Hilfe von unterschiedlichen schichtenspezifischen Markern für früh (Tbr1) (Hevner et al., 2001) und spät entstandene (SatB2 and Brn1) (Britanova et al., 2008, McEvilly et al., 2002) Neuronen, analysiert . Unsere Untersuchungen ließen die veränderte cortikale Schichtung in den rl/+; b3-/- Compound-Mäusen erkennen. So befanden sich früh entstandene Neuronen in den oberen cortikalen Schichten und spät entstandene in den unteren cortikalen Schichten, was für eine outside-in-Schichtung spricht, wie man sie von reeler kennt. Interessanterweise ist eine der frühesten strukturellen Abnormalitäten, die man im reeler-Cortex erkennen kann, die Unfähigkeit, die Preplate, die reich an extrazellulärer Matrix ist, in die Marginalzone und die Subplate aufzuspalten (Sheppard et al., 1997). Zum Zeitpunkt E17.5 zeigten rl/+; b3-/- Compound-Mäuse eine beachtliche Anhäufung von Chondroitin-Sulfat-Proteoglykan (CSPG), einer Komponente der extrazellulären Matrix, im gesamten Neocortex mit einer ungeteilten Schicht an der Oberfläche, welche übermäßig viel CSPG enthielt und somit die abnorme Teilung der Preplate der reeler-Maus nachahmte. Um zu bestätigen, dass die beobachteten Effekte auf die Schichtung des Cortex der rl/+; b3-/- Compound-Mäuse als Folge der Beeinträchtigung der neuronalen Migration auftritt, wurden zusätzlich BrdU-Puls-Experimente durchgeführt. BrdU wird in sich teilende Vorläuferzellen eingebaut und spiegelt deshalb das migratorische Verhalten von neu entstandenen Neuronen zum Zeitpunkt der Injektion wieder. Schwangeren Weibchen wurde BrdU zu den Zeitpunkten E12.5, E15.5 und E17.5 injiziert und die Gehirne wurden am postnatalen Tag 20 ausgewertet. Die Verteilung der mit BrdU gekennzeichneten Neuronen zu verschiedenen Zeitpunkten der Entwicklung in der Großhirnrinde bestätigte unsere Untersuchungen, die mit Hilfe der schichtspezifischen Marker durchgeführt worden waren. Deshalb deuten unsere Ergebnisse an, dass die beobachteten Defekte in der Schichtung des Cortex tatsächlich eine Folge von beeinträchtigter neuronaler Migration sind. Es wurde beobachtet, dass auch geschichtete Strukturen im Hippocampus in den rl/+; b3-/- Compound-Mäusen verändert sind, was für einen Crosstalk zwischen ephrinB3 und Reelin auch während der Entwicklung des Hippocampus spricht. Die CA1-Region des Hippocampus zeigte eine lockere Verbindung der pyramidalen Zellschichten, welche zu einer signifikanten Erhöhung der Dicke dieser Region und zu einer Einwanderung von Pyramidalzellen in das Stratum oriens führte. Darüber hinaus haben die Anomalien in den dendritischen Verzweigungen von Pyramidalneuronen der CA1-Region, die in Richtung der Reelin-produzierenden Cajal-Retzius-Zellen im stratum locunosum moleculare projizieren, in den rl/+; b3-/- Compound-Mäusen eine auffallende Ähnlichkeit mit denen, die in reeler-Mutanten beobachtet wurden. Reelin fungiert auch als Differenzierungsfaktor und Positionierungssignal für radiale Gliazellen, die positiv für glial fibrillary acidic protein (GFAP) sind und ein Gerüst für die korrekte Migration von neu entstandenen Granularzellen, die auf das Netzwerk der Granularzellen im Gyrus dentatus zuwandern (Forster et al., 2002) bilden. In rl/+; b3-/- Compound-Mäusen ist dieses Gerüst aus radialen Gliazellen schwerwiegend beeinträchtigt, was ebenfalls zu einer lockeren Organisation der Granularzellen im Gyrus dentatus führt. Die Ataxie in reeler-Mäusen ist das Ergebnis einer schwerwiegenden Fehlorganisation im Cerebellum dieser Mutanten (Tissir et al., 2003). Interessanterweise wurden nur milde Defekte in den Granularzellen, die sich in der internen Granularschicht des Cerebellums von rl/+; b3-/- Compound-Mäusen angesammelt haben, und keine Defekte in der Migration und der Verzweigung der Purkinjezellschicht, festgestellt. Stattdessen ist ephrinB2 in den Purkinjezellen des Cerebellums stark exprimiert (Liebl et al., 2003) und obwohl keine bedeutenden Defekte der Migration dieser Zellen festgestellt wurden, zeigte die Untersuchung der Verzweigung der Purkinjezellen in b2-/- Mäusen eindeutige Defekte, die bereits in einfachen ephrinB2-Mutanten auftraten. Bedeutend ist, dass die Defekte in der Verzweigung bei rl/+; b2-/- Compound-Mäusen signifikant verstärkt waren, was darauf hindeutet, dass der Reelin-Signalweg im Cerebellum spezifisch ephrinB2 benötigt. Um Einblicke in den Mechanismus zu erhalten, wie ephrinB-Liganden den Crosstalk mit Reelin durchführen, um die korrekte Positionierung von Neuronen in den geschichteten Strukturen des Gehirns zu kontrollieren, wurde als nächstes die biochemische Interaktion dieser beiden Signalwege untersucht. In einer gerichteten proteomischen Untersuchung mit Hilfe der Tandem affinity purification-mass spectometry-Methode (Angrand et al., 2006) von Proteinen aus eine Neuroblastom-Zelllinie, die ephrinB binden, wurde Reelin als ein Protein, das mutmaßlich mit ephrinB interagiert, identifiziert. Zunächst bestätigten wir die Fähigkeit von Reelin, mit ephrinBs zu assoziieren mit Ko-Immunpräzipitation beider endogener Proteine aus Gehirnlysaten. Das extrazelluläre Protein Reelin zeigte eine starke Bindung an die extrazelluläre Domäne von ephrinB3 und auch von ephrinB2, was andeutet, dass beide ephrin-Liganden die Funktionen von Reelin in vivo beeinflussen könnten. Die Stimulierung von cortikalen Neuronen mit Reelin führt zu einer effektiven Tyrosin-Phosphorylierung des Adapters Dab1. Da die Stimulation von cortikalen Neuronen mit einer löslichen, vorgeclusterten Form von EphB-Rezeptoren zur Rekrutierung und Aktivierung von Src-Kinasen in ephrinB-Clustern führt (Palmer et al., 2002), nehmen wir an, dass ephrinBs Src-Kinasen in VLDLR- und ApoER2-Rezeptor-Clustern rekrutieren und aktivieren könnten. Aktivierte Src-Kinasen phosphorylieren dann wiederum das Adapterprotein Dab1, das an VLDLR und ApoER2 gebunden ist und initiieren die weitere Signalgebung. In Übereinstimmung damit ko-immunpräzipitiert phosphoryliertes Dab1 zum Zeitpunkt E16.5 mit ephrinBs, während die neuronale Migration und die Schichtung des Cortex stattfindet. Darüber hinaus konnten wir beobachten, dass ephrinB3, das durch EphB3-Fc aktiviert wurde, sowohl Reelin, als auch ApoER2 und VLDLR in ephrinB3-Membranpatches in cortikalen Neuronen anhäuft. Die Aktivierung von ephrinB-Liganden durch Stimulation von cortikalen Neuronen mit EphB3-Fc führt zur Rekrutierung und Phosphorylierung von Dab1 in ephrinB-Clustern. Als nächstes befassten wir uns mit der Notwendigkeit von der durch ephrinB vermittelten Rekrutierung und Aktivierung von Src-Kinasen für den Reelin-Signalweg, indem wir Loss-of-function-Studien sowohl in cortikalen Neuronen in Kultur als auch in vivo in Mäusen durchführten. Cortikale Neuronen, die aus ephrinB3- und ephrinB2-Knockouts isoliert wurden, zeigten eine signifikante Beeinträchtigung der durch Reelin vermittelten Phosphorylierung von Dab1 und die Phosphorylierungslevels von Dab1 in ephrinB3 Mausmutanten waren stark verringert, was andeutet, dass ephrinBs Korezeptoren, die notwendig für einwandfreie Signalgebung durch Reelin sind, darstellen. Um die Bedeutung von ephrinBs für die Kontrolle der Funktion von Reelin zu untersuchen, arrangierten wir eine Reihe von Rescue-Experimenten sowohl in Neuronenkulturen als auch während der neuronalen Migration im Cortex in vivo. Aus reeler-Mäusen isolierte cortikale Neuronen zeigten die erwartet verringerte Phosphorylierung von Dab1, die rückgängig gemacht werden konnte, indem die Neuronen mit exogenem Reelin stimuliert wurden. Noch bedeutender ist die Tatsache, dass die Phosphorylierung von Dab1 durch die alleinige Aktivierung von ephrinBs mit EphB wiederhergestellt werden konnte, was die Bedeutung der ephrinBs als Korezeptoren für die Aktivierung des Signalwegs über die Rezeptoren für Reelin, VLDLR und ApoER2, wiederspiegelt. Um die Rolle von ephrinBs als Korezeptoren für den Reelin-Signalweg während der neuronalen Migration in der Großhirnrinde zu unterstreichen, setzten wir ähnliche Rescue-Experimente in organotypischen Schnittkulturen an. In den Schnitten von reeler-Mäusen und Wildtyp-Wurfgeschwistern wurde die Migration von Neuronen, die durch Fc als Kontrolle und EphB3-Fc stimuliert wurde, nach drei Tagen in Kultur untersucht. Die reeler-Schnitte zeigten den typischen reeler-Phänotyp in der Großhirnrinde. In Übereinstimmung mit der Annahme einer wirksamen Regulation des Reelin-Signalwegs war die Aktivierung von eprhinB mit EphB-Rezeptoren in der Lage, die migratorischen Defekte in reeler-Schnitten aufzuheben. Zusammengefasst identifizieren unsere Ergebnisse ephrinBs als Korezeptoren für den Reelin-Signalweg, die für die Funktion von Reelin in der neuronalen Migration während der Entwicklung der geschichteten Strukturen der Großhirnrinde, dem Hippocampus und dem Cerebellum notwendig sind. Unsere genetischen Analysen von ephrinB-Mutanten zeigen gemeinsam mit starken biochemischen Untersuchungen, dass ephrinBs in vivo für zahlreiche Aktivitäten von Reelin erforderlich sind.
LmrA is a member of the ATP Binding Cassette (ABC) transporter family of membrane proteins and a structural and functional homologue of P-glycoprotein1, 2. ABC-transporters share a common architecture of two transmembrane domains and two nucleotide binding domains. The NBDs are highly conserved in this transporter family whereas the TMDs are highly diverse3. The TMDs recognize the substrate and the NBDs bind and hydrolyze ATP and thus contribute the energy for substrate translocation. ABC transporters as a protein family transport a high number of substrates including peptides, nutrients, ions, bile acids, lipids and other lipophilic compounds. LmrA is a multidrug transporter that recognizes a number of hydrophobic substrates including fluorescent dyes and antibiotics1, 4-6. LmrA is a native protein of the gram-positive bacterium Lactococcus lactis. In this thesis, L. lactis was used as a homologous expression host for the preparation of LmrA for a variety of experiments. Wildtype LmrA as well as a number of cysteine mutants were successfully expressed in L. lactis, purified and subsequently characterized by a variety of biochemical assays (Chapter 4). LmrA can be expressed to very high amounts in L. lactis. The purification and reconstitution were optimized for the requirements of solid-state NMR experiments in this thesis. For the first time, an ABC transporter has been reconstituted in synthetic lipids to a ratio of up to 1:150 (mol/mol). LmrA was shown to be active under magic angle spinning conditions with these reconstitution ratios. By taking advantage of the slower ATP hydrolysis by LmrA ΔK388 (lysine deletion in the Walker A motif), a real-time 31P solid-state NMR ATPase assay was established (Chapter 5). This assay allowed, for the first time, the investigation of all phosphor nuclei during the ATP hydrolysis cycle of a membrane protein simultaneously and in real time7. This assay has been successfully adapted to investigate both ATP hydrolysis and substrate phosphorylation of diacylglycerol kinase (together with S. Wollschlag) and ATP hydrolysis at high temperatures of the thermophilic ABC transporter ABC1 from Thermos thermophilus (together with A. Zutz). In the course of this thesis, the gene for LmrA has been cloned into expression vectors suitable for Escherichia coli and the heterologous expression of LmrA was established (Chapter 4). The functionality of the heterologously expressed protein has been investigated and compared to L. lactis LmrA. In these experiments, LmrA was shown to yield a distinct multidrug resistance phenotype in its E. coli host and to show secondary active multidrug transport in the absence of ATP and presence of a proton gradient [Hellmich et al, in prep] (Chapter 4). Previously, it had been shown that LmrA acts as a seconadary active transporter when the NBDs are truncated8. The overexpression in minimal and defined medium and the purification of LmrA from E. coli have been optimized. Isotope labeling for ssNMR has been established and the first multinuclear ssNMR experiments have been carried out on a functional ABC transporter (Chapter 8). ABC transporters couple two cycles: upon ATP binding, the NBDs dimerize, hydrolyze the ATP, subsequently release Pi and ADP and finally dissociate. During this cycle, conformational changes are relayed to the TMDs which utilize the energy from ATP binding and/or hydrolysis to translocate the respective substrate. The prehydrolysis state can be trapped by beryllium fluoride, whereas the post-hydrolysis state of this cycle can be trapped by vanadate9-12. Trapping protocols for these reagents were successfully established for LmrA in this thesis (Chapter 4). This allowed for the investigation of different catalytic states by both ssNMR and EPR. A general 19F labeling protocol for membrane proteins has been established in the course of this thesis and successfully applied to proteorhodopsin (together with N. Pfleger)13 and LmrA (chapter 6). Single cysteine mutants of LmrA that line out the dimer interface have been labeled with a fluorine label for ssNMR. In the apo state, the 19F labeling indicates highly flexible transmembrane domains, a finding that is supported by 13C ssNMR and EPR measurements. The addition of drugs has a different effect on different positions within the LmrA dimer, therefore indicating that different drugs are recognized at a different position within the protein. For P-glycoprotein and LmrA it has been previously shown by biochemical methods that different drug binding sites co-exist. For a 19F label attached at position 314 (LmrA E314C), the spectra showed two distinct peaks with similar populations. This could hint towards a structural asymmetry within the LmrA dimer that might also be reflected in the alternating ATP hydrolysis at the NBDs. E314 has been specifically implicated with drug transport. Thus, structural asymmetry at this position might be functionally relevant for guiding a substrate through the transporter. Structural asymmetry within a homodimeric ABC transporter has also been shown for BtuCD, the E. coli vitamin B12 importer14. In addition, the conserved glutamates in EmrE, a small multidrug resistance protein, were shown to be asymmetric in the drug bound state15. Both, uniformly 13C/15N labeled as well as selectively amino acid type labeled LmrA has been investigated in different conformational states. Interestingly, significant dynamic changes in the b-sheet regions of LmrA (confined to the NBDs) were observed in the pre-hydrolysis (beryllium fluoride) and transition state (vanadate trapped) state. These were interpreted as the transition from a domain in fast conformational exchange in the apo state to one of intermediate exchange in the nucleotide bound state. A significant change in NBD mobility upon nucleotide binding was previously also shown with 2H ssNMR on LmrA16. By EPR it was shown that LmrA in both the vanadate and BeFx trapped states displays a significantly higher rigidity and therefore defined distances, whereas the apo state resembled a “floppy” protein with no preferred distance distribution. This concurs with data obtained from 19F ssNMR with fluorine labeled single-cysteine mutants. Here, in agreement with the EPR data, a higher label (and possibly) protein mobility was observed in the apo state displaying rather broad line widths. Upon trapping with vanadate, the line widths of the majority of fluorine-labeled mutants decreased due to an enhanced protein rigidity and a more homogenous environment of the fluorine labels. A similar observation was made when increasing the temperature that can be explained due to higher protein flexibility at increased temperatures. Solution NMR was employed to investigate the isolated soluble NBD of LmrA (Chapter 9). First 2D and 3D spectra were successfully obtained and could be utilized for a preliminary assignment of a significant fraction of residues. Additionally, binding of ATP and ADP in absence and presence of magnesium was investigated. Finally, the effects of peptides emulating the coupling helices of the full-length transporter on the soluble NBD were investigated. Strikingly, binding of one of these peptides only occurred in the presence of nucleotides (whereas the other showed no binding at all) hinting towards a tightly coupled regulation of the NBD and TMD during the substrate translocation/ATP hydrolysis cycle based on nucleotide binding.
ABCB9 is a peptide transporter belonging to the ATP-binding cassette (ABC) transporter subfamily B. Due to its high sequence identity to the transporter associated with antigen processing (TAP) the protein was named TAP-like (TAPL). The primary aim of this PhD thesis was the functional characterization of the TAPL transport complex. Despite the lack of TAPL function in the classical MHC class I pathway an involvement of TAPL in antigen presentation was still suggested. Apart from the crucial role of TAP for peptide delivery into the ER, TAP-independent translocation pathways in professional antigen presenting cells (pAPC) have been proposed, but not identified so far. Remarkably, TAPL mRNA and protein expression is strongly induced during differentiation of monocytes to immature and mature dendritic cells. This result was confirmed in the promonocytic cell line THP-1, which was used as a model system for monocyte to macrophage differentiation. By using quantitative immunofluorescence microscopy and subcellular fractionation, TAPL was detected in the lysosomal compartment co-localizing with the lysosome associated membrane protein 2 (LAMP-2) thus excluding the ER-localization formerly reported. Furthermore, by in vitro assays, a TAPL-specific and ATPdependent translocation of peptides into isolated lysosomes was demonstrated. Hence, TAPL is a candidate mediating peptide transport in alternative antigen presentation pathways in pAPCs. The presence of an extra N-terminal transmembrane domain (TMD0) lacking sequence homology to any known protein distinguishes TAPL from most other ABC transporters of its subfamily. By dissecting the TAPL translocation complex into its four putative transmembrane helices containing TMD0 and the core complex, distinct functions to the core complex and TMD0 were assigned. The core-TAPL complex composed of six predicted transmembrane helices and the nucleotide-binding domain (NBD) was expressed transiently in HeLa or stably in Raji cells. Crude membranes containing core-TAPL showed the same peptide transport activity as wt-TAPL demonstrating that the six core helices and the NBD are sufficient for peptide transport. This result also shows that the core transport complex is correctly targeted to and assembled in the membrane. Strikingly, in contrast to the wt transporter, the core complex localizes only partially to lysosomes and is mistargeted to the plasma membrane as observed by immunofluorescence microscopy and confirmed biochemically by cell surface biotinylation. Thus, a crucial role for TMD0 in proper subcellular targeting can be postulated. The vast majority of biological processes are mediated by protein complexes, hence characterization of such protein-protein-interactions is essential for understanding protein function on the cellular level. To identify interaction partners of TAPL, the transporter was isolated by tandem affinity purification. By tandem mass spectrometry the membrane proteins LAMP-1 and LAMP-2 were deciphered as specific proteins interacting with wt-TAPL. Notably, core-TAPL lacks these interactions indicating a role for TMD0 in recruiting other proteins. These results were verified for endogenous TAPL by co-immunoprecipitation. Using cells deficient in LAMP-1 and/or in LAMP-2 an escort function for the LAMP proteins was excluded. Very importantly, the physiological function of the LAMP-1and LAMP-2 interaction with TAPL is an increase in stability, since in their absence half-life of TAPL is drastically reduced.
Understanding the dynamics of recurrent neural networks is crucial for explaining how the brain processes information. In the neocortex, a range of different plasticity mechanisms are shaping recurrent networks into effective information processing circuits that learn appropriate representations for time-varying sensory stimuli. However, it has been difficult to mimic these abilities in artificial neural models. In the present thesis, we introduce several recurrent network models of threshold units that combine spike timing dependent plasticity with homeostatic plasticity mechanisms like intrinsic plasticity or synaptic normalization. We investigate how these different forms of plasticity shape the dynamics and computational properties of recurrent networks. The networks receive input sequences composed of different symbols and learn the structure embedded in these sequences in an unsupervised manner. Information is encoded in the form of trajectories through a high-dimensional state space reminiscent of recent biological findings on cortical coding. We find that these self-organizing plastic networks are able to represent and "understand" the spatio-temporal patterns in their inputs while maintaining their dynamics in a healthy regime suitable for learning. The emergent properties are not easily predictable on the basis of the individual plasticity mechanisms at work. Our results underscore the importance of studying the interaction of different forms of plasticity on network behavior.
Top-down and bottom-up approaches are the general methods used to analyse proteomic samples today, however, the bottom-up approach has been dominant in the last decade. Establishing a bottom-up method involves not only the choice of adequate instruments and the optimisation of the experimental parameters, but also choosing the right experimental conditions and sample preparation steps. LC-ESI MS/MS has widely been used in this field due to its advanced automation. The primary objective of the present study was to establish a sensitive high-throughput nLC-MALDI MS/MS method for the identification and characterisation of proteins in biological samples. The method establishment included optimisation and validation of parameters such as the capillaries in the HPLC systems, gradient slopes, column temperature, spotting frequencies or the MS and MS/MS acquisition methods. The optimisation was performed using two HPLC-systems (Agilent 1100 series and Proxeon Easy nLC system), three spotters and the 4800 MALDI-TOF/TOF analyzer. Furthermore, samples preparation protocols were modified to fit to the established nLCMALDI- TOF/TOF-platform. The potentials of this method was demonstrated by the successful analysis of complex protein samples isolated from lipid particles, pre-adipocytes/adipocytes tissues, membrane proteins and proteins pulled-down from protein-proteins interaction studies. Despite the small amount of proteins in the lipid particles or oil bodies, and the challenges encountered in studying such proteins, 41(6 novel + 14 mammal specific + 21 visceral specific) proteins were added to the already existing proteins of the secretome of human subcutaneous (pre)adipocytes and 6 novel proteins localised in the yeast lipid particles. Protein-protein interaction studies present another area of application. Here the analytical challenges are mostly due to the loss of binding partner upon sample clean-up and to differentiate from non-specific background. Novel interaction partners for AF4•MLL and AF4 protein complex were identified. Furthermore, a novel sample protocol for the analysis of membrane proteins, based on the less specific protease, elastase, was established. Compared to trypsin, a higher sequence coverage and higher coverage of the transmembrane domains were achieved. The use of this enzyme in proteomics has been limited because of its non specific cleavage. However, from the results obtained in these studies, elastase was found to cleave preferentially at the C-terminal site of the amino acids AVLIST. The advantage of the established protocol over conventional protocols is that the same enzyme can be used for shaving of the soluble dormains of intact proteins in membranes and the digestion of the hydrophobic domain after solubilisation. Furthermore, the solvents used are compatible with the nLC-MALDI method setup. In addition, it was also shown that for less specific enzymes, a higher mass accuracy is required to reduce the rate of false positive identifications, since current search engines are not perfectly adapted for these types of enzymes. A brief statistical analysis of the MS/MS data obtained from the LC-MALDI TOF/TOF system showed that for less specific enzymes, under high-energy collision conditions, approximately 43 % of the fragment ions could not be matched to the known y- b type ions and their resultant internal fragments. This limitation greatly influenced the search results. However, this limitation can be overcome by modifying the N-terminal amino acids with basic moieties such as TMT. The use of elastase as a digestion enzyme in proteomic workflow further increased the complexity of the sample. Therefore, orthogonal multidimensional separation was necessary. Offgel-IEF was used as the separation technique for the first dimension. Here peptides are separated according to the pI. However, the acquired samples could not be loaded to the nLC due to the high viscosity of the concentrated samples when using the standard protocol. In order to achieve compatibility of the Offgel-IEF to the nLC-MALDI-TOF/TOF-platform, the separation protocol of the Offgel-IEF was modified by omitting the glycerol, which was the cause of the viscous solution. The novel glycerol free protocol is advantageous over the conventional method because the samples could directly be picked-up and loaded onto the pre-column without resulting in an increase in back pressure or a subsequent pre-column clogging. The glycerol free protocol was then assessed using purple membrane and membrane fraction of C. glutamicum. The results obtained were comparable to those applied in published reports. Therefore, the absence of glycerol did not affect the separation efficiency of the Offgel-IEF. In addition the applicability of elastase and the glycerol free Offgel-IEF for quantitation of membrane proteins was assessed. Most of the unique peptides identified were in the acidic region and 85 % were focused only into one fraction and approximately 95 % in only two fractions. These results are in accordance with previously published results (Lengqvist et al., 2007). When compared with theoretical digests of the proteins identified in this study, it can be concluded that basic moiety (TMT) on the peptide backbone, did not affect the separation efficiency of the Offgel-IEF. In an applied study, changes in the protein content of yeast strain grown in two different media were relatively quantified. For example, prominent proteins, such as the hexose tranporter proteins responsible for transporting glucose accross the membrane, were successfully quantified. Last but not least, the nLC-MALDI-TOF/TOF platform also served as a basis for the development of a high-throughput method for the identification of protein phosphorylation. The establishment of such a method using MALDI has been challenging due to the lack of sensitive matrices, such as CHCA for non-modified peptides, which exhibit a homogenous crystallisation and thus yield stable signal intensity over a long period of time in an automated setup. The first step of this method was the establishment of a matrix/matrix mixture with better crystal morphology and higher analyte signal intensity than the matrix of choice, i.e. DHB. From MS and MS/MS measurements of standard phosphopeptides, a combination of FCCA and CHAC in a 3:1 ratio and 3 mM NH4H2PO4 facilitated high analyte signal intensities and good fragmentation behaviour. Combining a custom-packed biphasic column for the enrichment of phosphopeptides, the applicability of the matrix mixture was assessed in anautomated phosphopeptide analysis using standard phosphopeptides spiked to a 20-fold excess BSA digest. These analyses showed that this method is reproducibile and both flow throughs can be analysed. Applying the method to the analysis of 2 standard phosphoproteins, alpha/beta-casein, and a leukemia related protein, ENL, 13 phosphopeptides from both alpha/beta-Casein and 13 phosphopeptides with 6 phosphorylation sites from the ENL were identified. As a general conclusion, it can be stated that the nLC-MALDI-TOF/TOF method established here in various modifications for different analytical purposes is a robust platform for proteomic analyses.
In this study, I investigate the crustal and upper mantle velocity structure beneath the Rwenzori Mountains in western Uganda. This mountain range is situated within the western branch of the East African Rift and reaches altitudes of more than 5000 m. I use four different approaches that belong to the travel-time tomography method. The first approach is based on the isotropic tomographic inversion of local data, which contain information about 2053 earthquakes recorded by a network of up to 35 stations covering an area of 140×90 km2. The LOTOS-09 algorithm described here is used to realize this approach. The second approach is based on the anisotropic tomographic inversion of the same local dataset. This method employs the tomographic code ANITA, developed with my participation, which provides 3D anisotropic P and isotropic S velocity distributions based on P and S travel-times from local seismicity. For the P anisotropic model, four parameters for each parameterization cell are determined. This represents an orthorhombic anisotropy with one vertically-oriented predefined direction. Three of the parameters describe slowness variations along three horizontal orientations with azimuths of 0°, 60° and 120°, and one is a perturbation along the vertical axis. The third approach is based on tomographic inversion of the teleseismic data, which contain information about the traveltimes of P-waves coming from 284 teleseismic events recorded by the seismic network stations. The TELELOTOS code, which is my own modification of the LOTOS-09 algorithm, is used in this approach. The TELELOTOS code is designed to iteratively invert the local and/or teleseismic datasets. Finally, I present the results of the new tomographic approach, which is based on the simultaneous inversion of the joint local and teleseismic data. The simultaneous use of these datasets for the tomographic inversion has several advantages. In this case, the velocity structure in the study area can be resolved as deep as in the teleseismic approach. At the same time, in the upper part of the study volume, the resolution of the obtained models is as good as in the local tomography. The TELELOTOS algorithm is used to perform the joint tomographic inversion. Special attention is paid in this work to synthetic testing. A number of different synthetic and real data tests are performed to estimate the resolution ability and robustness of the obtained models. In particular, synthetic tests have shown that the results of the anisotropic tomographic inversion of the local data have to be considered as unsatisfactory. For all approaches used in this study, I present synthetic models that reproduce the same pattern of anomalies as that obtained by inverting the real data. These models are used to interpret the results and estimate the real amplitudes of the obtained anomalies. The obtained models exhibit a relatively strong negative P anomaly (up to -10%) beneath the Rwenzori Mountains. Low velocities are found in the northeastern part of the array at shallower depths and are most likely related to sedimentary deposits, while higher velocities are found beneath the eastern rift shoulder and are thought to be related to old cratonic crust. The presence of low velocities in the northwestern part of the array may be caused by a magmatic intrusion beneath the Buranga hot springs. Relatively low velocities were observed within the lower crust and upper mantle in the western and southern parts of the study area (beneath the rift valley and the entire length of the Rwenzori range). The higher amplitude of the low-velocity anomaly in the south can be related to the thinner lithosphere in the southern part of the Albertine rift. In the center of the study area, a small negative anomaly is observed, with the intensity increasing with depth. This anomaly is presumably related to a fluids rising up from a plume branch in the deeper part of the mantle. According to the interpretation of the local earthquake distribution, the Rwenzori Mountains are located between two rift valleys with flanks marked by normal faults. The Rwenzori block is bounded by thrust faults that are probably due to compression.
Capoeta damascina (Teleostei: Cyprinidae) is one of the most common freshwater fish species, found throughout the Levant, Mesopotamia, Turkey and Iran. According to the state of knowledge prior to this study, C. damascina, which is distributed over a wide range of isolated water bodies, was not a well-defined species. It was questionable whether it represents a single species or a complex of closely related species with high intraspecific and comparatively low interspecific variability. The goal of this study was to investigate the taxonomy, systematic position of the C. damascina species complex and the phylogenetic relationships among its members, based on morphological features as well as molecular phylogeny. Samples obtained from throughout the geographic range of this species complex were subjected to comparative morphological analyses in order to define, properly diagnose and separate species within the C. damascina complex. To elucidate phylogenetic relationships among members of the C. damascina species complex, samples were subjected to genetic analyses, using two molecular markers targeting the mitochondrial cytochrome oxidase I (COI, n = 103) and the two adjacent divergence regions (D1-D2) of the nuclear 28S rRNA genes (LSU, n = 65). Based on morphological and molecular genetic data, six closely related species were recognized within the C. damascina complex: C. buhsei, C. caelestis, C. damascina, C. saadii, C. umbla and an undescribed species, Capoeta sp.1. Analyses of the morphometric and meristic data obtained in this study revealed phenotypic variability among the various populations within a species and among the different species. Such differences in morphological characters reflect genetic differences, environmentally induced phenotypic variation or both, as the meristic phenotype of fish is sometimes a consequence of environmental parameters acting on the genotype. Based on phylogenetic analyses, two main lineages were identified within the C. damascina species complex: a western lineage represented by C. caelestis, C. damascina and C. umbla and an eastern lineage represented by C. buhsei, C. saadii and Capoeta sp.1. The close phylogenetic relationships between C. damascina and C. umbla and the sharing of same haplotypes between one specimen of C. damascina from Euphrates and another of C. umbla from Tigris reflect one of three possibilites: recent speciation, mitochondrial introgression or a combination of both. The results obtained in this study indicate that speciation of the above-mentioned six taxa is quite recent and that their dispersal and present-day distribution can be related to Pleistocene events. The drying out of the Persian Gulf, probably during one of the first glacials of the Pleistocene, led the ancestor of the C. damascina species complex in Mesopotamia to reach the rivers of the Gulf and of Hormuz basins and differentiate there, giving rise to the eastern lineage (ancestor of C. buhsei, C. saadii and Capoeta sp.1). As connections presumably existed among the different river drainages and basins in Iran during the wet periods of the Pleistocene, the ancestor of C. buhsei, C. saadii and Capoeta sp.1 was subsequently able to colonize the various Iranian drainages and differentiate there, giving rise to C. buhsei, C. saadii and Capoeta sp.1. After the separation from the eastern lineage, the western lineage, represented by the ancestor of C. damascina, C. umbla and C. caelestis, most likely reached the Levant from the Tigris-Euphrates system during the Pleistocene glacials, when river connections existed in the regions of the upper courses of Ceyhan Nehri (southern Turkey) and some western affluents to the Euphrates. From Ceyhan Nehri, it dispersed into other rivers in southern Turkey during Pleistocene periods of low sea levels until it reached Göksu Nehri and evolved into C. caelestis. The sister population differentiated into C. damascina and C. umbla. Based on the results obtained in this study, it is likely that C. damascina colonized the Levant and southern Turkey during the Pleistocene glacials. This is well supported by the low genetic variability among the C. damascina populations. Direct connections existed among the river drainages in the Levant during the Pleistocene periods of low sea level, thus serving as a pathway for the dispersal of C. damascina. The results of this study provide a coherent picture of the taxonomic position, phylogenetic relationships and evolutionary history of the C. damascina species complex and explain present patterns of distribution considering paleogeographic events.
Background: Although literature provides support for cognitive behavioral therapy (CBT) as an efficacious intervention for social phobia, more research is needed to improve treatments for children. Methods: Forty four Caucasian children (ages 8-14) meeting diagnostic criteria of social phobia according to the Diagnostic and Statistical Manual of Mental Disorders (4th ed.; APA, 1994) were randomly allocated to either a newly developed CBT program focusing on cognition according to the model of Clark and Wells (n = 21) or a wait-list control group (n = 23). The primary outcome measure was clinical improvement. Secondary outcomes included improvements in anxiety coping, dysfunctional cognitions, interaction frequency and comorbid symptoms. Outcome measures included child report and clinican completed measures as well as a diagnostic interview. Results: Significant differences between treatment participants (4 dropouts) and controls (2 dropouts) were observed at post test on the German version of the Social Phobia and Anxiety Inventory for Children. Furthermore, in the treatment group, significantly more children were free of diagnosis than in wait-list group at post-test. Additional child completed and clinician completed measures support the results. Discussion: The study is a first step towards investigating whether CBT focusing on cognition is efficacious in treating children with social phobia. Future research will need to compare this treatment to an active treatment group. There remain the questions of whether the effect of the treatment is specific to the disorder and whether the underlying theoretical model is adequate. Conclusion: Preliminary support is provided for the efficacy of the cognitive behavioral treatment focusing on cognition in socially phobic children. Active comparators should be established with other evidence-based CBT programs for anxiety disorders, which differ significantly in their dosage and type of cognitive interventions from those of the manual under evaluation (e.g. Coping Cat).
Using faculty-librarian partnerships to ensure that students become information fluent in the 21st century In the 21st century educators in partnership with librarians must prepare students effectively for productive use of information especially in higher education. Students will need to graduate from universities with appropriate information and technology skills to enable them to become productive citizens in the workplace and in society. Technology is having a major impact on society; in economics e-business is moving to the forefront; in communication e-mail, the Internet and cellular telephones have reformed how people communicate; in the work environment computers and web utilizations are emphasized and in education virtual learning and teaching are becoming more important. These few examples indicate how the 21st century information environment requires future members of the workforce to be information fluent so they will have the ability to locate information efficiently, evaluate information for specific needs, organize information to address issues, apply information skillfully to solve problems, use information to communicate effectively, and use information responsibly to ensure a productive work environment. Individuals can achieve information fluency by acquiring cultural, visual, computer, technology, research and information management skills to enable them to think critically.
Teaching information literacy: substance and process This presentation explores the concept of information literacy within the broader context of higher education. It argues that, certain assertions in the library literature notwithstanding, the concepts associated with information literacy are not new, but rather very closely resemble the qualities traditionally considered to characterize a well-educated person. The presentation also considers the extent to which the higher education system does indeed foster the attributes commonly associated with information literacy. The term information literacy has achieved the immediacy it currently enjoys within the library community with the advent of the so-called "information age" The information age is commonly touted in the literature, both popular and professional, as constituting nothing short of a revolution. Academic librarians and other educators have of course felt called upon to make their teaching reflect both the growing proliferation of information formats and the major transformations affecting the process of information seeking. Faced with so much novelty and uncertainty, it is no surprise that many have felt that these changes call for a revolution in teaching. It is within this context that the concept of information literacy has flourished. It is argued in this presentation, however, that by treating information literacy as an essentially new specialty that owes much of its importance to the plethora of electronic information, we risk obscuring some of the most fundamental and enduring educational values we should be imparting to our students. Much of the literature on information literacy assumes - rather than argues - that recent changes in the way we approach education are indications of progress. Indeed, much of the self-narrative that institutions produce (in bulletins, mission statements, web sites, etc.) endorses an approach to education that will result in lifelong learners who are critical consumers of information. After critically examining the degree to which such statements of educational approach reflect reality, this presentation concludes by considering the effects of certain changes in the culture of higher education. It considers particularly the transformation - at least in North America - of the traditional model of higher education as a public good to a market-driven business model. It poses the question of whether a change of this significance might in fact detract from, rather than promote, the development of information literate students.
Development of a computational method for reaction-driven de novo design of druglike compounds
(2010)
A new method for computer-based de novo design of drug candidate structures is proposed. DOGS (Design of Genuine Structures) features a ligand-based strategy to suggest new molecular structures. The quality of designed compounds is assessed by a graph kernel method measuring the distance of designed molecules to a known reference ligand. Two graph representations of molecules (molecular graph and reduced graph) are implemented to feature different levels of abstraction from the molecular structure. A fully deterministic construction procedure explicitly designed to facilitate synthesizability of proposed structures is realized: DOGS uses readily available synthesis building blocks and established reaction schemes to assemble new molecules. This approach enables the software to propose not only the final compounds, but also to give suggestions for synthesis routes to generate them at the bench. The set of synthesis schemes comprises about 83 chemical reactions. Special focus was put on ring closure reactions forming drug-like substructures. The library of building blocks consists of about 25,000 readily available synthesis building blocks. DOGS builds up new structures in a stepwise process. Each virtual synthesis step adds a fragment to the growing molecule until a stop criterion (upper threshold for molecular mass or number of synthesis steps) is fulfilled. In a theoretical evaluation, a set of ~1,800 molecules proposed by DOGS is analyzed for critical properties of de novo designed compounds. The software is able to suggest drug-like molecules (79% violate less than two of Lipinski’s ‘rule of five’). In addition, a trained classifier for drug-likeness assigns a score >0.8 to 51% of the designed molecules (with 1.0 being the top score). In addition, most of the DOGS molecules are deemed to be synthesizable by a retro-synthesis descriptor (77% of molecules score in the top 10% of the decriptor’s value range). Calculated logP(o/w) values of constructed molecules resemble a unimodal distribution centred close to the mean of logP(o/w) values calculated for the reference compounds. A structural analysis of selected designs reveals that DOGS is capable of constructing molecules reflecting the overall topological arrangement of pharmacophoric features found in the reference ligands. At the same time, the DOGS designs represent innovative compounds being structurally distinct from the references. Synthesis routes for these examples are short and seem feasible in most cases. Some reaction steps might need modification by using protecting groups to avoid unwanted side reactions. Plausible bioisosters for known privileged fragments addressing the S1 pocket of trypsin were proposed by DOGS in a case study. Three of them can be found in known trypsin inhibitors as S1-adressing side chains. The software was also tested in two prospective case studies to design bioactive compounds. DOGS was applied to design ligands for human gamma-secretase and human histamine receptor subtype 4 (hH4R). Two selected designs for gamma-secretase were readily synthesizable as suggested by the software in one-step reactions. Both compounds represent inverse modulators of the target molecule. In a second case study, a ligand candidate selected for hH4R was synthesized exactly following the three-step synthesis plan suggested by DOGS. This compound showed low activity on the target structure. The concept of DOGS is able to deliver synthesizable and bioactive compounds. Suggested synthesis plans of selected compounds were readily pursuable. DOGS can therefore serve as a valuable idea generator for the design of new pharmacological active compounds.