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Background and Purpose of this Meeting With an opening reception sponsored by Thomson Scientific on the evening of Thursday, October 5, the University Library of Frankfurt and the German-North American Resources Partnership (GNARP) and will be hosting an important two-day conference this Autumn in Frankfurt, Germany: »The World According to GNARP: Prospects for Transatlantic Library Partnership in the Digital Age« Sessions at this meeting will explore the wealth of library resources - archival, print, and digital - available to students and researchers (in Germany and the United States) in five selected subject areas: North American Studies, German Studies, Judaica, Africana, and South Asia/India, highlighting both existing avenues (and obstacles) for transatlantic resource sharing along with future prospects. In addition, several other important topics will be highlighted through individual presentations and panel discussions: the future of German as a language of the sciences; existing and planned electronic journal archives in Germany and the U.S.; print and digital repositories; and a special panel on »comparative cataloging cultures« on both sides of the Atlantic. The »World According to GNARP« conference will be taking place simultaneously with the Frankfurt Book Fair, the largest book-related event in the world, attracting annually 285,000 visitors (2005), thus giving participants who arrive early the chance to combine attendance at both the Book Fair and Conference. A cultural event and dinner in Frankfurt are planned for Friday 6th October.
The rate of species extinctions due to anthropogenic activities has dramatically increased within the past few centuries (Dirzo & Raven, 2003; Novacek & Cleland, 2001). Although the mechanisms and ultimate causes leading to the extinction of species remain largely unclear (Frankham et al., 2002), five threats to global biodiversity have frequently been referred to as the most important: habitat destruction and fragmentation, global climate change, hunting and overuse of food resources, biological invasions and environmental pollution (Dudgeon et al., 2006; Lewis, 2006; Novacek & Cleland, 2001). Different research fields, as conservation biology, ecology and ecotoxicology, investigate the effects of these factors on organisms and found strong evidence for their negative impact on regional and global biodiversity.
In most cases, natural populations will be impacted not only by one threat, but rather a combination of them (Buckley & Roughgarden, 2004; Kappelle et al., 1999). Multiple environmental stress factors can have cumulative negative effects on the survival of populations (Sih et al., 2004). To understand, how natural populations respond to combinations of different stress factors is thus of crucial importance in order to understand our present and future impact on all scales of biodiversity (Warren et al., 2001).
The effects of anthropogenically introduced chemicals on organisms and ecosystems are investigated in the field of ecotoxicology. Research in this area has led to a large body of information concerning the impact of chemical stress on the fitness of model species in the laboratory. In contrast to this, there is an obvious lack of knowledge on the effects of contaminants on natural populations and communities (Bickham et al., 2000; Bourdeau et al., 1990). For instance, ecotoxicologists have just started to investigate the impact of environmental pollution on the genetic variability of natural populations (Bickham et al., 2000; Whitehead et al., 2003). Genetic variation provides the raw material for populations in order to adapt to changing environmental conditions and is thus the substrate for evolution and long-term survival of populations and species (Frankham, 2005). The amount of genetic variation in populations is positively correlated with the effective population size (Frankham, 1996). Habitat destruction and fragmentation has divided the ranges of many species into small and isolated refuges. Without migration from adjacent habitats, isolated populations will decrease in their level of genetic diversity through random loss of alleles (Hedrick, 2000). Frankham (1995) for instance, showed that 32 of the 37 endangered species (which occur in small populations per definition) of different animals and plant taxa display reduced levels of heterozygosity compared to closely related and more frequent species.
In strongly human impacted landscapes, both factors, environmental pollution and habitat destruction, can be expected to occur frequently together. It is thus of crucial importance to investigate the impact of reduced genetic diversity and inbreeding on the response to chemical stress. In addition, chemical exposure has frequently been discussed to have an impact on the extent of genetic variability in exposed populations (Guttman, 1994; Staton et al., 2001; van Straalen & Timmermans, 2002). However, evidence for this 'genetic erosion hypothesis' remained scarce to date, most likely because of the difficulty to single out the impact of pollution stress from a background of multiple factors which influence patterns of genetic variability in natural populations (Belfiore, 2001; Staton et al., 2001; van Straalen & Timmermans, 2002).
The Frankfurt University Library possesses one of the outstanding Africana Collections in continental Europe; its regional anddisciplinary scope is unique in Germany. Today about 5,000 new acquisitions a year have accumulated over 200,000 items on Africa south of the Sahara. Some 50,000 historical and rare photographs are fully digitized and freely accessible. Together with a collection of around 18,000 books stemming from the collections of the German Colonial Society at the end of the 19th and the beginning of the 20th century they constitute the historical foundations of the collection. Recently the University Library Frankfurt and the library of the GIGA Institute of African Affairs, Hamburg, started the project ilissAfrica (internet library sub-Saharan Africa), a central subject gateway for online resources and a powerful tool for bibliographic research. These new services will be indispensable for researchers and librarians of African Studies and will promote African studies worldwide.
A commentary on the Synopsis Fungorum in America Boreali Media Degentium, by L. D. de Schweinitz
(1856)
Experimente zum radiativen Elektroneneinfang (REC, Radiative Electron Capture), der Zeitumkehrung der Photoionisation, wie er in Stößen hochgeladener, relativistischer Schwerionen mit leichten Gasatomen auftritt, ermöglicht einen einzigartigen Zugang zum Studium der Photonen-Materie-Wechselwirkung im Bereich extrem starker Coulombfeldern. So ist die REC-Strahlung im relativistischen Bereich zum einen geprägt durch das Auftreten von höheren elektrischen und magnetischen Multipolordnungen und zum anderen durch starke Retardierungseffekte. In Folge dessen wurde der REC-Prozeß in den vergangen Jahren sehr detailliert untersucht, wobei sich die experimentelle und theoretische Forschung auf die Emissionscharakteristik der REC-Photonen konzentrierte, wie z.B. auf Untersuchungen von Winkelverteilungen und Linienprofilen. Mittlerweile kann der REC-Prozeß als ein - selbst für die schwersten Ionen - wohlverstandener Effekt angesehen werden. Allerdings entzog sich den Experimenten bislang eine zur Beschreibung der Photonenmission wesentlich Größe, näamlich die Polarisation der Strahlung. Die lineare Polarisation der REC-Strahlung, wie sie in Stößen zwischen leichten Atomen und den schwersten, hochgeladenen Ionen vorhergesagt wird, war der Gegenstand der vorliegende Arbeit, in der es erstmals gelang, die diese für den konkreten Fall des Einfangs in die K-Schale von nackten Uranionen nachzuweisen und im Detail zu untersuchen. Die hierzu notwendigen experimentellen Untersuchungen erfolgten am Speicherring ESR der GSI-Darmstadt für das Stoßsystem U92+ -> N2 und für Projektilenergien, die im Bereich zwischen 98 und 400 MeV/u lagen. Besonders hervorzuheben ist der Einsatz eines segmentierten Germaniumdetektors, der speziell für den Nachweis linear polarisierter Strahlung im Energiebereich oberhalb 100 keV entwickelte wurde. Die lineare Polarisation der Strahlung wurde hierbei durch eine Analyse der Comptonstreuung innerhalb des Detektors gewonnen. Die durch eine präzise Analyse der Comptonstreuverteilungen gewonnenen Daten zeigen eine ausgeprägte lineare Polarisierung der REC-Strahlung in der Streuebene, die zudem eine starke Abhängigkeit als Funktion der Stoßenergie und des Beobachtungwinkels aufweist. Der detaillierte Vergleich mit nicht-relativistischen und relativistischen Vorhersagen ermöglichte darüberhinaus den Nachweis für das Auftreten starker relativistischer Effekte, die sich allerdings depolarisierend auswirken. Das Experiment wurde am internen Target des ESR-Speicherrings durchgeführt, wobei der Photonennachweis mittels mehrerer Ge(i)-Detektoren erfolgte, die die Ionen-Target-Wechselwirkungszone unter Beobachtungswinkeln zwischen nahe Null und 150 Grad einsahen. Alle Photonendetektoren wurden in Koinizidenz mit einem Teilchendetektor betrieben, um so die volle Charakteristik des REC-Prozesses zu erfassen, also den Einfang eines Targetelektrons in die nackten Uranionen (U92+) unter Emission eines Photons. Für den Polarisationsnachweis entscheidend war der Einsatz eines Germanium-Pixel-Detektors, der abwechselnd unter den Winkeln von 60 und 90 Grad betrieben wurde. Dieser Detektor verfügt über eine 4x4 Pixelmatrix (Pixelgröße: 7x7 mm), wobei die elektronische Information jedes Pixels (Energiesignale und schnelle Zeitsignale) separat registriert und aufgezeichnet wurde. Hierdurch war es möglich Ereignisse, die koinzident in zwei Pixeln erfolgten, zu detektieren und zu analysieren. Dies ist die eigentliche Voraussetzung für den Nachweis der linearen Polarisation bei hohen Photonenenergien, bei dem die Abhängigkeit des differenziellen Wirkungsquerschnitts für Comptonstreuung von der linearen Polarisation der einfallenden Photonen ausgenutzt wird (siehe Klein-Nishina Formel Eq. 2.7). Der Nachweis der Comptonstreuung erfolgt hierbei durch die Detektion des Compton-Rückstoßelektrons (deltaE) und des gestreuten Comptonphotons (hw'), die jeweils separat, aber koinzident in zwei unterschiedlichen Segmenten des Detektors nachgewiesen werden. Hier sei betont, dass für Germanium bereits ab Photonenenergien von ca. 160 keV die Absorption der Strahlung durch den Compton-Effekt über die Photoabsorption dominiert und somit das Ausnutzen des Compton-Effekts prinzipiell eine sehr effektive Technik ist. Der Auswertung der Datenfkam wesentlich zugute, dass der Germanium-Detektor über eine im Vergleich zu Szintillations- oder Gaszählern gute Energieauflösung von ca. 1.8 keV bei 122 keV verfügt. Somit kann durch Bilden der Summenenergie hw = hw' + deltaE für koinzidente Ereignisse die Energie des einfallenden Photons (hw) rekonstruieren werden und als zwingende Bedingung dafür herangezogen werden, dass es sich bei dem Ereignis im Detektor um ein Compton-Event gehandelt hat. Für den Fall linearer Polarisation ist eine wesentliche Aussage der Klein-Nishina-Formel, dass die maximale Intensität für die Compton gestreuten Photonen senkrecht zur Polarisationsebene zu erwarten ist. Tatsächlich zeigen bereits die während des Experiments aufgenommenen Rohdaten für den Fall der untersuchten REC-Strahlung, die durch den Einfang in die K-Schale des Projektils entsteht, dass es sich hierbei um eine stark polarisierte Strahlung handelt, wobei eine erhöhte Intensität für Comptonstreuung senkrecht zur Stoßebene (für den REC-Prozeß definiert durch die Ionenstrahlachse und den Impuls des REC-Photons) festgestellt wurde (vgl. Fig. 7.3). Zur genauen qualitativen Analyse der Meßdaten wurden alle möglichen Pixelkombinationen der (4x4) Detektorgeometrie ausgewertet, wobei jedoch koinzidente Ereignisse benachbarter Segmente ausgeschlossen wurden, um den hier vorhandenenen Einfluß elektronischer Übersprecher zu eliminieren. Zudem erfolgte die Analyse der Daten unter Berücksichtigung verschiedenster Effekte, die einen Einfluß auf die Nachweiseffizienzen für die Compton gestreuten Photonen haben könnten. An prominenter Stelle ist hier die Korrektur zu nennen, die durch die Detektordicke von 1,5 cm und der Pixelgröße von 7x7 cm2 hervorgerufen wird. Zu betonen ist hier, dass für die Auswertung nur relative Effizienzen eine Rolle spielen und so der Einfluß systematischer Fehler, hervorgerufen durch Effizienzkorrekturen, stark reduziert werden konnte (für eine so gewonnene, vollständige Compton-Streuverteilung sei auf Abbildung 9.1 verwiesen, in der die Intensitätsverteilung für Compton-Streuung dargestellt ist). Es sei auch hervorgehoben, dass der Nachweis der Polarisation durch Messungen von vollständigen Compton-Intensitätverteilung im Detektor erfolgte, was das hier diskutierte Experiment wesentlich von konventionellen Polarisationsexperimenten für harte Röntgen- und gamma-Strahlung unterscheidet. Üblicherweise wird in diesen Experimenten die Comptonstreuung ausschließlich in der Reaktionsebene und senkrecht dazu nachgewiesen. Generell weisen die in der vorliegenden Arbeit gewonnen Compton-Streuverteilungen für den K-REC-Prozeß ein ausgeprägtes Maxium senkrecht zur Reaktionsebene auf und bestätigen somit den bereits aus den Rohdaten abgeleiteten Befund, dass die Polarisationsebene der KREC Strahlung in der Reaktionsebene des Stosses liegt. In der Tat kann dieser Befund für alle Energien und Beobachtungswinkel bestätigt werden, die in dem hier diskutierten Experiment verwendet wurden. Hier sei zudem darauf hingewiesen, dass es durch die Erfassung der vollständigen Compton-Streuverteilung möglich war, die Orientierung der Polarisationsebene in Bezug auf die Stoßebene mit hoher Präzision zu erfassen. So konnte z.B. bei der Stossenergie von 400 MeV/u und dem Winkel von 90 Grad, die Orientierung der Comptonstreuverteilung in Bezug auf die Stoßebene zu ph=90 Grad bestimmt werden. Dieser Befund könnte für die Planung zukünftiger Experimente zum Nachweis polarisierter Ionenstrahlen entscheidend sein, da eine Abweichung von der ph = 90 Grad Symmetrie nur durch das Vorhandensein polarisierter Teilchen erklärt werden kann. Dieser Effekt, der in neuesten theoretischen Behandlungen im Detail untersucht wurde, stellt gleichsam einen neuen Zugang zur Bestimmung des Polarisationsgrads der Projektile dar. Hierdurch wird die Stärke der hier angewandten Technik verdeutlicht, die auf dem Einsatz eines ortsempfindlichen Germanium-Pixel- Detektors beruht. Die Bestimmung des genauen Polarisationsgrades für die K-REC-Strahlung erfolgte durch eine X2-Anpassung der Klein-Nishina-Formel an die experimentellen Daten. Die hieraus resultierenden Daten zeigen für alle Strahlenergien und Beobachtungsgwinkel eine starke Polarisation von etwa 80%, wobei die experimentelle Unsicherheit im 10% Bereich liegt. Letztere ist im wesentlichen auf die statistische Genauigkeit zurückzuführen. Die Daten wurden zudem eingehend mit theoretischen Vorhersagen verglichen. Die Theorie stützt sich auf eine vollständige relativistische Beschreibung des REC-Prozesses unter Verwendung exakter Wellenfunktionen für das Kontinuum und den 1s Zustand in wasserstoffartigem Uran. Typischer weise mußten bei den Rechnungen sowohl elektrische wie auch magnetische Multipolterme bis hin zu L=20 verwendet werden, um Konvergenz zu erreichen. Der Vergleich zeigt eine hervorragende Übereinstimmung zwischen Experiment und Theorie. Zudem verdeutlicht der Vergleich mit der ebenfalls diskutierten Vorhersage der nicht-relativistischen Dipolnäherung die Bedeutung relativistischer Effekte (vor allem das Auftreten höherer elektrischer und magnetischer Multipole), die für die Emission der REC-Strahlung bei hohen, relativistischen Energien und hohem Z charakteristisch sind. Offensichtlich wirken sich diese Effekte stark depolarisierend aus. Dass in der Tat eine Zunahme der depolarisierenden Effekte mit einer Zunahme der Strahlenergie verbunden ist, wird auch durch die Daten dokumentiert, die für den Beobachtungswinkel von 60 Grad als Funktion des Projektilenergie untersucht wurden. Die in der vorliegenden Arbeit gewonnenen Resultate für die Polarisation der REC-Strahlung ebenso wie die neuartige Experimenttechnik, die hierbei zum Einsatz kam, lassen für die nahe Zukunft eine Serie von weiteren Polarisations-Experimenten erwarten. Hierbei könnte der REC-Strahlung und deren Polarisation als Mittel zur Diagnostik und zum Nachweis des Polarisationsgrades gespeicherter Ionenstrahlen eine Schlüsselrolle zukommen. Als Detektorsysteme werden hierzu zwei-dimensionale Germanium- und Silizium-Streifen-Detektoren zum Einsatz kommen bzw. Kombinationen aus zweidimensionalen Silizium- und Germanium-Detektoren, sogenannte Compton-Teleskope. Diese Compton-Polarimeter, die gegenwärtig für neue Experimentvorhaben am ESR-Speicherring entwickelt werden, verfügen über eine wesentlich verbesserte Ortsauflösung (z.B. 1x1 mm2) und somit über eine wesentlich gesteigerte Nachweiseffizienz für die Comptonstreuung (ein bis zwei Größenordnungen). Hierdurch sollte es möglich sein, den für Polarisationexerperimente zugänglichen Energiebereich wesentlich auszudehnen, sodass selbst die charakteristische Strahlung der Schwerionen (ca. 50 bis 100 keV) für solche Experimente zugänglich wird.
Physical soil properties feature high spatial variabilities which are known to affect geophysical measurements. However, these variations are not considered in most cases. The challenging task is to quantify the influence of soil heterogeneities on geophysical data. This question is analysed for DC resistivity and GPR measurements which are frequently used for near-surface explorations. To determine the pattern of electric soil properties in situ with the required high spatial resolution, geophysical measuring techniques are methodically enhanced. High-resolution dipole-dipole resistivity measurements are used to determine the electric conductivity distribution of the topsoil. Due to the small electrode separations, the actual electrode geometry has to be considered and an analytic expression for geometric factors is derived instead of assuming point electrodes. Two methods are used to determine soil permittivity with GPR:(i) the coefficient of reflection at the interface air-soil is measured with an air-launched horn antenna, (ii) the velocity of the groundwave is measured with a new setup using two receiver antennas enhancing the lateral resolution from in the best case 0.5 m for standard techniques to approximately 0.1 m with the new technique. With the optimised measuring techniques, the electric properties of sandy soils are determined in the field. Conductivity and permittivity show high spatial variability with correlation lengths of a few decimetres. Geostatistical simulation techniques are used to generate synthetic random media featuring the same statistical properties as in the field. FD calculations are carried out with this media to provide realistic synthetic data of resistivity and GPR measurements. Conductivity variations as determined in the field generate significant variations of simulated Schlumberger sounding curves resulting in uncertainties of the inverted models. Even in pedologically homogeneous sandy soil, moisture pattern and resulting permittivity variations cause strong GPR diffractions as demonstated by FD calculations. This influences the detectability of small objects such as e.g. landmines or of large reflectors as e.g. the groundwater table. Conductivity variations as typical for soils showed to have a minor effect on GPR measurements than variations of permittivity. In summary, geostatistical analysis and simulation provide a powerful tool to simulate geophysical measurements under field conditions including soil heterogeneity which can be used to quantify the uncertainty of field measurements by geologic noise.
The present publication is intended to be a monograph on the family of Burmanniaceae. It is divided into three parts: General Part, Critical Part and Taxonomical Part. The first part, General Part, contains general remarks on the taxonomy, distribution and use of the family. The second part, Critical Part, contains general and geobotanical remarks on the genera of the family, whereas the third part, the Taxonomical Part, gives the determination keys to the tribes, subtribes, genera, sections, subsections and species, the description of these groups with literature, distribution and the indications of the types. New varieties, species and larger groups are described in the taxonomical part in foot-notes.
Shaped by some of the most dramatic tectonic events of the Cenozoic, the parts of southern and eastern Asia that have become known as the Oriental faunal region comprise vast areas of great geological complexity and ecological diversity. One of the four major groups of terrestrial elapid snakes in this region is the genus Bungarus. These nocturnal and predominantly ophiophagous snakes are widely known as kraits and are an important cause of snakebite mortality throughout their wide range that extends from Afghanistan to Vietnam and eastern China, and south to the Indonesian islands of Java and Bali. Although present on Borneo, kraits have not been found on any island of the Philippines, nor on Lesser Sunda Islands east of Bali. Despite their medical significance and the great importance of Bungarus toxins as tools in neuropharmacology, krait systematics and taxonomy have remained largely unstudied. Twelve species of Bungarus were recognized at the beginning of the present study. Many of these are rare in collections, and most aspects of their biology are unknown. While some species are highly distinct, most kraits are conservative morphologically, rendering molecular methods invaluable for the study of their diversity and biogeography. This study is the first to address the relationships within Bungarus and the historical biogeography of kraits based on molecular evidence. I inferred phylogeographic relationships based on analyses of new nucleotide sequences of the entire mitochondrial cytochrome b gene of 51 kraits and partial NADH dehydrogenase subunit 4 sequences of 40 kraits which I analyzed together with a representative sample of 32 published elapid and non-elapid outgroup taxa using Bayesian, maximum-likelihood, maximum-parsimony and neighbor-joining methods. I then used the recovered phylogeny to investigate the evolution of selected morphological characters and, together with collections-based geographical distribution information, in dispersal-vicariance analyses with models of variable taxonomic and biogeographic complexity. The phylogenetic analyses demonstrate that the current taxonomy of kraits does not adequately represent either the relationships or the genetic diversity in this genus. In contrast, I identified monophyletic groups that are congruent with recognized biogeographic units as well as extensive ecomorph evolution and morphologically cryptic speciation. The following additional conclusions are collectively supported by the mitochondrial phylogeny and morphological as well as biochemical synapomorphies: (1) Kraits are monophyletic with respect to the remaining taxa of the Elapidae; (2) Bungarus flaviceps and Bungarus bungaroides form the monophyletic sister clade of a clade formed by B. fasciatus, black-and-white-banded, and uniformly black taxa; (3) the remaining taxa are divisible into two sister clades, the South Asian species (Bungarus sindanus (Bungarus caeruleus, Bungarus ceylonicus)) vs. Himalayan, Burmese, Southeast and East Asian taxa; (4) within the latter, Burmese taxa form the sister clade to Southeast and East Asian taxa; (5) the widespread and medically significant species Bungarus candidus and Bungarus multicinctus are paraphyletic. The results of this study highlight the importance of vicariant geological events and sea level fluctuations for the cladogenesis of kraits. Events of particular importance in the evolution of kraits include the uplift of the Indo-Burman ranges (Arakan-Naga Hills) which separated black-and-white banded kraits in India and Southeast Asia, and the uplift of mountain ranges in Yunnan, China (e.g., the Gaoligong Shan), which coincided with lineage separation in two distantly related clades of kraits. Alternating dispersal and vicariance events due to Pleistocene climatic and sea level changes have caused complex phylogeographic patterns in kraits in Southeast Asia. Zones of contact between closely related evolutionary lineages of the B. candidus complex are identified in Thailand, Vietnam, and southern China (Hainan). Within this complex, two main clades are revealed. One includes populations from the Southeast Asian mainland and is in contact with B. multicinctus in southern China. The other consists of populations from Thailand, southern Vietnam, Java, and Bali. The phylogeny as well as genetic distances suggest a scenario in which a Pleistocene southward dispersal of B. candidus to Sumatra, Java, and Bali during times of low sea levels was temporarily interrupted by vicariant events (rising sea levels, especially flooding of the Malacca Strait between Sumatra and the Malay Peninsula, and of the Bali Strait between Java and Bali). In this context, the close phylogenetic relationship between haplotypes from southern Vietnam and those from Java and Bali suggests that "southern" B. candidus dispersed directly via colonization of the widely receded South Chinese Sea, and not by taking a detour via the Malay Peninsula and Thailand, which were already inhabited by other populations of B. candidus. Using these phylogenetic estimates as the framework for a study on the diversity and evolution of krait venom components, I applied biochemical and molecular genetic approaches to identify and quantify polypeptide and protein toxins in krait venom, focusing on the distribution and molecular evolution of alpha-bungarotoxin, an irreversible competitive antagonist of nicotinic acetylcholine receptors with an exceptionally high applied significance as a receptor probe. I was specifically interested in the medically relevant question of intraspecific and interspecific variability in toxin diversity, and whether receptor-binding postsynaptic toxins evolve at rates different from those of presynaptic neurotoxins like beta-bungarotoxin, which act by destroying the nerve terminal and are believed to exhibit hypervariable functional diversification due to an accelerated mode of molecular evolution. In the context of this question, I isolated and purified the major lethal neurotoxins from B. candidus venoms by sequential steps of liquid chromatography for structural and functional characterization studies. Cloning and sequence analysis of toxin-coding genomic DNAs showed that the gene encoding the alpha-bungarotoxin alanine-31 variant, originally isolated from B. multicinctus venom, is widely present and highly conserved in multiple populations of B. candidus and is expressed as the principal postsynaptic neurotoxin at least in Javan B. candidus. In addition to the widespread presence of genomic DNAs encoding the alpha-bungarotoxin alanine-31 variant, the present study also revealed the partial genes of three novel alpha-bungarotoxin isoforms in addition to the previously known alanine-31 and valine-31 variants, all of which share an invariant exon 3 coding region. While alpha-bungarotoxin is the principal postsynaptic neurotoxin of Taiwanese B. multicinctus and Javan B. candidus, the main postsynaptic neurotoxin of Thai B. candidus both by quantity and lethality was a novel polypeptide of similar toxicity with a mass of 8030 Da and 73 amino acid residues, whose characterization at the genetic and protein levels revealed a novel subgroup of krait neurotoxins, here named alpha-delta-bungarotoxins and represented by four sequences from Bungarus caeruleus and B. candidus. alpha-delta-Bungarotoxins share high sequence homology with alpha-bungarotoxins but the purified, 8030 Da alpha-delta-bungarotoxin-1 exhibits only reversible, low affinity binding to nicotinic receptors and high site-selectivity for the acetylcholine binding site at the alpha-delta-subunit interface of the receptor. These properties render alpha-delta-bungarotoxin not only the first snake long-chain neurotoxin with reversible binding and binding-site selectivity, but also an exciting natural tool with which to address structure-function relationships at the subunit interfaces of the human receptor. The results of comparisons of the number of non-synonymous nucleotide substitutions per nonsynonymous site (dN) to the number of synonymous nucleotide substitutions per synonymous site (dS) strongly suggest that positive selection is acting on exon 2 of the alpha-bungarotoxin and probably also of the alpha-delta-bungarotoxin genes. In addition, the numbers of nucleotide substitutions per site of intron (dI) compared to the dS value of the toxin-coding exon regions provide strong evidence for accelerated molecular evolution in exon 2 of alpha-delta-bungarotoxins —whose value of dI is only one-eighth of the value of dS—whereas the hypothesis of accelerated evolution is rejected for 13 unique genomic DNAs encoding five alpha-bungarotoxin isoforms from B. candidus and B. multicinctus....
This paper documents the methodology underlying the construction of a global database of gross foreign asset and liability positions for 153 countries over the period 1970 to 2004 and illustrates some key data characteristics. The data cover both inflows and outflows of capital and thus allow for an assessment of the degree of international financial integration. In addition to net foreign asset stocks, we also provide details on the composition of the main asset and liability categories, namely the foreign direct investment, equity investment and debt components. Finally, we report on valuation changes as one of the main sources of discrepancy between transaction-based capital flow data and stock values of investment positions. The dataset is available for download at www.ifk-cfs.de/fileadmin/downloads/data/cfs-icfd.zip. or http://publikationen.ub.uni-frankfurt.de/volltexte/2007/4855/original/cfs-icfd.zip JEL Classification: F21; F34; F32
In this paper we revisit medium- to long-run exchange rate determination, focusing on the role of international investment positions. To do so, we develop a new econometric framework accounting for conditional long-run homogeneity in heterogeneous dynamic panel data models. In particular, in our model the long-run relationship between effective exchange rates and domestic as well as weighted foreign prices is a homogeneous function of a country’s international investment position. We find rather strong support for purchasing power parity in environments of limited negative net foreign asset to GDP positions, but not outside such environments. We thus argue that the purchasing power parity hypothesis holds conditionally, but not unconditionally, and that international investment positions are an essential component to characterizing this conditionality. Finally, we adduce evidence that whether deterioration of a country’s net foreign asset to GDP position leads to a depreciation of that country’s effective exchange rate depends on its rate of inflation relative to the rate of inflation abroad as well as its exposure to global shocks. JEL Classification: F31, F37, C23
An evaluation scheme is presented in this paper which can be used to assess groundwater vulnerability according to the requirements of the European Water Framework Directive (WFD). The evaluation scheme results in a groundwater vulnerability map identifying areas of high, medium and low vulnerability, as necessary for the measurement planning of the WFD. The evaluation scheme is based on the definition of the vulnerability of the Intergovernmental Panel on Climate Change (IPCC). It considers exposure, sensitivity and the adaptive capacity of the region. The adaptive capacity is evaluated in an actors' platform, which was constituted for the region in the PartizipA ("Participative modelling, Actor and Ecosystem Analysis in Regions with Intensive Agriculture") project. As a result of the vulnerability assessment, 21% of the catchment area was classified as being highly vulnerable, whereas 73% has medium vulnerability and 6% has low vulnerability. Thus, a groundwater vulnerability assessment approach is presented, which can be used in practice on a catchment scale for the WFD measurement planning.
Global modelling of continental water storage changes : sensitivity to different climate data sets
(2007)
Since 2002, the GRACE satellite mission provides estimates of the Earth's dynamic gravity field with unprecedented accuracy. Differences between monthly gravity fields contain a clear hydrological signal due to continental water storage changes. In order to evaluate GRACE results, the state-of-the-art WaterGAP Global Hydrological Model (WGHM) is applied to calculate terrestrial water storage changes on a global scale. WGHM is driven by different climate data sets to analyse especially the influence of different precipitation data on calculated water storage. The data sets used are the CRU TS 2.1 climate data set, the GPCC Full Data Product for precipitation and data from the ECMWF integrated forecast system. A simple approach for precipitation correction is introduced. WGHM results are then compared with GRACE data. The use of different precipitation data sets leads to considerable differences in computed water storage change for a large number of river basins. Comparing model results with GRACE observations shows a good spatial correlation and also a good agreement in phase. However, seasonal variations of water storage as derived from GRACE tend to be significantly larger than those computed by WGHM, regardless of which climate data set is used.
Metabotropic glutamate receptor subtype 7 (mGluR7) belongs to the family of G-protein coupled receptors. mGluR7 is widely distributed in the brain and primarily localized at presynaptic terminals, where it is thought to regulate neurotransmitter release and synaptic plasticity. Studies have shown that the intracellular C-terminal tail of mGluR7 binds a variety of proteins in addition to trimeric G-proteins. These newly identified protein interactions are believed to play a key role in the synaptic targeting and G-protein dependent signaling of mGluR7. Protein interacting with C kinase 1 (PICK1), a PDZ-domain protein, is a strong interaction partner of mGluR7a. In order to investigate the role of PICK1 in the synaptic trafficking and signaling of mGluR7a, a knock-in mouse line in which the interaction of mGluR7a and PICK1 is disrupted was generated. Analysis of the mutant mice by immunocytochemistry and immunoelectron microscopy showed that the synaptic targeting and clustering of mGluR7a was not altered, indicating that PICK1 is not required for mGluR7a receptor membrane trafficking and synaptic localization. However, when the spontaneous synaptic activity of cerebellar granule cell cultures prepared from both wild-type and knock-in mice was monitored, and L-AP4 (400μm) was found to decrease the frequency, but not the amplitude, of spontaneous excitatory currents in wild-type neurons, while no effect of L-AP4 on spontaneous synaptic activity was observed in knock-in neurons. This indicates that PICK1 binding to the C-terminal region of mGluR7a plays an essential role in mGluR7a mediated G-protein signaling. We examined the threshold sensitivity for the convulsant pentetrazole (PTZ) in knock-in mice. It was found that mGluR7a knock-in mice had a greater sensitivity to PTZ than wild-type mice. Moreover, the surface parietal cortex EEG recordings of the mutant mice revealed spontaneous synchronous oscillation, or "spike-and-wave discharges" (SWD), which displayed similar characteristics to absence-like seizures. It was also observed that the knock-in mice responded to pharmacology as human absence epilepsy. These data suggests that the knock-in mice displayed the phenotype of absencelike epilepsy. Furthermore, the behavioral analysis of the mGluR7a knock-in mice showed no deficits in motor coordination, pain sensation, anxiety as well as spatial learning and memory, thus the interaction of mGluR7a and PICK1 appears not to contribute to these physiological processes. Taken together, our data provides evidence for an important role of PICK1 in Gprotein dependent signaling of mGluR7a, whereas PICK1 is not required for synaptic targeting and clustering of mGluR7a. Our results also provide an animal model of absencelike epilepsy generated by disruption of a single mGluR7a-PDZ interaction, thus creating a novel therapeutic target against this neurological disease.
The main subject of the thesis is the investigation of low-temperature-grown (LTG) GaAs-based photoconductive switches used in the generation of continuous-wave (CW) and pulsed terahertz (THz) radiation. The use of photoconductive switches based on low-temperature-grown GaAs proved to be a viable option in generating electromagnetic transients on a subpicosecond time-scale, corresponding to frequencies of ~1012 Hz (between microwave and far-infrared). The most appealing property of LTG-GaAs is the ultra-short carrier lifetime obtained by incorporation of a large number of As defects when GaAs is grown at low temperatures. However, the reason for poor THz emission efficiency (low CW-THz power lrvrls) is still up to this date not fully understood. The various reasons are to be found in both, optoelectronic properties of the active layer (photoconducting material) as well as in the device characteristics. The thesis focuses primarily on the limitation imposed to the performance of the THz emitters by the material of choice for the active layer (LTG-GaAs) and secondarily, on the impact of a particular emitter design on the THz radiation efficiency. In the beginning of the thesis one finds an ample overview on the electrical and optical properties of the LTG-GaAs material. A special chapter deals with the main features of current-voltage and CW-THz emission characteristics measured from a photoconductive antenna employed as photomixer. We observed deviations from the theoretical predictions of photomixing theory which were explained by considering the high-field electrons effects (velocity overshoot and elongation of the carrier trapping time). With the scope to provide a better understanding of the correlation between device and material properties when the LTG-GaAs material is integrated with a planar antenna (photoswitch), a special THz double-pulse technique (THz-pump and -probe) was implemented. The experimental results assisted by modeling of the double-pulse THz data provide a gainful insight into the ultrafast dynamics of the electrical field and photogenerated carriers. The outcome of the double-pulse experiments is the evidence for long-living carriers in the LTG-GaAs-based photoconductive antenna under applied bias, with a deleterious impact upon the emitter performance (especially for the CW case). Additionally, by measuring the THz transients generated by a constant laser pulse with and without a CW laser background illumination, we obtained further evidence of strong field-screening effects. This phenomenon was also attributed to the existence of long-living space-charge effects. For both cases (pulsed as well as CW) we derived the de-screening time constant. The principal conclusion of the present study is that, besides shortcomings imposed by the THz-circuitry, photomixers based on materials with traps (defects) exhibit great “affinity” for space-charge screening effects with cumulative and therefore long-lived deleterious impact upon device’s performance. An alternative would be the usage of a transient-time limited device where the response time is given by the carrier collection time, possibly with only one type of carrier responsible for THz signal generation.
As if to bear out the tenet of this study, the field of black British literature has been transformed enormously over the last ten years or so, while this book was in the making. And for myself, too, this has been a formative process. During this time I’ve been supported, challenged, and encouraged by more colleagues and friends than I can acknowledge here. ...
Constructive waterfalls
(1911)
The excavation of valleys by waterfalls is one of the best known and most effective processes by which rivers cut down the surface of the earth. The influence of waterfalls is usually regarded as solely destructive, and as always helping to lower the land. They undermine and cut backward the rock faces over which they fall : by this recession they excavate deep gorges ; and the existence of these gorges enables the adjacent country to be lowered to the level of the valIey floors. The waterfalls, moreover, empty any lakes they rnay reach in their retreat, while the ravines below the falls may drain the springs and thus desiccate the neighbouring hihlands. Observations in various countries had suggested to me that waterfalls may sometimes be constructive in stead of destructive, and that they may reserse their usual procedure, advancing instead of retreating, filling valleys instead of excavating them, and forrning alluvial plains and lakes instead of destroying them. The best illustrations I have seen of such advancing, constructive waterfalls are on some rivers of Dalmatia and Bosnia, where they occur in various stages of development. ...
Safety concerns associated with the use of viral vectors in gene therapy applications have attracted considerable attention towards the development of nonviral vectors as alternatives for DNA delivery. While nonviral vectors are commonly not associated with safety problems, they are still very inefficient compared to viral vectors, and require significant improvements to approach the efficiency of their viral counterparts. Meanwhile ligands or single-chain antibody fragments that bind to cell surface receptors for increased and/or specific cellular uptake, endosome escape activities, and nuclear localization sequences (NLSs) to enhance transport of plasmid DNA into the nucleus, have become available that can be incorporated into nonviral vectors to improve their efficacy. However, as gene delivery is a multistep process, the challenge is to incorporate multiple of these functional elements into a single nonviral vector system, while retaining their specific activities. A promising method to attach such entities to plasmid DNA is the use of multifunctional fusion proteins that bind to DNA through a DNA-binding domain. In principle, two types of DNA-binding domains/proteins can be used to anchor additional functional domains or peptides to a plasmid, namely sequence-specific DNA-binding domains, described in the first part of this thesis, or those that bind DNA independent of its sequence, exemplified in the second part of this work by a derivative of the human HMGB2 protein. The first fusion protein constructed and analyzed contained the E. coli LexA repressor as a sequence-specific DNA-binding domain. In addition, this DNA-carrier protein, termed TEL, included a bacterial translocation domain as an integrated endosome escape activity, and human TGF-a for specific targeting to the EGF-receptor (EGFR). TEL was expressed in E. coli and purified under both native and denaturing conditions. Purified, denatured TEL was refolded and subsequently shown to bind specifically to EGFR-expressing cells. However, inclusion of TEL in complexes of plasmid DNA and poly-L-lysine (pL) did not lead to increased gene delivery into EGFR-expressing COS-1 cells. Most likely this was due to the absence of DNA-binding activity of the LexA moiety in TEL. In contrast, native TEL was able to interact specifically with DNA. Nevertheless, since this interaction was rather weak, and refolding of denatured TEL had not resulted in functional activity of all of its protein domains, it seemed unlikely that fusion proteins containing LexA would exhibit gene transfer capabilities superior to those of similar DNA-carrier proteins previously constructed in our group. Further work therefore focused on the use of the E2C-Sp1C protein as an alternative sequencespecific DNA-binding domain. This artificial zinc-finger protein was fused to the single-chain antibody fragment scFv(FRP5), directed against the human ErbB2 growth factor receptor. The resulting 5-E2C fusion protein was expressed in E. coli and purified under native and denaturing conditions. Refolded and native 5-E2C were found to bind specifically to ErbB2-expressing cells, indicating that scFv(FRP5) in 5-E2C was functional in both preparations. In contrast, whereas refolded 5-E2C bound DNA only weakly, significant DNA binding was observed for native 5-E2C. In addition, it could not only be shown that the interaction of native 5-E2C with DNA containing its recognition sequence was specific, but also that this protein was able to bind DNA and recombinant ErbB2 simultaneously, demonstrating the functionality of both domains in native 5-E2C. Despite these encouraging results, the inclusion of native 5-E2C in pL- or polyethyleneimine (PEI)-DNA complexes did not lead to an (5-E2C-specific) enhancement of gene transfer efficiency, irrespective of the presence of the endosome-disruptive reagent chloroquine during transfection. In the second part of this thesis an alternative approach for the development of DNA-carrier proteins for nonviral gene delivery is described, based on human HMGB2, a DNA-binding protein without sequence specificity. HMGB2 contains an acidic C-terminus that has been found to decrease the affinity of the protein for DNA. Therefore, this C-terminal tail was deleted, resulting in an HMGB2-variant consisting of amino acids 1-186. HMGB2186, purified under native conditions from E. coli lysates, was able to interact with DNA and bound to the surface of different cell lines. Importantly, after binding to plasmid DNA HMGB2186 mediated gene delivery into COS-7 cells with higher efficiency than pL. In addition, HMGB2186-mediated gene transfer was strongly enhanced in the presence of chloroquine, indicating that the endocytic pathway was involved in cellular uptake. To improve internalization and intracellular routing of HMGB2186 as a DNA-carrier, a derivative containing the TAT47-57 cell-penetrating peptide (CPP), reported to facilitate cell entry independent of endocytosis, was constructed. Since this peptide also contains an NLS, in addition an HGMB2186-variant containing the SV40-NLS was constructed to investigate the effect of a peptide that has only nuclear localizing properties. Interestingly, the resulting TAT-HMGB2186 and SV40-HMGB2186 fusion proteins displayed DNA-binding activities similar to HMGB2186, but mediated gene delivery into different cell lines clearly more efficiently than the parental molecule. Furthermore, the efficacy of both fusion proteins was enhanced markedly in the presence of chloroquine, an indication that endocytosis was involved in the transfection process mediated by these proteins. This suggests that the increased transfection efficiency observed for TAT-HMGB2186 was more likely due to the NLS function present in the TAT47-57 peptide, rather than to its ‘cell penetrating properties’. Finally, the incorporation of functional peptides derived from human proteins into HMGB2186 was investigated. An uncharged CPP originating from Kaposi-FGF, reported to facilitate efficient cellular uptake of fused protein domains in an endocytosis-independent manner, was fused to HMGB2186 together with the SV40-NLS. Interestingly, the resulting KSV40-HMGB2186 fusion protein bound DNA similarly as previously tested DNA-carrier proteins, but did not mediate enhanced transfection compared to HMGB2186. In addition, the importin-b-binding (IBB) domain derived from human importin-a2 was investigated as a component of a DNA-carrier protein. Since the IBB domain can function as an NLS, it was fused to HMGB2186 resulting in the DNA-carrier protein IBBHMGB2186. Although IBB-HMGB2186 bound DNA in a similar manner as the other HMGB2186-derivatives, gene delivery mediated by IBB-HMGB2186 was only as effective as HMGB2186 mediated transfection, suggesting no significant role of the IBB domain. However, addition of chloroquine resulted in a remarkable enhancement of IBB-HMGB2186-mediated gene transfer, which was now more efficient than with any other HMGB2186-variant tested, and not much lower than gene transfer mediated by PEI, one of the most efficient transfection reagents available to date. To enhance nonviral gene delivery even further, the HMGB2186-based DNA-carrier proteins described in this thesis might now serve as building blocks for novel fusion proteins that include additional complementing activities. In this respect it seems particularly promising that, under conditions of effective end some escape, IBB-HMGB2186, which consists entirely of protein domains of human origin, was the most efficient of all proteins tested in this work.
On seatangle tent
(1869)
RcsB is a central transcriptional regulator in enteric bacteria involved in exopolysaccharide (EPS) biosynthesis, in cell division, in the expression of osmoregulated genes, and regulates at least 20 other genes and operons. It is a member of a phosphorelay system and signal transfer is mediated by phosphorylation through the RcsC/YojN phosphorelay. RcsB proteins modified with the phosphorylation mimic BeF3- as shown by its conformational changes and DNA binding properties and resulted phosphorylated RcsB derivatives with sufficient stability. Both, the wild type RcsB protein and the mutant RcsBD11A could be modified with BeF3-. Non-phosphorylated RcsB has been shown to bind as a heterodimer with the coinducer RcsA at the conserved RcsAB box in Rcs regulated promoters. In this study, it has been shown that the modification of RcsB by BeF3 - (I) has a negative effect on its homodimerization, (II) abolishes the complex formation of RcsAB with the RcsAB box as shown by the EMSA and SPR technique. All the effects were found to be reversible by increasing the NaF concentration in the assays presumably leading to the formation of the inactive BeF4 2- salt. This hypothesis of RcsB being modified by BeF3- was also supported by other phosphodonors like ATP and acetyl phosphate, both of them showed the same negative effect on DNA binding by RcsAB heterodimer giving evidence that BeF3- could be used as a phosphorylation mimic. In addition, the phosphorylation mimic BeF3- was found to be a better phosphorylating agent than ATP and acetyl phosphate. This is the first evidence that phosphorylation of RcsB might have a negative effect on the activation of RcsAB regulated operons. Autophosphorylation of RcsB proves that it has the ability to take up phosphoryl groups and the mutant protein also become autophosphorylated with less efficiency or stability than the wild type protein. RcsB probably takes up phosphoryl groups through RcsC -> YojN -> RcsB phosphorelay pathway. To study the interaction among the proteins in this pathway, fluorescence spectroscopy, NMR spectroscopy, and an in vivo ß galactosidase assay were performed by using two domains of RcsC (T-RcsC and R-RcsC), HPt domain of the protein YojN, and RcsB. The interactions between R-RcsC/YojN-HPt and YojN-HPt/RcsB supports the proposed pathway of phosphorylating RcsB. RcsB might also be phosphorylated by YojN-HPt that is phosphorylated by other sensor kinase other than RcsC in a cross-talk mechanism. The phosphorylation of RcsB by YojN-HPt probably has the same negative effect on cps induction as obtained with BeF3 - effect on DNA binding by RcsAB heterodimer.
The biomarker record in two different lakes in central Europe, Lake Albano and Lake Constance, is used to reflect environmental changes and lake system response during the Late Glacial and Holocene. Extractable organic compounds in lake sediments, which can be assigned to their biological source (biomarkers) function as fingerprints of past aquatic or land plant organisms. Using gas chromatography coupled with mass spectrometry, 21 different biomarkers (predominantly steroids and triterpenoids) as well as a variety of n-alkanes, nalkanols, and n-alkanoic acids could be identified in the sediment records of Lake Albano and Lake Constance. In the Holocene sediments of Lake Albano, the distribution of biomarkers such as dinosterol (dinoflagellates), isoarborinol, and diplopterol (aquatic organisms) indicate three biomarker zones: The period between 0-3,800 years BP (zone 3) is characterized by high concentrations of these biomarkers and others such as tetrahymanol and diploptene. Conversely, zone 2 (3,800-6,500 years BP) shows very low concentrations of all autochthonous biomarkers. In zone 1 (6,500–11,480 years BP), dinosterol, isoarborinol, and diplopterol range on a relatively high level, whereas diploptene and tetrahymanol display comparatively low concentrations. The results suggest at least two distinct changes in the predominance of primary producers during the Holocene, which are related to changes in the lake system such as lake mixing and water column stratification. This interpretation is consistent with previous investigations of Lake Albano sediments including pigment and hydrogen index data (Ariztegui et al., 1996b; Guilizzoni et al., 2002). Allochthonous biomarkers such as long-chain n-alkanes, amyrenones and friedelin indicate a development from forest to a more open landscape from 6,000 and 5.000 years BP, respectively. After a period of high concentrations during the first half of the Holocene, all biomarkers derived from deciduous trees exhibit relatively low values until around 1,000 years BP. Again, this is consistent with results from previous pollen investigations (Ariztegui et al., 2000). The sediment core from Upper Lake Constance comprises the Late Glacial and Holocene. It was analysed for biomarkers and inorganic tracers in order to compare the biomarker results with other proxy data from the same core. Magnetic susceptibility (MS) was measured to get a high-resolution stratigraphic framework of the core and to obtain further information about changes of the proportions of allochthonous and autochthonous input. Enhanced concentrations and accumulation rates of dinosterol (biomarker for dinoflagellates) and biogenic calcite give evidence of increasing lake productivity at the beginning of the Holocene followed by a decrease in bioproductivity after around 7,000 years BP. Younger Dryas sediments are characterized by low amounts of both dinosterol and biogenic calcite indicating a low productivity. The comparison of the concentrations and accumulation rates of b-sitosterol and stigmastanol with parameters reflecting lake productivity suggests that both steroids in Lake Constance sediments are mainly derived from terrigenous sources. Biomarkers as well as concentrations and accumulation rates of allochthonous inorganic compounds such as titanium, magnesium and strontium indicate a slightly enhanced allochthonous input after 8,500 years BP. Significant increase of erosive matter input from enhanced soil erosion is not observed before 4,000 years BP. This can be attributed to the combined effects of precipitation increase as a result of climatic deterioration and anthropogenic deforestation which is consistent with observations from other lakes in Central Europe. The MS record of Lake Constance confirms these results by tracing the climatically induced shifts of more intense bioproduction (low MS caused by increased calcite deposition) during the ‘climatic optimum’. This is followed by increasing input of terrigenous sediment compounds during colder and wetter periods which lead to higher MS values in the lake sediments. The occurrence of tetrahymanol in Lake Constance sediments questions the unambiguous use of tetrahymanol as an indicator for water column stratification. Anaerobic organic macroaggregates within the oxygenated, photic zone of the water column have to be considered as a possible living space for anaerobic microorganisms containing tetrahymanol. The direct comparison of two very different lakes Albano and Constance with respect to biomarkers indicating climate or environmental change provides a contribution to the recent biomarker research for a better understanding of biomarkers in lacustrine sediments.
P2X receptors are ligand (ATP)-gated ion channels that open an intrinsic cation permeable pathway in response to extracellular ATP released from both neuronal and non-neuronal cells. P2X receptors are abundantly distributed and mediate a wide variety of physiological functions, ranging from fast synaptic transmission in the central, peripheral, and enteric nervous system, to proinflammatory cytokine release from immune cells. The primary aim of this work was to elucidate the pathway that leads to the finally assembled trimeric P2X receptors, including the assessment of a possible role of ER chaperones and folding factors in this process. Additionally, the study was conducted to investigate the various ER quality control processes involved in the selection of “properly folded and assembled” P2X receptors that are suitable for the surface expression.
The heat stress (hs) response is universal to all organisms. As the cell senses increase in temperature, heat stress transcription factors (Hsfs) are activated to upregulate the expression of a number of genes encoding heat stress proteins (Hsp) which act as molecular chaperones to protect cells against heat damages. In higher plants, the phenomenon seems to be unusually complex both at the level of Hsfs and Hsps (e.g., 21 Hsf encoding genes in Arabidopsis and at least 17 in tomato). Upon prolonged hs, another characteristic property of plant cells is the assembly of large cytosolic aggregates called heat stress granules (HSG), which are composed of Hsps, HsfA2, RNA and RNA-binding proteins. The present work was aimed to understand plant hs response using tomato as a model system. To study the function of tomato Hsfs in their native system, we generated transgenic tomato lines altered in expression of HsfA1, HsfA2, and HsfB1. Tomato plants with 10-fold overexpression of HsfA1 (OE plants) were characterised by integration of a single HsfA1 expression cassette, whereas the plants harbouring a tandem inverted repeat (IR) of the cassette showed cosuppression of HsfA1 (CS plants). The lack of HsfA1 expression in CS plants results from posttranscriptional gene silencing connected with the formation of small interfering RNA (siRNA). Under normal growth conditions, major developmental features were similar for wild-type (WT), OE and CS plants. However, in contrast to the former two, CS plants and fruits were extremely sensitive to elevated temperature because hs-induced synthesis of major chaperones and Hsfs was strongly reduced or lacking. Despite the complexity of the plant Hsf family, the function of tomato HsfA1 is unique as master regulator of induced thermotolerance. On the other hand, maintenance of essential chaperones in CS plants during seed development suggests involvement of other Hsfs and/or transcription factor(s). HsfB1 and HsfA2 transgenic tomato plants, unaffected in thermotolerance, further supported the function of HsfA1 as the major factor regulating hs-inducible genes. Hs87 independent phenotypes of plants with altered expression of HsfB1 indicates developmental role of this Hsf. Using transient reporter assays with mesophyll protoplasts from WT tomato, we demonstrated that plasmids encoding Hsfs A1, A2 and A3 were well expressed which could function as activators for reporter gene expression. However, in protoplasts derived from CS plants, plasmids encoding HsfA2 and HsfA3 were normally expressed but even higher amounts of HsfA1 expression plasmids were completely silenced. Therefore, silencing of HsfA1 in CS plants was also reproduced in its mesophyll protoplasts. Lacking thermotolerance in CS protoplasts could be restored after transformation with expression plasmids encoding functionally equivalent HsfA2 or HsfA3 resulting in (i) expression of chaperones, (ii) survival of the cells at otherwise lethal temperature, (iii) thermoprotection of firefly luciferase, and (iv) assembly of heat stress granules (HSGs). The strong silencing caused by an IR in CS plants opened the possibility of a broad use of RNAi for gene knock-down also in the transient system of mesophyll protoplasts. Using this technology, we attempted to dissect essential components of thermotolerance and HSG assembly. We demonstrated the previously reported function of chaperones such as Hsp70 and Hsp101, and could discriminate the in vivo chaperone functions of different isoforms of Hsp20 and Hsp70 proteins. Hsp17-CI, Hsp70 (hs-inducible isoforms), and Hsp101 are absolutely essential chaperones for thermotolerance in plants. Furthermore, the results also show that despite Hsp17-CI and -CII being major components of HSG complexes, they are dispensable for assembly of these complexes. Based on these results, it is proposed that in the transient protoplast system an approach with gene-specific IRs can be used to discriminate functions of closely related isoforms among protein-families and to dissect complex protein networks.
Vascular occlusive diseases are one of the leading mortality causes in westernised countries. Occlusions of one of the major arteries can be overcome without devastating consequences provided a timely induction of compensating collateral arteries occurs. Perhaps the most outstanding feature of collateral vessel growth is the proliferation of smooth muscle cells (SMCs). Understanding the molecular mechanisms and identifying key molecular players of SMC proliferation would contribute significantly to the development of efficient therapies to intervene with all processes involving neointima formation, including collateral growth. mRNA and protein coding for co-transcription factor Egr1 were found to be up-regulated in growing collateral vessels 6, 12 or 24 hours following femoral artery ligation in mice. Since Egr1 is required for SMC proliferation in vitro and in vivo and likely to be implicated in the initiation of collateral artery growth, the key signalling mediators regulating Egr1 expression specifically in proliferating vascular SMCs were investigated. Northern blot and Western blot analysis revealed a strong up-regulation of Egr1 within 2 hours of stimulation with PDGF-AB and FGF-2. These two potent SMC mitogens involved in neointima formation were used to stimulate vascular SMCs not only to delineate the regulators of Egr1 expression but also to identify additional key mediators of SMC proliferation. FGF-2 but not PDGF-AB led to a drastic reduction of desmin amount in proliferating SMCs, correlating closely with the phenotypic modulation of SMCs in vivo. Both growth factors triggered a dramatic increase in DNA-synthesis rate with a concomitant loss of p27 exp Kip1. Stimulation with PDGF-AB and FGF-2 triggered a rapid and transient activation of PDGFRβ and FGFR1 respectively, thus providing the basis for activation of down-stream targets. Analysis of an array of signalling pathways demonstrated a strong activation of the Ras-Raf-MEK-ERK cascade in response to both factors as measured by the level of phosphorylation of prominent members MEK, ERK1/2 and c-Myc. SAPK/JNK and p38, which also belong to the superfamily of MAP kinases, did not become activated following stimulation with either PDGF-AB or FGF-2. The analysis of various PKC isoforms identified PKCδ and PKCθ to be the key mediators of PDGF-AB- and FGF-2-induced mitogenesis in proliferating SMCs. Whereas PDGF-AB potently stimulated PKB/Akt with concomitant GSK3β phosphorylation, FGF-2-induced inactivation of GSK3β was independent of PKB/Akt. Specific inhibition in order to evaluate the contribution of individual pathways to Egr1 expression and vascular SMC proliferation revealed that inhibition of the Raf-MEK-ERK module by UO126 completely abolished DNA-synthesis and Egr1 expression without a compensation by alternative pathways. Surprisingly, inhibition of PI3K led to a switch to the mitogenic RafMEK-ERK signalling cascade which resulted in an augmented Egr1 expression. In conclusion, in porcine vascular SMCs, activation of the Ras-Raf-MEK-ERK signalling module appears to be the main prerequisite for Egr1 expression and DNA synthesis induction in response to PDGF-AB and FGF-2 whereas related kinases SAPK/JNK and p38 play no significant role. Inhibition of the PI3K-Akt cascade represents an alternative way to activate ERK1/2 and induce Egr1 expression. Whereas MEK is the central regulator of mitogenic effects in proliferating vascular SMCs, the PI3K-Akt pathway most likely exerts survival function. Inactivation of MEK by its specific inhibitors identified hyperphosphorylation as ayet unknown mechanism of kinase inhibition.
Summary and Outlook The aim of this work was the investigation of the Mn2+ binding sites in hammerhead and the Diels-Alder ribozymes. This project consists of three main topics. In the first part quantification and structural characterization of Mn2+ binding sites in the m- and the tsHHRz using Electron Paramagnetic Resonance (EPR) spectroscopy are described. The second part summarizes the newest results obtained for the cleavage activity of both mand tsHHRzs in the presence of different Mg2+ and Mn2+ and Na+ ion concentrations using the new method with fluorescent-labeled RNAs. Here the influence of neomycin B on the structure of Mn2+ binding pockets and on the catalytic activity of both HHRzs is discussed. In addition, a possible role of Mn2+ ions is suggested from correlation of the EPR data with the kinetic results. The last chapter is devoted to quantification and differentiation of Mn2+ binding sites of the Diels-Alder ribozyme using continuous wave (cw) EPR experiments in solution. In this work EPR spectroscopy was used to study the binding of Mn2+ ions to the cis tsHHRz and to compare it with the binding to the trans mHHRz and to the Diels-Alder ribozyme. Cw EPR measurements showed that the tsHHRz possesses a single highaffinity Mn2+ binding site with a KD of < 10 nM at a NaCl concentration of 0.1 M. This dissociation constant is three orders of magnitude smaller than the KD determined for the single high-affinity Mn2+ site in the mHHRz (KD = 4.4 μM). The measurements of catalytic activity have been performed using fluorescent-labeled RNAs. Compared to the mHHRz, the cis tsHHRz cleaves up to 20-fold faster in the presence of Mg2+/Mn2+ ions with no saturation of the cleavage rates at high metal(II) ion concentrations. This is in good agreement with the last investigations on the trans tsHHRz (Nelson et al. 2005). Thus, the much stronger Mn2+ binding and higher cleavage activity were attributed to the interaction between the two external loops of the tsHHRz which reduces the RNA dynamics and traps the Mn2+ in the tightly folded conformation. Intriguingly, according to the EPR studies the binding constants for Mn2+ ions are several orders higher than the concentration of Mn2+ ions required for the catalytic activity (mHHRz: KD = 4.4 ± 0.5 μM and the Mn2+ concentration required to achieve half of the maximum cleavage rate [Mn2+]1/2 = 4.1 ± 0.6 mM respectively). Therefore, strongly bound Mn2+ ions seem to be needed for the folding of the HHRz, whereas weakly bound metal(II) ions are required to achieve full catalytic activity, and may be directly involved in catalysis. A comparison between the Electron Spin Echo Envelope Modulation (ESEEM) and Hyperfine Sublevel Correlation (HYSCORE) spectra of m- and tsHHRz demonstrates that both binding sites in HHRzs are structurally very similar. This suggests that the Mn2+ is located in both ribozymes between the bases A9 and G10.1 of the sheared G•A tandem basepair, as shown previously and in detail for the mHHRz (Vogt and DeRose 1998, Schiemann et al. 2003). However, the hyperfine spectra of the tsHHRz with 15N labeled G10.1 revealed no difference in comparison with the ones with 14N. This leads to an interpretation that the Mn2+ binding sites in both ribozymes are not identical. In addition, aminoglycoside antibiotic neomycin B inhibits the cleavage activity of both despite of the fact that it displaces the high-affinity Mn2+ ion only from the mHHRz. Hence, binding of neomycin B to the m- and the tsHHRzs probably occurs at different sites and neomycin B displaces only loosely bound Me2+ ions from the tsHHRs, whereas in the mHHRz both the high-affinity ion and the weakly bound ions are replaced. Therefore, it cannot be excluded that weakly bound Mg2+/Mn2+ ions, together with looploop interactions, induce a structural rearrangement which brings the high-affinity ion closer to the cleavage site. In the case of the Diels-Alder ribozyme it possesses five Mn2+ binding sites with KD = 0.6 ± 0.2 μM in solution under conditions where it is catalytically active. The competition experiment with Cd2+ allows to distinguish three different types of Mn2+ binding sites in the Diels-Alder ribozyme including inner-sphere monomeric Mn2+, monomeric Mn2+ bound through water-mediated contacts and electronically coupled dimeric Mn2+. Three Mn2+ ions are more strongly bound to the ribozyme via inner-sphere contacts, whereas two other Mn2+ ions form water-mediated outer-sphere contacts with the nucleotides of the ribozyme. The inner-sphere Mn2+ with the highest affinity and the fourth Mn2+ ions added to the ribozyme form a dimer with a Mn2+-Mn2+ distance of ~6 Å (as arises from simulations). Moreover, an addition of the product analog inhibitor (AMDA) to the [Diels-Alder ribozymes/ Mn2+] complex shows no conformational changes in the Mn2+ binding pockets. This is in good agreement with the recent studies which suggest that the Diels-Alder ribozyme is preorganized (Keiper et al. 2004). Some considerations on the evolution of the project (Outlook) There may be several venues of continuation of this project, which exploit on unique combination of EPR experiments and biochemical studies on RNA. This combination may allow us to significantly contribute to understanding of metal role in HHRz catalysis. Since the tsHHRz possesses the high affinity Mn2+ binding site (Kd < 10 nM) it creates a possibility to find conditions where the structural site is occupied by Mn2+, while catalytic sites are occupied by Mg2+ ions. If these conditions will be established by EPR titration, a set of standard biochemical experiments may be designed to look at the kinetic of cleavage and differentiate the “structural” and catalytic effects. The other experiment would be to look at the Mn2+ binding site in the tsHHRz in comparison with P1 and P1/P2 complexes and compare the results with the ones for the mHHRz. No matter the answer, P1 can be used as a simpler model to study the effect of tertiary structure on Mn2+ binding. A set of the tsHHRz mutants can be created to observe the mutations affect on Mn2+ binding sites, Mn2+ affinity and correlate the data with the kinetic analysis. FRET-based kinetic assay with fluorophore pairs on P1 and P2 can be designed for the kinetic experiments. Having this system one will be able to perform kinetic measurements 100-fold faster comparing to standard gel procedures (everything will be done in 96-wells). By manipulating the lengths and the sequence of P2 we most likely will be able to use FRET assay for the chemical step analysis (provided Kd > k2), and measure it using stop-flow system with time resolution of microseconds. And finally, one will be able to quantitatively measure the effect of neomycin B on the tsHHRz. Another interesting possibility would be to look at the state of metal(II) in the tsHHRz – enzyme alone (dissociated product) and in the enzyme-product complex and compare with the full-length tsHHRz. It will provide the information about the local rearrangements upon catalysis and the role of metal(II) ions. Furthermore, additional pulse-EPR experiments using 15N labeling have to be performed in order to reveal the location of the high-affinity Mn2+ binding site in the tsHHRz. Additionally, paramagnetic Mn2+ ions can be localized within the global fold of HHRzs using PELDOR and site-directed spin labeling. Further characterization of the high-affinity binding site in the tsHHRz can be performed using high-field ENDOR measurements in order to obtain the 14N and 31P tensors.
Unlimited self-renewal is an absolute prerequisite for any malignancy, and is the ultimate arbiter of the continuous growth and metastasis of tumors. It has been suggested that the self-renewal properties of a tumor are exclusively contained within a small population, i.e., the so-called cancer stem cells. Enhanced self-renewal potential plays a pivotal role in the development of leukemia. My data have shown that APL associated translocation products PML/RARalpha and PLZF/RARalpha increased the replating efficiency of mouse lin-/Sca1+ hematopoietic stem cells (HSCs). This effect is partly mediated by induction of gamma–catenin which is an important mediator of the Wnt signaling pathway and has been shown to be up regulated by the AML associated translocation products(AATPs). Suppression of gamma–catenin by siRNA can abrogate the increased replating efficiency induced by AATPs. Transduction of gamma–catenin in lin-/Sca1+ HSCs led to increased replating efficiency and the expression of stem cell markers Sca1 and c-kit. Additionally it induced accelerated cell cycle progression of mouse bone marrow HSCs. Transduction/transplantation mouse models have shown that ectopic expression of gamma–catenin in HSCs led to acute myeloid leukemia without maturation. These data suggest important roles of Wnt signaling pathway in the leukemogenesis induced by PML/RARalpha, PLZF/RARalpha and AML1/ETO. In contrast to AATPs, CML and Ph+-ALL associated translocation products p185(BCR-ABL) and p210(BCR-ABL) did not affect the self-renewal potential of hematopoietic stem/progenitor cells. However my studies indicated that their reciprocal translocation products p40(ABL/BCR) and p96(ABL/BCR) actually increased the replating efficiency of hematopoietic stem/progenitor cells. The effect is stronger when induced by p96(ABL/BCR) than by p40(ABL/BCR). It is very intriguing that p96(ABL/BCR) can activate Wnt signaling and up regulate the expression of HoxB4. Transduction/transplantation mouse model has shown that p40(ABL/BCR) and p96(ABL/BCR) both have their own leukemogenic potential. Given the fact that leukemic stem cells maintain the growth of tumor and are the origin of relapse, the cure of leukemia is dependent on the eradication of the leukemic stem cell and abrogation of aberrantly regulated self-renewal capability. Both t-RA and As2O3 have been shown to induce complete remission in APL patients with PML/RARalpha translocation product. However, t-RA as a single agent achieves completeremission (CR) but not complete molecular remissions (CMR). Therefore, virtually all patients will experience a relapse within a few months. In contrast to t-RA, As2O3 as a single agent is able to induce CR as well as CMR followed by long-term relapse-free survival in about 50% of APL patients even if relapsed after treatment with t-RA-containing chemotherapy regimens. Nothing is known about the mechanisms leading to the complete different clinical outcomes by the two compounds although both have been shown to induce differentiation of blast cells, proliferation arrest, induction of apoptosis and degradation of PML/RARalpha. We investigated the effect of t-RA and arsenic on PML/RARalpha-expressing cell population with stem cell capacity derived from the APL cell line NB4 as well as Sca1+/lin- murine bone marrow cells. We found that t-RA did not reduce the replating efficiency in PML/RARalpha- and PLZF/RARalpha-infected Sca1+/lincells whereas it selected small compact colonies representing very early progenitor cells. T-RA was unable to reduce the capacity to form colony forming units-spleen (CFU-S) of Sca1+/lin-cells expressing PML/RARalpha, additionally t-RA did not impair the capability of engraftment of NB4 cells in NOD/SCID mouse. On the contrary to t-RA, As2O3 abolished the aberrant self-renewal potential of Sca1+/lin- cells expressing PML/RARalpha. As2O3 not only abolished the replating efficiency of PML/RARalpha positive cells but also completely abrogated the ability of PML/RARalpha-positive HSC to produce CFU-S in vivo. On the contrary to As2O3, t-RA increased the absolute cell number and the percentage of cells in the side population with respect to the whole cell population in NB4 cells. Taken together these data suggest that arsenic but not all-trans retinoic acid overcomes the aberrant stem cell capacity of PML/RARalpha positive leukemic stem cells. My data prove for the first time that there is a direct relationship between the capacity of compounds to effectively target the LSC and their capacity to eradicate the leukemia, and, thereby, to induce complete molecular remission and long-term relapse-free survival. Thus, in order to increase the curative potential of leukemia therapies, future studies need to include the effect of given compounds on the stem cell compartment to determine their ability to eradicate the LSC.
The experience of pain is mediated by a specialized sensory system, the nociceptive system. There is considerable evidence that the cGMP/cGMP kinase I (cGKI) signaling pathway modulates the nociceptive processing within the spinal cord. However, downstream targets of cGKI in this context have not been identified to date. In this study we investigated whether cysteine-rich protein 2 (CRP2) is a downstream effector of cGKI in the spinal cord and is involved in nociceptive processing. Immunohistochemistry of the mouse spinal cord revealed that CRP2 is expressed in superficial laminae of the dorsal horn. CRP2 is colocalized with cGKI and with markers of primary afferent C fibers. Importantly, the majority of CRP2 mRNA-positive dorsal root ganglion (DRG) neurons express cGKI and CRP2 is phosphorylated in a cGMP-dependent manner. To elucidate the functional role of CRP2 in nociception, we investigated the nociceptive behavior of CRP2-deficient (CRP2-/-) mice. Touch perception and acute thermal nociception were unaltered in CRP2-/- mice. However, CRP2-/- mice showed an increased nociceptive behavior in models of persistent pain as compared to wild type mice. Intrathecal administration of cGKI activating cGMP analogs increased the nociceptive behavior in wild type but not in CRP2-/- mice, indicating that the presence of CRP2 was essential for cGMP/cGKI-mediated nociception. These data indicate that CRP2 is a new downstream effector of cGKI-mediated spinal nociceptive processing and point to an inhibitory role of CRP2 in the generation of inflammatory pain.
cGMP- and cAMP-dependent protein kinases (cGK and cAK) mediate the inhibitory effects of endothelium-derived messenger molecules nitric oxide and prostacyclin on platelets. To understand the mechanisms involved in platelet inhibition we searched for new substrates of cGK and cAK. We identified Rap1GAP2, the only GTPase-activating protein of Rap1 in platelets. Rap1 is a guanine-nucleotide binding protein that controls integrin activity, platelet adhesion and aggregation. Rap1GAP2 is required to turn over Rap1-GTP to Rap1-GDP resulting in the inactivation of integrins and reduced cellular adhesion. Using phospho-specific antibodies we demonstrate phosphorylation of endogenous Rap1GAP2 on serine 7 by cGK and cAK in intact platelets. Yeast-two-hybrid screening revealed an interaction of the phosphoserine/-threonine binding adapter protein 14-3-3 with Rap1GAP2, and we mapped the 14-3-3 binding site to the N-terminus of Rap1GAP2 close to the cGK/cAK phosphorylation site. We could show that 14-3-3 binding to Rap1GAP2 requires phosphorylation of serine 9. Platelet activation by ADP and thrombin treatment induces Rap1GAP2 serine 9 phosphorylation and enhances the attachment of 14-3-3 to Rap1GAP2. In contrast, phosphorylation of serine 7 by cGK/cAK leads to the detachment of 14-3-3. Furthermore, Rap1GAP2 serine 7 phosphorylation correlates with the inhibition of Rap1-GTP formation by cGMP and cAMP in platelets. Cell adhesion experiments provide additional evidence that Rap1GAP2 is activated by the detachment of 14-3-3. Point mutants of Rap1GAP2 deficient in 14-3-3 binding inhibit Rap1-mediated cell adhesion significantly stronger than a Rap1GAP2 mutant that binds 14-3-3 constitutively. Our findings define a novel regulatory mechanism that might contribute to both platelet activation and endothelial inhibition of platelet adhesion and aggregation.
Oxidative stress attenuates the NO-cGMP pathway, e.g. in the vascular system, through scavenging of free NO radicals by superoxide O2•-, by inactivation of soluble guanylyl cyclase (sGC) via oxidation of its central Fe2+ ion, and by down-regulation of sGC protein levels. While the former pathways are well established, the molecular mechanisms underlying the latter are still obscure. Using oxidative sGC inhibitor ODQ we demonstrate rapid down-regulation of sGC protein in mammalian cells. Co-incubation with proteasomal inhibitor MG132 results in accumulation of ubiquitinated sGC whereas sGC activator BAY 58–2667 prevents ubiquitination. ODQ-induced down-regulation of sGC is mediated through selective ubiquitination of its b subunit, and BAY 58–2667 abrogates this effect. Ubiquitination of sGC-b is dramatically enhanced by E3 ligase CHIP. Our data indicate that oxidative stress promotes ubiquitination of sGC b subunit through E3 ligase CHIP, and that sGC activator 58–2667 reverts this effect, most likely through stabilization of the heme-free b subunit. Thus the deleterious effects of oxidative stress can be counter-balanced by an activator of a key enzyme of vascular homeostasis.
Much has been written on the success of the Indian software industry, enumerating systemic factors like first-class higher education and research institutions, both public and private; low labour costs, stimulating (state) policies etc. However, although most studies analyzing the 'Indian' software industry cover essentially the South (and West) Indian clusters, this issue has not been tackled explicitly. This paper supplements the economic geography explanations mentioned above with the additional factor social capital, which is not only important within the region, but also in transnational (ethnic) networks linking Indian software clusters with the Silicon Valley. In other words, spatial proximity is complemented with cultural proximity, thereby, extending the system of innovation. The main hypothesis is that some Indian regions are more apt to economic development and innovation due to their higher affinity to education and learning, as well as, their more general openness, which has been a main finding of my interviews. In addition, the transnational networks of Silicon Valley Indians seem to be dominated by South Indians, thus, corroborating the regional clustering of the Indian software industry. JEL Classifications: O30, R12, Z13, L86
Bypassing of DNA lesions by damage-tolerant DNA polymerases depends on the interaction of these enzymes with the monoubiquitylated form of the replicative clamp protein, PCNA. We have analyzed the contributions of ubiquitin and PCNA binding to damage bypass and damage-induced mutagenesis in Polymerase {eta} (encoded by RAD30) from the budding yeast Saccharomyces cerevisiae. We report here that a ubiquitin-binding domain provides enhanced affinity for the ubiquitylated form of PCNA and is essential for in vivo function of the polymerase, but only in conjunction with a basal affinity for the unmodified clamp, mediated by a conserved PCNA interaction motif. We show that enhancement of the interaction and function in damage tolerance does not depend on the ubiquitin attachment site within PCNA. Like its mammalian homolog, budding yeast Polymerase {eta} itself is ubiquitylated in a manner dependent on its ubiquitin-binding domain.
To facilitate the measurement of intramolecular distances in solvated RNA systems, a combination of spin-labeling, electron paramagnetic resonance (EPR), and molecular dynamics (MD) simulation is presented. The fairly rigid spin label 2,2,5,5-tetramethyl-pyrrolin-1-yloxyl-3-acetylene (TPA) was base and site specifically introduced into RNA through a Sonogashira palladium catalyzed crosscoupling on column. For this purpose 5-iodouridine, 5-iodo-cytidine and 2-iodo-adenosine phosphoramidites were synthesized and incorporated into RNA-sequences. Application of the recently developed ACE (R) chemistry presented the main advantage to limit the reduction of the nitroxide to an amine during the oligonucleotide automated synthesis and thus to increase substantially the reliability of the synthesis and the yield of labeled oligonucleotides. 4-Pulse Electron Double Resonance (PELDOR) was then successfully used to measure the intramolecular spin–spin distances in six doubly labeled RNA-duplexes. Comparison of these results with our previous work on DNA showed that A- and B-Form can be differentiated. Using an all-atom force field with explicit solvent, MD simulations gave results in good agreement with the measured distances and indicated that the RNA A-Form was conserved despite a local destabilization effect of the nitroxide label. The applicability of the method to more complex biological systems is discussed.
Riboswitches are highly structured elements in the 50-untranslated regions (50-UTRs) of messenger RNA that control gene expression by specifically binding to small metabolite molecules. They consist of an aptamer domain responsible for ligand binding and an expression platform. Ligand binding in the aptamer domain leads to conformational changes in the expression platform that result in transcription termination or abolish ribosome binding. The guanine riboswitch binds with high-specificity to guanine and hypoxanthine and is among the smallest riboswitches described so far. The X-ray-structure of its aptamer domain in complex with guanine/ hypoxanthine reveals an intricate RNA-fold consisting of a three-helix junction stabilized by longrange base pairing interactions. We analyzed the conformational transitions of the aptamer domain induced by binding of hypoxanthine using highresolution NMR-spectroscopy in solution. We found that the long-range base pairing interactions are already present in the free RNA and preorganize its global fold. The ligand binding core region is lacking hydrogen bonding interactions and therefore likely to be unstructured in the absence of ligand. Mg2+-ions are not essential for ligand binding and do not change the structure of the RNA-ligand complex but stabilize the structure at elevated temperatures. We identified a mutant RNA where the long-range base pairing interactions are disrupted in the free form of the RNA but form upon ligand binding in an Mg2+-dependent fashion. The tertiary interaction motif is stable outside the riboswitch context.
Background Cryptic species are two or more distinct but morphologically similar species that were classified as a single species. During the past two decades we observed an exponential growth of publications on cryptic species. Recently published reviews have demonstrated cryptic species have profound consequences on many biological disciplines. It has been proposed that their distribution is non-random across taxa and biomes. Results We analysed a literature database for the taxonomic and biogeographical distribution of cryptic animal species reports. Results from regression analysis indicate that cryptic species are almost evenly distributed among major metazoan taxa and biogeographical regions when corrected for species richness and study intensity. Conclusion This indicates that morphological stasis represents an evolutionary constant and that cryptic metazoan diversity does predictably affect estimates of earth´s animal diversity. Our findings have direct theoretical and practical consequences for a number of prevailing biological questions with regard to global biodiversity estimates, conservation efforts and global taxonomic initiatives.
Membranes are essential for life, because a cell must separate itself from the environment to keep its molecules from dissipating away and also must keep out foreign molecules that disturb them or their cell components. However, the cell must communicate with the environment and adapt to the external conditions, needs to pump in nutrients and release toxic products of its metabolism. Membrane proteins present in the membranes of the cell and cell organelles, help the cell to gather information about the environment and perform various biological processes. Membrane proteins perform a wide range of biological functions including respiration, signal transduction and transport. Despite their high importance in biological function, only few structures have been determined because of the difficulties in producing high amounts of membrane proteins and obtaining good quality crystals. This Ph. D. thesis involves the study of different kinds of cytochrome oxidases and a membrane anchored cytochrome oxidase electron donor. Though structures of many cytochrome oxidases are known to date, there exist many different types of oxidases in different organisms, which help the organism to survive under unfavorable environmental conditions. The structural differences between these terminal oxidases which make the organism to survive in extreme environments are unclear. To investigate these, structures of different types of oxidases are necessary. Therefore, we are interested in revealing the structural details of different types of oxidases. The different types of oxidase I worked with were the caa3 HiPIP:oxygen oxidoreductase from Rhodothermus marinus, the aa3-type quinol oxidase from Acidianus ambivalens and bd-type quinol oxidase from three different organisms (Escherichia coli, Bacillus thermodenitrificans and Aquifex aeolicus). Besides the protein from E. coli all other proteins are from thermophilic organisms from which the proteins obtained are generally believed to be highly stable. The presence of a high content of charged amino acids that enhances the occurrence of salt bridges contributes to the stability of thermophilic proteins. ....
In this thesis the three dimensional solution strucutre of the RbfA protein from Thermotoga maritima was solved using multidimensional heteronuclear NMR spectroscopy. The RbfA protein binds to the helix I region of the 16S rRNA. To gain insights into the binding mode of RbfA to its target, a second RbfA construct from Helicobacter pylori was used. Comparison of the RbfA proteins with the published structure of RbfA from Escherichia coli, led to studies concerning the differences between proteins from thermophile and mesophile systems. In the second part of this thesis the native binding motive of the RbfA protein was identified. The RbfA protein binds to an alternate helix fold within the pre-sequence of the immature 16S rRNA.
Membrane proteins play vital role in a variety of cellular processes, such as signal transduction, transport and recognition. In turn they are involved in numerous human diseases and currently represent one of the most prevalent drug targets. A comprehensive understanding of the mechanisms mediated by membrane proteins requires information about their structures at near-atomic resolution, although structural studies of membrane proteins remain behind those of soluble proteins. A bottleneck in the study of membrane proteins resides in the difficulties that are encountered during their high-level production in cell based systems. However, many toxic effects attributed to the over production of membrane proteins are eliminated by cell-free expression, as viable host cells are no longer required. Therefore, the objective of this study was to obtain adequate amounts of selected membrane transport proteins for their structural studies using a cell-free expression system. For the establishment of the cell-free system for membrane proteins, the transporters YbgR and YiiP from Salmonella typhimurium LT2, PF0558 and PF1373 from Pyrococcus furiosus, from the cation diffusion family (CDF), BetP from Corynebacterium glutamicum from the betaine/carnitine/choline transporter (BCCT) family and Aq-2030 from Aquifex aeolicus VF5 from the monovalent cation/proton antiporter-2 (CPA2) family were selected. An Escherichia coli S-30 extract based cellfree system was established by generating the best expression constructs of the target proteins, preparing T7 RNA polymerase and an S-30 extract with high translation efficiency. The functionality of the S-30 extract was shown by the cell-free expression of correctly folded Green Fluorescent Protein (GFP). Essential factors of the cell-free system such as the Mg2+ concentration, the bacterial S-30 extract proportion in the reaction mixture and the time-course of cell-free reactions have been optimized. For the cell-free production of membrane proteins in soluble form, the possibility to supplement cell-free reactions with detergents was explored. A wide range of non-ionic or zwitterionic detergents, were found to be compatible with cell-free synthesis, while ionic detergents and non-ionic detergents at high concentrations had an inhibitory effect. Moreover, high concentrations of polyoxyethylene-alkyl-ethers (Brij) detergents were found to have enhancing effect on the production levels as well as on the solubility of cell-free produced proteins. As membrane proteins tend to misfold and aggregate in a membrane-free translation system, the possibility to supplement the cell-free reactions with inner membrane vesicles (IMVs) to obtain correctly folded target transport proteins was explored. All the target proteins were successfully produced in the batch cell-free reactions and were found to be incorporated in the IMVs. A continuous exchange cell-free (CECF) system was established, where consumable substrates (amino acids, nucleotides and energy regenerating compounds) were supplied to the cell-free reaction mixture through a dialysis membrane, which in consequence resulted in high-level production of target proteins compared to the batch system. The osmosensing and osmoregulated sodium-coupled symporter BetP from C. glutamicum was chosen for the large scale production in CECF set-up. The protein is easily produced in E. coli and is functional as assayed by its transport activity, after purification and reconstitution in liposomes. It is therefore possible to compare in-vivo and cell-free production. High-level cell-free production of BetP was achieved in CECF mode in different forms: (i) as precipitate, (ii) as soluble form in detergent, and (iii) incorporated in IMVs. Cell-free production of BetP resulted in the yield of about 0.5 mg of purified BetP from 1 ml of CECF reaction. The yield of purified BetP was increased to 1.6 fold by addition of 1% polyoxyethylene-(20)-cetyl-ether (Brij58) detergent in the reaction mixture. Moreover, the high level cell-free production of BetP (0.5 mg purified BetP/ml reaction mixture) incorporated in IMVs was shown for the first time in this work.However, it was observed that oligomerization of BetP was not efficient in the cell-free system. Factors that can promote the folding of membrane proteins such as lipids and chaperones were investigated. Addition of lipids and molecular chaperone GroE facilitated correct folding of BetP resulting in increased yield and stability of cell-free produced BetP. The results obtained indicate that most of the cell-free produced BetP exists in functional oligomeric form. The possibility of obtaining milligram amounts of BetP, a 12 trans-membrane protein from the cell-free reactions holds promise for structural and functional studies of other membrane proteins. In any case, the strategies adapted in this study should prove extremely valuable for the production of membrane proteins in the E. coli cell-free expression system.
First milestone of this Ph.D. thesis was the successful extension of conventional NTA/His-tag technique to self-assembling, multivalent chelator thiols for high-affinity recognition as well as stable and uniform immobilization of His-tagged proteins on chip surfaces. Bis-NTA was linked via an oligoethylene glycol to alkyl thiols by an efficient modular synthesis strategy yielding a novel, multivalent compound for formation of mixed SAMs with anti-adsorptive matrix thiols on gold. Multivalent chelator chips allow a specific, high-affinity, reversible, long-term immobilization of His-tagged proteins. In AFM studies reversibility of the specific protein immobilization process was visualized at single molecule level. The entire control over the orientation of the immobilized protein promotes this chip surface to an optimal platform for studies focusing on research targets at single molecule level and nanobiotechnology. Based on the constructed protein chip platform above and a novel AFM mode (contact oscillation mode, COM) – developed during the current Ph.D. work – protein nanolithography under physiological conditions enabling fabrication of active biomolecular patterns in countless variety has been established. Reversible COM-mediated nanostructuring is exceptionally suitable for multiplexed patterning of protein assemblies in situ. The first selfassembled protein layer acts as a biocompatible and ductile patterning material. Immobilized proteins can be replaced by the AFM tip applying COM, and the generated structures can be erased and refilled with different proteins, which are immobilized in a uniform and functional manner. Multi-protein arrays can be systematically fabricated by iterative erase-and-write processes, and employed for protein-protein interaction analysis. Fabrication of two-dimensionally arranged nanocatalytic centres with biological activity will establish a versatile tool for nanobiotechnology. As an alternative chip fabrication approach, the combined application of methodologies from surface chemistry, semiconductor technology, and chemical biology demonstrated successfully how pre-patterned templates for micro- and nanoarrays for protein chips are fabricated. The surface physical, as well the biophysical experiments, proved the functionality of this technology. The promises of such process technology are fast and economic fabrication of ready-to-use nanostructured biochips at industrial scale. Membrane proteins are complicated in handling and hence require sophisticated solutions for chip technological application. A silicon-on-insulator (SOI) chip substrate with microcavities and nanopores was employed for first technological investigation to construct a protein chip suitable for membrane proteins. The formation of an artificial lipid bilayer using vesicle fusion on oxidized SOI cavity substrates was verified by CLSM. Future AFM experiments will give further insights into the chip architecture and topography. This will provide last evidence of the sealing of the cavity by the lipid bilayer. Transmembrane proteins will be employed for reconstitution experiments on this membrane protein chip platform. Highly integrated microdevices will find application in basic biomedical and pharmaceutical research, whereas robust and portable point-of-care devices will be used in clinical settings.
Background Synchronous neuronal firing has been discussed as a potential neuronal code. For testing first, if synchronous firing exists, second if it is modulated by the behaviour, and third if it is not by chance, a large set of tools has been developed. However, to test whether synchronous neuronal firing is really involved in information processing one needs a direct comparison of the amount of synchronous firing for different factors like experimental or behavioural conditions. To this end we present an extended version of a previously published method NeuroXidence [1], which tests, based on a bi- and multivariate test design, whether the amount of synchronous firing above the chance level is different for different factors.
Background The synchrony hypothesis postulates that precise temporal synchronization of different pools of neurons conveys information that is not contained in their firing rates. The synchrony hypothesis had been supported by experimental findings demonstrating that millisecond precise synchrony of neuronal oscillations across well separated brain regions plays an essential role in visual perception and other higher cognitive tasks [1]. Albeit, more evidence is being accumulated in favour of its role as a binding mechanism of distributed neural responses, the physical and anatomical substrate for such a dynamic and precise synchrony, especially zero-lag even in the presence of non-negligible delays, remains unclear. Here we propose a simple network motif that naturally accounts for zero-lag synchronization for a wide range of temporal delays [3]. We demonstrate that zero-lag synchronization between two distant neurons or neural populations can be achieved by relaying the dynamics via a third mediating single neuron or population. Methods We simulated the dynamics of two Hodgkin-Huxley neurons that interact with each other via an intermediate third neuron. The synaptic coupling was mediated through alpha-functions. Individual temporal delays of the arrival of pre-synaptic potentials were modelled by a gamma distribution. The strength of the synchronization and the phase-difference between each individual pairs were derived by cross-correlation of the membrane potentials. Results In the regular spiking regime the two outer neurons consistently synchronize with zero phase lag irrespective of the initial conditions. This robust zero-lag synchronization naturally arises as a consequence of the relay and redistribution of the dynamics performed by the central neuron. This result is independent on whether the coupling is excitatory or inhibitory and can be maintained for arbitrarily long time delays (see Fig. 1). Conclusion We have presented a simple and extremely robust network motif able to account for the isochronous synchronization of distant neural elements in a natural way. As opposed to other possible mechanisms of neural synchronization, neither inhibitory coupling, gap junctions nor precise tuning of morphological parameters are required to obtain zero-lag synchronized neuronal oscillation.
Die Verarbeitung von Informationen im zentralen Nervensystem beruht auf dem Zusammenspiel von erregender und hemmender Neurotransmission. Die Übertragung von Signalen zwischen Neuronen erfolgt chemisch über die Ausschüttung von Neurotransmittern an spezialisierten Kontaktstellen, den Synapsen. Glyzin und gamma-Aminobuttersäure (GABA) sind die bedeutendsten inhibitorischen Neurotransmitter im zentralen Nervensystem von Säugern, welche Rezeptoren vom Glyzin- (GlyR) und GABAA-Typ (GABAAR) aktivieren. Diese ligandengesteuerten Ionenkanäle sind in postsynaptischen Membranen angereichert und mit intrazellulären Proteinen assoziiert. Die Rekrutierung der Rezeptoren in postsynaptischen Domänen ist ein an das zytoplasmatisch lokalisierte Protein Gephyrin gekoppelter Prozess. So bindet Gephyrin spezifisch an die intrazelluläre Domäne der beta-Untereinheit des GlyR (GlyR beta) und bildet für die Verankerung des Rezeptors ein gerüstartiges Netzwerk unterhalb der synaptischen Membran. Die gezielte Inaktivierung des Gephyrin-Gens führt in Mäusen zu einem postnatal letalen Phänotyp und zu dem Verlust der synaptischen Anreicherung des GlyR und bestimmter GABAA-Rezeptoren auf zellulärer Ebene. Gephyrin ist ein 93 kDa großes Protein, das nicht nur im zentralen Nervensystem (ZNS), sondern auch in anderen Organen wie Leber und Niere exprimiert wird, in denen es an der Synthese des Molybdän-Kofaktors von Oxido-Reduktasen beteiligt ist. Das Gephyrin-Protein wird durch 30 Exons codiert, von denen zehn als sogenannte Kassetten alternativ gespleißt werden können. Die bestuntersuchte Spleißvariante besitzt 736 Aminosäuren und ist in eine N- und eine C-terminale Domäne (Aminosäuren 1-181 bzw. 318-736) sowie eine zentrale Linker-Domäne unterteilt. Die N- und die C-terminalen Bereiche von Gephyrin sind den Proteinen MogA und MoeA aus E. coli homolog und werden daher auch als G-Domäne (N-terminal) bzw. E-Domäne (C-terminal) bezeichnet. In kristallographischen Untersuchungen wurde gezeigt, dass die G- und E-Domänen zur Tri- bzw. Dimerisierung befähigt sind. Diese speziellen Oligomerisierungseigenschaften der beiden Gephyrindomänen bilden wahrscheinlich die Grundlage für die Entstehung von Gephyrin-Clustern sowie eines hexagonalen Gephyrin-Gerüstes. Dieses Gerüst stellt den Verknüpfungspunkt zwischen Rezeptoren und dem Zytoskelett dar und ermöglicht somit die effiziente Clusterbildung und die zielgerichtete Anordnung einer großen Anzahl inhibitorischer Rezeptoren. In der vorliegenden Arbeit sollten die Rolle dieser beiden Domänen bei der Bildung membranassoziierter Gephyrinaggregate und die molekularen Mechanismen der Clusterbildung des Gephyrinmoleküls untersucht werden. Zu diesem Zweck wurden durch zielgerichtete Mutagenese unterschiedliche Gephyrin-Mutanten hergestellt, um die Fähigkeit der Oligomerisierung der G- und E-Domäne gezielt zu modifizieren. Dadurch sollte die Bedeutung der Oligomerisierung hinsichtlich der Aggregat- bzw. Clusterbildung untersucht werden. Außerdem sollten die Wechselwirkungen zwischen Gephyrin und anderen Proteinen und deren Einfluss auf die synaptische Lokalisation analysiert werden. Für diese Untersuchungen wurden auf der Basis von Röntgenstruktur-Daten spezifische Aminosäurereste an den bei der Oligomerisierung beteiligten Kontaktstellen ausgetauscht. In der G-Domäne wurden zu diesem Zweck vier separate Aminosäuren des Trimer-Interface durch Arginin ersetzt (GephRRRR). Analog hierzu wurden in der EDomäne einzelne Aminosäuren durch Arginin bzw. Glutamat substituiert (GephRER), um dadurch eine Dimersierung zu verhindern. Für die Kassette C5’ wird angenommen, dass deren Vorhandensein die Interaktion zwischen Gephyrin und GlyR beeinträchtigt, wodurch GlyR aus GABAergenen Synapsen ausgeschlossen wird. Daher wurde der Einfluss dieser Gephyrin-Spleißvariante (GephC5’), die zu einer Peptidinsertion innerhalb der G-Domäne führt, und einer Gephyrin-Mutante (Gephmut), die den Verlust der Wechselwirkung mit dem GlyR bedingt, auf die Aggregatbildung von Gephyrinoligomeren untersucht. Bei dem Konstrukt Gephmut wurden, basierend auf Daten von Röntgenstrukturuntersuchungen, neun Aminosäuren (713-721) am Cterminalen Ende der E-Domäne durch den homologen Bereich des bakteriellen MoeA Proteins aus E. coli ersetzt. Zunächst wurden die einzelnen isolierten Domänen mittels Gelfiltration hinsichtlich ihres Oligomerisierungsverhaltens untersucht. Die Mutationen wurden hierzu in verkürzte Proteine eingeführt, bei denen nur die G- bzw. die E-Domäne exprimiert wurden. Diese Konstrukte wurden daher als GRRRR, GC5’ bzw. ERER und Emut bezeichnet. Bei diesen zeigte sich, dass die G-Domäne des Gephyrin-Wildtyps zu trimeren Proteinkomplexen oligomerisiert. Im Gegensatz hierzu war die Mutante GRRRR nicht in der Lage, Trimere zu bilden. Das Einfügen der C5’-Kassette führte ebenfalls zu einer Störung der Trimerisierung. Gelfiltrationsexperimente mit der E-Domäne ergaben, dass die mutierte Domäne ERER, im Gegensatz zum Wildtyp-Konstrukt, keine Dimere ausbildet. Bisherige Studien haben jedoch gezeigt, dass das Emut Polypeptid zur Dimerisierung befähigt ist. Das Oligomerisierungsverhalten des kompletten Gephyrin-Proteins wurde mittels blauer nativer Gelelektrophorese (BN-PAGE) analysiert. Für die hier beschriebenen Untersuchungen mit BN-PAGE wurde rekombinantes Gephyrin in Xenopus laevis Oozyten heterolog exprimiert. Die Analyse ergab, dass Wildtyp Gephyrin nativ als Hexamer vorliegt, welches durch ansteigende Konzentrationen des Detergenzes Natriumdodecylsulfat (SDS) in Trimere, Dimere und Monomere zerfällt. Sowohl GephRRRR und GephC5’ liegen nativ fast ausschließlich als Dimere vor, während GephRER nur trimere Aggregate formt. Die entsprechende Doppelmutante mit Mutationen in Gund E-Domäne war wie erwartet nur noch als Monomer existent. Die als Kontrolle eingesetzte Glyzinrezeptor-Bindungsmutante Gephmut bildete, ebenso wie der Wildtyp, Hexamere aus. Daraus folgt, dass die Oligomere der G- bzw E-Domäne Zwischenprodukte der Hexamerbildung darstellen. Die Analyse der Oligomerisierungseigenschaften der Mutanten wurde nachfolgend in humanen embryonalen Nierenzellen (HEK 293T) untersucht. Nach heterologer Expression von Wildtyp Gephyrin in HEK 293T-Zellen formen sich große, charakteristische Gephyrinaggregate. Die Oligomerisierungs-Mutanten GephRRRR, GephRER und GephC5’ aggregierten jedoch nicht, sondern waren diffus im Zytoplasma verteilt. Die wiederum als Kontrolle eingesetzte Bindungsmutante Gephmut hingegen wies eine normale Aggregation auf. Diese Ergebnisse bestätigen die grundlegende Rolle der Oligomerisierung von G- und E- Domänen für die Aggregatbildung von Gephyrin. Mittels GST-Pulldown und Kolokalisationsanalysen in HEK Zellen wurde die Wechselwirkung der Gephyrinmutanten mit der GlyR beta, dem Motorkomplexprotein Dynein light chain-1 (Dlc-1) und dem Guanin-Nukleotid-Austauschfaktor Collybistin (Cb) untersucht. Beide Ansätze weisen darauf hin, dass die Trimerisierung der G-Domäne an der Interaktion von Gephyrin mit Dlc-1 und die Dimerisierung der E-Domäne bei der Bindung an GlyR beta und Cb beteiligt ist. Die Mutante Gephmut zeigte in beiden Fällen einen totalen Verlust der Bindungsfähigkeit sowohl an das GlyR beta Bindungsmotiv als auch an Cb. Der Einbau der C5’ Kassette in Gephyrin scheint jedoch nicht dessen Bindung an den GlyR zu beeinflussen. Für die Analyse der Clusterbildung und des zielgerichteten Transports in Neuronen wurden Wildtyp und mutiertes Gephyrin in hippocampalen und spinalen Primärkulturen der Ratte exprimiert. Zur Überprüfung einer synaptischen Lokalisation wurde Gephyrin gemeinsam mit dem vesikulären inhibitorischen Aminosäure-Transporter (VIAAT), einem präsynaptischen Marker-Protein, detektiert. In beiden Kulturen wies Gephyrin eine punktartige Verteilung in den Neuriten auf und wurde gezielt an Synapsen angereichert. Im Kontrast dazu zeigten alle Oligomerisierungsmutanten, GephRRRR, GephC5’ und GephRER keine Ausbildung von Clustern sondern eine diffuse Verteilung im Zellkörper und in Dendriten. Das Konstrukt Gephmut wies jedoch Clusterbildung und eine punktförmige Verteilung auf. Diese Daten belegen, dass die Oligomerisierung der G- wie auch der E-Domänen für die Clusterbildung und synaptische Lokalisation von Gephyrin unerlässlich ist. Die Wechselwirkung mit dem GlyR und/oder Collybistin ist ebenfalls für die Anreicherung in der Synapse erforderlich, nicht jedoch für die Bildung der Gephyrin-Cluster. Die dargestellten Ergebnisse belegen die Rolle der spezifischen Oligomerisierungseigenschaften der G- und E-Domäne für die Ausbildung des hexagonalen Gephyringerüstes und dessen grundlegende Bedeutung für die spezifische Anreicherung von Gephyrin an inhibitorischen Synapsen in Neuronen.
The Indian IT industry has received great attention. Although most studies cover South Indian locations, clustering has rarely been a topic. This study focuses on Bangalore addressing questions related to Bangalore’s successful development and lessons thereof for other regions in and outside India. The approach pertains to economic geography and international business; hypotheses have been developed from a multi-disciplinary literature survey and interview fieldwork in Bangalore. I emphasize human and social capital and networks. While the first chapter delineates cultural foundations of human capital formation, the second and third deal with bonding and bridging social capital (or dense and loose networks), respectively; the fourth is an outlook on future opportunities through intersectoral upgrading. The main hypothesis is that a combination of both forms of social networks - contingent upon sub-sectors – has helped Bangalore developing a successful IT industry. Positive attitudes towards education led to relatively more human capital spawning two positive feedbacks: 1) establishment of national research and educational institutes resulting in large inflows of a diversity of people providing the required setting for creativity and innovation; 2) transnational networks linking to Silicon Valley are dominated by people from South India, allowing for additional knowledge spillovers corroborating the regional clustering.
The goal of this thesis was to gain further insight into the binding behavior of ligands in the heptahelical domain (HD) of group I metabotropic glutamate receptors (mGluRs). This was realized by the establishment of strategies for the detection and optimization of molecules acting as non-competitive antagonists of group I mGluRs (mGluR1/5). These strategies should guarantee high diversity in the retrieved chemotypes of the detected compounds not resembling original reference molecules (“scaffold-hopping”). The detection of new scaffolds, in turn, was divided into two approaches: First the development of pharmacological assays to screen compounds at a certain target for bioactivity (here: affinity towards the allosteric recognition site of mGluR1 and mGluR5), and second the evaluation of computer assisted methods for the identification of virtual hits to be screened afterwards on the pharmacological assays established before. Promising molecules should be optimized with respect to activity/affinity and selectivity, their binding mode investigated and, finally, compared to existing lead compounds. Initially, membrane based binding assays for the HD of mGlu1 and mGlu5 receptors with enhanced throughput (shifting from 24-well plates to 96-well plates) were set up. For the mGluR1 assay the potent antagonist EMQMCM exhibited high affinity towards the binding site (Ki ~3nM), which is in accordance with published data from Mabire et al. (functional IC50 3nM). For mGluR5 the reference antagonist MPEP binds with high affinity to the receptor (binding IC50 13.8nM), which confirmed earlier findings from Anderson et al. (binding IC50 15nM). In another series of experiments the properties of rat cerebellar (mGluR1) and corticalmembranes (mGluR5) as well as of radiotracers were investigated by means of binding saturation studies and kinetic experiments. Furthermore, the influence of the solvent DMSO, necessary for compound screening of lipophilic substances, on positive and negative controls was evaluated. As the precise architecture of the HD of mGluR1 is still not known our efforts in identifying new ligands for this receptor focused on the ligand-based approach. All computer assisted methods that were applied to virtually screen large compound collections and to retrieve potential hits (“activity-enriched subsets”) acting at the heptahelical domain of mGluR1 relied on the existence of a valid dataset of reference molecules. This was realized by an initial compilation of a mGluR reference data collection comprising in total 357 entries predominantly negative but also some positive allosteric modulators for mGluR1 and mGluR5. In the next step a pharmacophore model for non-competitive mGluR1 antagonists was constructed. It was based upon six selective, potent and structurally diverse ligands. Prospective virtual screening was performed using the CATS atom-pair descriptor. The Asinex Gold-Collection was screened for each seed compound and some of the most similar compounds (according to the CATS descriptor) were ordered and tested forbinding affinity and functional activity at mGluR1. A high hit rate of approximately 26% (IC50 < 15 micro M) was yielded confirming the applicability of this method. One compound exerted functional activity below one micro molar (IC50-value of C-07:362nM ± 0.03). Moreover, non-linear principal component analysis was employed. Again the Asinex vendor database served as test database and was filtered by the pharmacophore model for mGluR1 established before. Test molecules that were adjacently located with mGluR1 antagonist references were selected. 15 compounds were tested on mGluR1 in binding and functional assays and three of them exhibited functional activity (IC50) below 15 micro M. The most potent molecule P-06 revealed an IC50-value of 1.11 micro M (± 0.41). The COBRA database comprising 5,376 structurally diverse bioactive molecules affecting various targets was encoded with the CATS descriptor and used for training two selforganizing maps (SOM). The encoded mGluR reference data collection was projected onto this map according to the SOM algorithm. This projection allowed to clearly distinguish between antagonists of mGluR1 and mGluR5 subtype. 28 compounds were ordered and tested on activity and affinity for mGluR1. They exhibited functional activity down to the sub-micro molar range (IC50-value of S-08: 744nM ± 0.29) yielding a final hit rate of 46% (<15 micro M). Then, the Asinex collection was screened using the SOM approach. For a predicted target panel including the muscarinic mACh (M1) receptor, the histamine H1-receptor and the dopamine D2/D3 receptors, the tested mGluR ligands exhibited the calculated binding pattern. This virtual screening concept might provide a basis for early recognition of potential sideeffects in lead discovery. We superimposed a set of 39 quinoline derivatives as non-competitive mGluR1 antagonists that were recently published by Mabire and co-workers. A CoMFA model (QSAR) was established and the influence of several side chains on functional activity was investigated. The coumarine derivative C-07 was obtained as a result of similarity searching. Starting from this compound a series of chemical derivatives was synthesized. This led to the discovery of potent (B-28, IC50: 58nM ± 0.008; Ki: 293nM ± 0.022) and selective (rmGluR5 IC50: 28.6 micro M) mGluR1 antagonists. From a homology model of mGluR1 we derived a potential binding mode for coumarines within the allosteric transmembrane region. Potential interacting patterns with amino acids were proposed considering the difference of the binding pockets between rat and human receptors. The proposed binding modes for quinolines (here:EMQMCM) and coumarines (here:B-04) were compared and discussed considering in particular the influence on activity of several side chains of quinolines obtained from the QSAR studies. The present studies demonstrated the applicability of ligand-based virtual screening for non-competitive antagonists of a G-protein coupled receptor, resulting in novel, potent and selective agents.
The strong nuclear force is described by Quantum Chromodynamics (QCD), the parallel field theory to Quantum Electrodynamics (QED) that describes the electromagnetic force. It is propagated by gluons analogously to photons in the electromagnetic force, but unlike photons, which do not carry electric charge, gluons carry color, and they can self-interact. However, as individual quarks have never been observed in nature, it is postulated that the color charge itself is confined, and hence all baryons and mesons must be colorless objects. To study nuclear matter under extreme conditions, it is necessary to create hot and dense nuclear matter in the laboratory. In such conditions the confinement between quarks and gluons is cancelled (deconfinement). This state is characterized with a qusi-free behavior of quarks and gluons. The strange (s) and anti-strange (anti-s) quarks are not contained in the colliding nuclei, but are newly produced and show up in the strange hadrons in the final state. It was suggested that strange particle production is enhanced in the QGP with respect to that in a hadron gas. This enhancement is relative to a collision where a transition to a QGP phase does not take place, such as p+p collisions where the system size is very small. Therefore the energy- and system size dependence is studied to receive a picture about the initial state. In this thesis experimental results on the energy- and system size dependence of Xi hyperon production at the CERN SPS is shown. All measurements were performed with the NA49 detector at the CERN SPS. NA49 took central lead-lead collisions from 20 - 158 AGeV, minimus bias lead-lead collisions at 40 and 158 AGeV, and semi-central silicon-silicon colisions at 158 AGeV. The NA49 experiment features a large acceptance in the forward hemisphere allowing for measurements of Xi rapidity spectra. At the SPS accelerator at CERN Pb+Pb collisions are performed with beam energies to 158 AGeV. The analyzed data sets were taken in the period from 1999 to 2002. The NA49 experiment is a large acceptance hadron spectrometer, which measures charged hadrons in a wide acceptance. The main components are the four TPCs (Time Projection Chamber). The centrality of nucleon-nucleon collisions was done by measuring the not in the collision participating (spectator-) nucleons in the VETO-calorimeter. The study of strangeness is motivated by its role as a signature for the Quark Gluon Plasma. Any enhancement in the yield must be with respect to a ’normal’ yield, where a QGP is not formed. This is usually taken to mean suitably scaled p+p collisions, where the volume of the system created is too small for a QGP to occur. The results at SPS and RHIC energies show an enhancement, with the doubly strange Xi? being enhanced more than the Lambda, in accordance with the original prediction. However, the enhancement at SPS energies is higher than at RHIC energies.
We investigate unary regular languages and compare deterministic finite automata (DFA’s), nondeterministic finite automata (NFA’s) and probabilistic finite automata (PFA’s) with respect to their size. Given a unary PFA with n states and an e-isolated cutpoint, we show that the minimal equivalent DFA has at most n exp 1/2e states in its cycle. This result is almost optimal, since for any alpha < 1 a family of PFA’s can be constructed such that every equivalent DFA has at least n exp alpha/2e states. Thus we show that for the model of probabilistic automata with a constant error bound, there is only a polynomial blowup for cyclic languages. Given a unary NFA with n states, we show that efficiently approximating the size of a minimal equivalent NFA within the factor sqrt(n)/ln n is impossible unless P = NP. This result even holds under the promise that the accepted language is cyclic. On the other hand we show that we can approximate a minimal NFA within the factor ln n, if we are given a cyclic unary n-state DFA.
Background The cell cycle of all organisms includes mass increase by a factor of two, replication of the genetic material, segregation of the genome to different parts of the cell, and cell division into two daughter cells. It is tightly regulated and typically includes cell cycle-specific oscillations of the levels of transcripts, proteins, protein modifications, and signaling molecules. Until now cell cycle-specific transcriptome changes have been described for four eukaryotic species ranging from yeast to human, but only for two prokaryotic species. Similarly, oscillations of small signaling molecules have been identified in very few eukaryotic species, but not in any prokaryote. Results A synchronization procedure for the archaeon Halobacterium salinarum was optimized, so that nearly 100% of all cells divide in a time interval that is 1/4th of the generation time of exponentially growing cells. The method was used to characterize cell cycle-dependent transcriptome changes using a genome-wide DNA microarray. The transcript levels of 87 genes were found to be cell cycle-regulated, corresponding to 3% of all genes. They could be clustered into seven groups with different transcript level profiles. Cluster-specific sequence motifs were detected around the start of the genes that are predicted to be involved in cell cycle-specific transcriptional regulation. Notably, many cell cycle genes that have oscillating transcript levels in eukaryotes are not regulated on the transcriptional level in H. salinarum. Synchronized cultures were also used to identify putative small signaling molecules. H. salinarum was found to contain a basal cAMP concentration of 200 uM, considerably higher than that of yeast. The cAMP concentration is shortly induced directly prior to and after cell division, and thus cAMP probably is an important signal for cell cycle progression. Conclusions The analysis of cell cycle-specific transcriptome changes of H. salinarum allowed to identify a strategy of transcript level regulation that is different from all previously characterized species. The transcript levels of only 3% of all genes are regulated, a fraction that is considerably lower than has been reported for four eukaryotic species (6% - 28%) and for the bacterium C. crescentus (19%). It was shown that cAMP is present in significant concentrations in an archaeon, and the phylogenetic profile of the adenylate cyclase indicates that this signaling molecule is widely distributed in archaea. The occurrence of cell cycle-dependent oscillations of the cAMP concentration in an archaeon and in several eukaryotic species indicates that cAMP level changes might be a phylogenetically old signal for cell cycle progression.
Im Zeitalter von Internet und digitaler Wissensvermittlung hat auch die Geschichtswissenschaft die Photographie als Quellenmaterial zur Dokumentation historischer Lebensbedingungen und Ereignisse schätzen gelernt. Neben dem geisteswissenschaftlichen Aspekt solcher Photodokumente gibt es einen technisch-konservatorischen Aspekt.
Chalcogen-based species are common ligands in transition-metal chemistry and display a variety of coordination modes. Like alkyl- and arylchalcogenolates, silylchalcogenolates are able to stabilize transition-metal complexes. Metal chalcogenolates LnM-ESiR3 with small organic residues R can serve as precursors for larger metal–chalcogenide clusters, which can be accessed by cleaving the E-Si bond. Furthermore, large silyl residues at the chalcogen atom serve to kinetically stabilize reactive systems. To explore the diverse chemistry of this class of compounds, a number of different silyl chalcogenolates were synthesized, including the sodium siloxide Ph2MeSiONa and the chalcogen derivatives of the extremely sterically hindered silyl residues tBu2PhSi- und tBu3Si-. The anionic silyl species tBu2PhSiNa and tBu3SiNa nucleophilically degrade elemental chalcogens (S, Se, and Te), thus producing the silyl chalcogenolates tBu2PhSiENa and tBu3SiENa (E = S, Se, Te). The chemical and structural properties of these compounds were studied. Protonolysis produces the corresponding chalcogenols tBu2RSiEH, while oxidation leads to the dichalcogenides tBu2RSiE-ESiRtBu2 (R = tBu, Ph; E = S, Se, Te). Oxidative addition of the dichalcogenides to metal centers in low oxidation states offers one route to chalcogenolate complexes. To investigate the realm of this approach, three oligochalcogen compounds R3SiE-E′n-ESiR3 were synthesized. The tetrasulfane tBu3SiS-S2-SSitBu3 and the chalcogen(II)dithiolates (tBu3SiS)2Se and (tBu3SiS)2Te were produced, and their stability was investigated. The direct comparison of isoelectronic species allows for a deeper understanding of their similarities and differences. The silanides R3Si– can be considered as anionic phosphane analogues in which a phosphorus atom has been formally replaced with a Si– unit. Phosphanylborhydrides R2BH3P– also belong to this isoelectronic series. The same analogy holds true for the chalcogen derivatives related to the phosphane chalcogenides R3P=E. With this in mind, complexes of the CpFe(CO)2 fragment with the different isoelectronic ligands were synthesized and compared. The silyl-based ligands were found to be the strongest donors of the two isoelectronic series. The differences in donor strength were roughly twice as large for the nonchalcogen species as for the chalcogen-based ligands. To further investigate the chemistry of transition-metal silyl chalcogenolate complexes, the coordination behavior of the chalcogenolates tBu2RSiE– (R = tBu, Ph; E = S, Se, Te) was studied. Salt metathesis of silyl thiolates with appropriate metal halides leads to the multinuclear complexes [Cu(SSitBu2Ph)]4 and [ZnCl(SSitBu3)(THF)]2. Metathesis products were identified in the reactions of BrMn(CO)5 with one or two equivalents of tBu3SiSNa(THF)2. Diproporationation of these compounds leads to dimeric Mn(I)Mn(II) complexes. The crystal structure of the dinuclear disproportionation product [(CO)3Mn(mu-SSitBu3)3Mn(SSitBu3)]– displays a terminal tBu3SiS– ligand, which coordinates with a Mn-S-Si angle of 180°. This geometry indicates that the thiolate can be considered as a six-electron donor (2 sigma e–, 4 pie–), analogous to the cyclopentadienyl ligand. Photoinduced oxidative addition of the dichalcogenides to Fe(CO)5 leads to the dimeric complexes [(CO)3Fe(ESitBu3)]2 (E = S, Se, Te). The tellurolate complex forms quantitatively within 8 h. The thiolate complex, on the other hand, is formed slowly over a period of six months. IR-spectroscopic investigation of the CO vibrations of the three homologous complexes indicates that the tellurolate is the strongest donor of the series.
Koalas are popular zoo animals, but difficult in husbandry. In addition to their specialised diet of eucalyptus leaves, they are prone to “stress” and disease. Particularly in European zoos, themonitoring of theirwell-being has high priority and they are protected from possible stressors. However, stress signs in koalas are vague and monitoring techniques like weighing might result in discomfort itself. Additionally, husbandry routines are planned according to keeper’s schedule, not to the endogenous rhythms of the koalas. Therefore it is necessary to investigate activity pattern in captive koalas and the signals influencing them. These signals have to be assessed on the strength and quality of their impact. A total of 17 koalas have been observed in three zoological gardens in Australia and Europe. Koalas kept in outdoor enclosures with little human contact (Koala Walkabout, Taronga Zoo, Sydney) showed a uniform activity pattern, which was clearly entrained by light. Activity levels were higher during the night, and there was a pronounced resting period in the morning which corresponds with low body temperature measured by Degabriele and Dawson (1979). Activity peaks were related to twilight and changed during the year related to day lengths. However, there was a clear influence from the introduction of fresh browse which resulted in a distinct feeding peak in the afternoon. With short day lengths, this stimulus competed with dusk. Activity patterns from koalas in indoor enclosures (Zoo Duisburg, Vienna Zoo) varied between individuals and in some cases lacked a detectable rhythm. Though activity peaks were related to light, entrainment to sunlight was weak. In winter, koalas reacted primarily to the artificial light, but some also showed activity peaks related to sunlight. Activity patterns in these koalas were less structured and differed severely from patterns expected according to literature. Activity was often related to the keeper’s presence and food introduction. Frequency of feeding bouts was considerably higher at Vienna Zoo compared to the other zoos and the bouts were shorter in duration. Time budgets of the koalas were within the range given in free-range studies. Feeding showed seasonal changes and was increased in lactating females. Koalas at Vinna Zoo had a high level of locomotor activity compared to the size of the enclosure. Koalas at Koala Walkabout were not used to handling, so they resisted the keeper. The koalas at the two European zoos were handled regularly and settled down quickly. However, handling took place in the morning; in most koalas, there was no activity prior to it. In Vienna, resting periods were interrupted daily due to weighing. Food introduction at KoalaWalkabout took place in the afternoon. It was preceded by locomotor activity and triggered a long feeding bout in the koalas. It is not clear, whether food had true Zeitgeber properties or masked the endogenous rhythm. In the two European zoos, food was introduced in the morning. The peaks related to this were smaller than those at Koala Walkabout. Activity was rarely observed prior to food introduction. The koalas at Koala Encounter, Taronga Zoo (Sydney),were regularly confronted with visitors, though no contact was allowed. Direct observation by the keepers did rarely show any stress signs. Activity patterns at night were strikingly similar to Koala Walkabout, but differed dramatically during the day. Food was introduced three times a day, which usually resulted in activity that interrupted a resting period. Generally, the koalas at Koala Encounter were more active than those at KoalaWalkabout. They also displayed a high level of locomotor activity, especially on the ground, which is an accepted sign of discomfort in koalas (Wood 1978; Zoological Society of San Diego 2001; Yusuf& Rosenthal unpublished data). In summary, this chronoethological study of the captive koalas showed that there are several problems with koala husbandry. Artificial light regimes for koalas are not sufficient for entrainment and result in unstructured activity pattern. This is especially the case in winter, when the day in Europe is artificially extended. Due to the mainly nocturnal behaviour of koalas, such an extension might not be necessary and therefore should be avoided. Handling in Europe took place during the physiological resting time of the koalas. Interruptions of resting times are considered as stressors (Wood 1978) and should be avoided. Handling in the afternoon would be more suitable for the koalas and triggered activity in the two koalas at Vienna Zoo. It is also arguable if daily weighing is necessary to monitor health in captive koalas or if the frequent interruption of resting countervail the advantages of constant monitoring. Frequent contact with visitors, evenwithout the so-called cuddling, has a considerable impact on activity patterns and time budget of koalas, even if no immediate stress signs are displayed. Such contact should therefore be reduced to a minimum and chronoethological observations of the koalas should be used. A study on koalas with direct visitor contact is also advisable to revise the current legislation on “koala cuddling”. Koalas frequently rested in living trees if they had access to it. Since no food-poisoning has been reported from koalas using living non-food trees, the provision of living trees with an appropriate canopy should be included in the husbandry guidelines. Increased locomotor activity has been shown to be related to conditions of discomfort or stress and possibly to oestrus. This is in accordance with literature (Wood 1978; Zoological Society of San Diego 2001). Further observation, combined with hormone analysis, are advisable to establish this parameter for evaluation of well-being. Chronoethology has proven to be useful for the evaluation of husbandry conditions and group dynamics. Different to other, traditional ethologicalmethods, it indicated problems and enabled me to advise more appropriate times for handling and food introduction. It is desirable that zoos already using 24-hour video observation include chronoethological aspects into their analysis.
This thesis exhibits skeins based on the Homfly polynomial and their relations to Schur functions. The closures of skein-theoretic idempotents of the Hecke algebra are shown to be specializations of Schur functions. This result is applied to the calculation of the Homfly polynomial of the decorated Hopf link. A closed formula for these Homfly polynomials is given. Furthermore, the specialization of the variables to roots of unity is considered. The techniques are skein theory on the one side, and the theory of symmetric functions in the formulation of Schur functions on the other side. Many previously known results have been proved here by only using skein theory and without using knowledge about quantum groups.
Epstein and Penner constructed in [EP88] the Euclidean decomposition of a non-compact hyperbolic n-manifold of finite volume for a choice of cusps, n >= 2. The manifold is cut along geodesic hyperplanes into hyperbolic ideal convex polyhedra. The intersection of the cusps with the Euclidean decomposition determined by them turns out to be rather simple as stated in Theorem 2.2. A dual decomposition resulting from the expansion of the cusps was already mentioned in [EP88]. These two dual hyperbolic decompositions of the manifold induce two dual decompositions in the Euclidean structure of the cusp sections. This observation leads in Theorems 5.1 and 5.2 to easily computable, necessary conditions for an arbitrary ideal polyhedral decomposition of the manifold to be a Euclidean decomposition.
The development of a drug product, beginning with the synthesis of the drug substance through approval for marketing, may take up to 15 years and a total amount of investment of up to half a billion Euro. After the discovery of a potential drug substance, many different investigations have to be performed: e.g. characterization of the physical-chemical properties, the pharmacological and toxicological profile and, especially relevant for this work, the development of the first dosage forms. After achieving these steps, first investigations in human studies can be carried out. After a positive assessment of the benefit to risk ratio, further investigations, such as food effects on the pharmacokinetics, multiple dosing studies and further studies on patients can be implemented. After successfully completing this second part the new drug product can be approved. With broader clinical experience it often becomes apparent that changes in relevant aspects of the formulation of the registered drug product e.g. excipients, concentration of the drug substance or excipient versus drug substance ratio, are necessary to optimise the therapy. This often leads to additional clinical investigations and a new registration, a procedure which is time and cost intensive. A possible way to reduce the financial and time investments, is to establish an appropriate in vivo- in vitro correlation (IVIVC). If it is possible to predict the in vivo performance of a drug product adequately with in vitro methods (dissolutions tests), it will no longer be necessary to perform additional clinical investigations. In this work, IVIVCs were investigated for three different drug substances and several different types of formulations.... ...Results of this work clearly show that successful IVIVCs can be achieved for the fasted state using biorelevant dissolution media. A prerequisite of achieving a good IVIVC is the availability of in vivo data of a reference product (i.v., oral solution or IR) tested within the same group of volunteers as the product of interest. Only with this procedure, one can obtain adequate IVIVCs for drug substances with high inter-individual variability of the plasma concentrations and with high first-pass metabolism. This work also shows that predictions of the in vivo behavior of a modified release dosage form after administration with a high fat meal are more difficult to obtain. This is mainly related to an absence of a medium, which could mimic the situation of the fed stomach adequately. Ensure plus®, which was chosen in this work, failed to simulate the fed stomach adequately in several cases; it suppressed the release of rosiglitazone from lipid formulations and led to rapid disruption of the HPMC-matrix of the 5-ISMN Geomatrix formulations. Future work should be directed towards optimization of the test media in the BioDis apparatus. This work clearly shows the inability of Ensure plus® to predict the in vivo performance of a drug under fed state conditions and indicates that alternative media must be developed. It is known that the pH of the stomach rises up to six after the intake of a meal. During the following hours the pH decreases until reaching the baseline value of approximately 1.8. One possibility of simulating the fed state stomach more precisely will be to divide the overall residence time into 4 different parts: 1. half a hour at pH 6 2. half a hour at pH 4 3. one hour at pH 3 4. two hours at pH 1.8 Another option is not only to modify the pH of the medium, but also to change its composition. During the decomposition of the food contents, the composition of the gastric juice changes, the ionic strength, the buffer capacity and the osmolarity rises, while the pH value decreases. A third possibility will be the addition of enzymes, mainly pepsin, lipases and amylases. Again, the quantity of the enzymes differs during the residence time of the food in the stomach. Highest quantities are expected in the first two hours after food intake and decreases in the remaining two hours. Another issue of this work was an assessment of the two dissolution apparatus, Paddle and BioDis. In general, the choice of the dissolution apparatus should be done primarily with respect to the solubility behavior of the drug substance. For high soluble drugs the USP apparatus II, Paddle, is sufficient (e.g. diltiazem or 5-ISMN). In cases of a poorly soluble drug (rosiglitazone), where the release strongly depends on the medium used, the USP apparatus III (BioDis) is favored, due to the advantage of simulating the GI-tract with a gradient of different dissolution media, each simulating one part of the GI-tract. In summary, the results of this work indicate that it is acurrently possible to predict fasted state behavior of a variety of controlled release products using in vitro tests. Prognoses was also made in terms of predicting food effects on the behavior of controlled release products, although it is clear that the media compositions will have to be revised to establish releiable predictive methods for the fed state.
G protein-coupled receptors (GPCRs) comprise the largest membrane protein family and play an essential role in signal transduction through the cell membrane. They are currently the targets of approximately 50 % of the pharmaceuticals on the market (Klabunde and Hessler, 2002). However, only one high-resolution GPCR structure has been determined up to now, that of bovine rhodopsin (Palczewski et al., 2000). The GPCR activation and regulation mechanisms are still unknown and other GPCR structures are thus required. MePNet (Membrane Protein Network) was a European consortium dedicated to structural studies of GPCRs. The approach was to produce 100 GPCRs in three expression systems (Escherichia coli, Pichia pastoris and Semliki Forest Virus infected mammalian cells) in order to select at each step of the process (production, solubilization, purification) the constructs that fulfilled quantity and quality (functionality) requirements for crystallization trials. In our team, we screened 38 of the 100 targets in P. pastoris. For each receptor, the clone with the highest production level was identified by dot-blot. The size and homogeneity of each receptor were then analyzed by Western-blot. The human adenosine A2A receptor showed a well-defined and pronounced single band and was thus selected for further characterization. The adenosine A2A receptor is a GPCR mainly localized in the central nervous system and, as it antagonizes dopaminergic activity, it has great potential as a drug target for the treatment of Parkinson’s disease. Functional characterization by binding assays with the specific antagonist [3H]-ZM241385 demonstrated a Bmax of 56 +/- 3 pmol/mg i.e. pmol of binder per milligram of total membrane protein, and a KD of 0.40 +/- 0.02 nM. Receptor production was then improved by lowering the induction temperature, decreasing the induction time and adding DMSO to the medium. For large-scale production, fermention reached around 300 g cells (wet weight)/L culture, which provided 43 mg of functional receptor in membranes per liter of culture. Functional solubilization was achieved with dodecyl-β-D-maltoside and the soluble yield was increased to 70-80 % of the membrane content by addition of cholesteryl hemisuccinate and increasing the ionic strength. The receptor was successfully purified via Ni-NTA and monomeric avidin chromatography in the presence of the antagonist ZM241385. This strategy produced a pure, homogeneous and stable receptor preparation with functionality demonstrated by radioligand binding assays. The total receptor yield after purification was routinely around 20 % of the membrane functional receptor content and 2 g of membranes provided 4 mg of pure receptor for crystallization trials. GPCRs are very difficult targets for crystallization, and co-crystallization with antibody fragments has been shown to be a successful method for crystallization of membrane proteins. In order to develop such a tool for the adenosine A2A receptor, a single-chain Fv (scFv) fragment specific to the purified receptor was selected by phage display. The receptor was functionally immobilized on the surface of streptavidin beads and after two rounds of selection, 6 different phages were identified several times. After production in E. coli and purification via Ni-NTA affinity chromatography, 4 out of the 6 scFv fragments were sufficiently enriched to be tested by ELISA. For the ELISA, the receptor was functionally immobilized via the biotinylation domain of the construct in a 96-well streptavidin-coated plate. The antibody fragments binding to the receptor were identified based on interaction with HRP-conjugated protein L. One scFv fragment gave a positive ELISA signal 10 fold above background and titration of the scFv fragment binding to the receptor was specific and saturable. However no complex of scFv fragment and receptor was observed on gel filtration. In order to have a more sensitive detection method, the scFv fragment was labeled with fluorescein: a complex was then observed up on gel filtration but the binding appeared to be non-specific. A pull-down assay with immobilized non-labeled scFv fragment finally confirmed the specificity of the binding, but also the low affinity of the interaction. Affinity maturation of this specific scFv fragment by a random mutagenesis and selection process should improve this parameter in order to obtain an adapted tool for co-crystallization.
Background: West Nile virus (WNV) infection can cause severe meningitis and encephalitis in humans. Apoptosis was recently shown to contribute to the pathogenesis of WNV encephalitis. Here, we used WNV-infected glioma cells to study WNV-replication and WNV-induced apoptosis in human brain-derived cells. Results: T98G cells are highly permissive for lytic WNV-infection as demonstrated by the production of infectious virus titre and the development of a characteristic cytopathic effect. WNV replication decreased cell viability and induced apoptosis as indicated by the activation of the effector caspase-3, the initiator caspases-8 and -9, poly(ADP-ribose)polymerase (PARP) cleavage and the release of cytochrome c from the mitochondria. Truncation of BID indicated cross-talk between the extrinsic and intrinsic apoptotic pathways. Inhibition of the caspases-8 or -9 inhibited PARP cleavage, demonstrating that both caspases are involved in WNV-induced apoptosis. Pancaspase inhibition prevented WNV-induced apoptosis without affecting virus replication. Conclusions: We found that WNV infection induces cell death in the brain-derived tumour cell line T98G by apoptosis under involvement of constituents of the extrinsic as well as the intrinsic apoptotic pathways. Our results illuminate the molecular mechanism of WNV-induced neural cell death.
Anomalous monism and mental causality : on the debate of Donald Davidson’s philosophy of the mental
(2004)
The English version of the first chapter of Erwin Rogler and Gerhard Preyer: Materialismus, anomaler Monismus und mentale Kausalität. Zur gegenwärtigen Philosophie des Mentalen bei Donald Davidson und David Lewis (2001) "Anomaler Monismus und Mentale Kausalität. Ein Beitrag zur Debatte über Donald Davidsons Philosophie des Mentalen" is a contribution to the current debates on the philosophy of the mental and mental causality initiated from Donald Davidson's philosophy with his article "Mental Events" (1970). It is the intent of the English version to give a response to the controversy among American, British and Australian philosophers in the context of a global exchange of ideas on problems understanding the mental. Contents 1. Preliminary Remarks 2. The Critique of Property-Epiphenomenalism and Counterarguments (a) The Enlargement of Nomological Reasoning (b) The Counterfactual Analysis (c) Supervenient Causality 3. Are Mental Properties real or unreal (fictive)? Abstract Things and events are fundamental entities in Davidson's ontology. Less distinct is the ontological status of properties, especially of mental types. Despite of some eliminative allusions there are weighty reasons to understand Davidson's philosophy of mind as including intentional realism. With it, the question of mental causality arises. There are two striking solutions to this problem: the epiphenomenalism of mental properties and the downward causation of mental events. Davidson cannot accept either. He claims to justify the mental as supervenient causality in order to thus integrate it into physicalism (his version of monism). But his argument at best proves the explanatory, not the causal relevance of mental properties. For this and for other reasons, Davidson fails the aspired synthesis of a sufficiently strong physicalism and the autonomy of the mental; a project whose realization is anyhow hard to achieve.
Hard physics in STAR
(2005)
The hot and dense matter created in high-energy nuclear collisions is believed to undergo a transition into a deconfined phase where partonic degrees of freedom determine the dynamics of the medium. High-p⊥ partons, that are produced in the initial collisions between nucleons of the incoming nuclei, lose energy as they propagate through the medium. This effect, called jetquenching, is observed in high-p⊥ particle spectra, in azimuthal correlations with the reaction plane (elliptic flow) and jet-like two-particle correlations.
STAR consists of tracking detectors and electromagnetic calorimetry with large and azimuthally symmetric acceptance and is exceptionally well suited for single particle detection and correlation studies at high p⊥. In the last five years, it has collected a large dataset including Au+Au and Cu+Cu collisions at different energies and reference data from p+p and d+Au collisions.
We present particle spectra and two-particle correlations at high-p⊥, and relate these measurements to the properties of the medium.
A new imaging method that combines high-efficiency fast-neutron detection with sub-ns time resolution is presented. This is achieved by exploiting the high neutron detection efficiency of a thick scintillator and the fast timing capability and flexibility of light-pulse detection with a dedicated image intensifier. The neutron converter is a plastic scintillator slab or, alternatively, a scintillating fibre screen. The scintillator is optically coupled to a pulse counting image intensifier which measures the 2-dimensional position coordinates and the Time-Of-Flight (TOF) of each detected neutron with an intrinsic time resolution of less than 1 ns. Large-area imaging devices with high count rate capability can be obtained by lateral segmentation of the optical readout channels.
The CERN Axion Solar Telescope (CAST) is searching for axions produced in the Sun's core by the Primakoff process. CAST is using a decommissioned Large Hadron Collider (LHC) test magnet where axions could be converted back into X-rays with energies up to 10 keV. Analysis of the 2003 data showed no signal above background implying an upper limit for the axion-photon coupling constant gagg < 1.16 X 10 ^-10 GeV exp -1 at 95% C.L. for ma . 0.02 eV [1]. The higher quality 2004 data is presently under analysis. CAST Phase II is scheduled to start in late 2005. This will be the first step in extending CAST's sensitivity to axion rest masses up to ~ 1 eV.
The freeze out of the expanding systems, created in relativistic heavy ion collisions, is discussed. We combine kinetic freeze out equations with Bjorken type system expansion into a unified model. The important feature of the proposed scenario is that physical freeze out is completely finished in a finite time, which can be varied from 0 (freeze out hypersurface) to infinit. The dependence of the post freeze out distribution function on the freeze out time will be studied. Model allows analytical analyses for the simplest systems such as pion gas. We shall see that the basic freeze out features, pointed out in the earlier works, are not smeared out by the expansion of the system. The entropy evolution in such a scenario is also studied.
We compute neutrino emissivities, specific heat, and the resulting cooling rates in four spin-one color superconductors: color-spin locked, planar, polar, and A phases. In particular, the role of anisotropies and point nodes in the quasiparticle excitation spectra are investigated. Furthermore, it is shown that the A phase exhibits a helicity order, giving rise to a reflection asymmetry in the neutrino emissivity.
The elliptic flow for Lambda hyperons and K0s mesons was measured by the NA49 experiment in semicentral Pb+Pb collisions at 158A GeV. The standard method of correlating particles with an event plane has been used. Measurements of v2 near mid-rapidity are reported as a function of centrality, rapidity and transverse momentum. Elliptic flow of Lambda and K0s particles increases both with the impact parameter and with the transverse momentum. It is compared with v2 for pions and protons as well as with various model predictions. The NA49 results are compared with data from NA45/CERES and STAR experiments.
The multiplicity of hadronic species created in elementary, and in nucleus-nucleus collisions, are known to be well reproduced by the statistical hadronization model, in its canonical and grand-canonical versions.To understand the origin of the implied equilibrium we revisit the hadronization models developed for e+e- annihilation to hadrons which imply spatial color pre-confinement clusters forming at the end of the pQCD evolution, which decays into on-shell hadrons/resonances. The classical ensemble description arises as a consequence of decoherence and phase space dominance during cluster formation, and decay.For A+A collisions we assume that hadronization occurs from similar singlet clusters which will overlap spatially owing to the extreme density. This is imaged in the transition to the grand-canonical ensemble.This transition sets in with increasing A and collision centrality. It can be described by a percolation model.
The effects of the onset of deconfinement on longitudinal and transverse flow are studied. First, we analyze longitudinal pion spectra from Elab = 2A GeV to √sNN = 200 GeV within Landau’s hydrodynamical model and the UrQMD transport approach. From the measured data on the widths of the pion rapidity spectra, we extract the sound velocity c2s in the early stage of the reactions. It is found that the sound velocity has a local minimum (indicating a softest point in the equation of state, EoS) at Ebeam = 30A GeV. This softening of the EoS is compatible with the assumption of the formation of a mixed phase at the onset of deconfinement. Furthermore, the energy excitation function of elliptic flow (v2) from Ebeam = 90A MeV to √sNN = 200 GeV is explored within the UrQMD framework and discussed in the context of the available data. The transverse flow should also be sensitive to changes in the equation of state. Therefore, the underestimation of elliptic flow by the UrQMD model calculation above Elab = 30A GeV might also be explained by assuming a phase transition from a hadron gas to the quark gluon plasma around this energy. This would be consistent with the model calculations, indicating a transition from hadronic matter to “string matter” in this energy range.
The energy dependence of multiplicity fluctuations was studied for the most central Pb+Pb collisions at 20A, 30A, 40A, 80A and 158A GeV by the NA49 experiment at the CERN SPS. The multiplicity distribution for negatively and positively charged hadrons is significantly narrower than Poisson one for all energies. No significant structure in energy dependence of the scaled variance of multiplicity fluctuations is observed. The measured scaled variance is lower than the one predicted by the grand-canonical formulation of the hadron-resonance gas model. The results for scaled variance are in approximate agreement with the string-hadronic model UrQMD.
A new SPS programme
(2006)
A new experiemntal program to study hadron production in hadron-nucleus and nucleus-nucleus collisions at the CERN SPS has been recently proposed by the NA49-future collaboration. The physics goals of the program are: (i) search for the critical point of strongly interacting matter and a study of the properties of the onset of deconfinemnt in nucleus-nucleus collisions, (ii) measurements of correlations, fluctuations and hadron spectra at high transverse momentum in proton-nucleus collisions needed as for better understanding of nucleus-nucleus results, (iii) measurements of hadron production in hadron-nucleus interactions needed for neutrino (T2K) and cosmic-ray (Pierre Auger Observatory and KASCADE) expriments. The physics of the nucleus-nucleus program is reviewed in this presentation.
The J/psi-hadron interaction is a key ingredient in analyzing the J/psi suppression in hot hadronic matter as well as the propagation of J/psi in nuclei. As a first step to clarify the J/psi-hadron interactions at low energies, we have calculated J/psi-pi, J/psi-rho and J/psi-nucleon scattering lengths by the quenched lattice QCD simulations with Wilson fermions for beta=6.2 on 24^3*48 and 32^3*48 lattices. Using the Luscher's method to extract the scattering length from the simulations in a finite box, we find an attractive interaction in the S-wave channel for all three systems: Among others, the J/psi-nucleon interaction is most attractive. Possibility of the J/psi-nucleon bound state is also discussed.
We discuss the present collective flow signals for the phase transition to quark-gluon plasma (QGP) and the collective flow as a barometer for the equation of state (EoS). A study of Mach shocks induced by fast partonic jets propagating through the QGP is given. We predict a significant deformation of Mach shocks in central Au+Au collisions at RHIC and LHC energies as compared to the case of jet propagation in a static medium. Results of a hydrodynamical study of jet energy loss are presented.
The energy dependence of various hadronic observables is reviewed. The study of their evolution from AGS over SPS to the highest RHIC energy reveals interesting features, which might locate a possible onset of deconfinement. These observables include transverse spectra of different particle types and their total multiplicities, as well as elliptic flow. In this context especially the observation of a maximum of the strangeness to pion ratio is of particular interest, since on one hand it has been predicted as a signal for the onset of deconfinement but on the other hand also statistical model calculations exhibit qualitatively similar structures. The sharpness of these features is however not reproduced by hadronic scenarios. The significance of these structures will be discussed in this contribution. Other observables, such as radius parameters from Bose-Einstein correlations, on the other hand do not exhibit any structure in their energy dependence.
We present quantitative and qualitative arguments in favor of the claim that, within the present cosmological epoch, the U(1)gamma factor in the Standard Model is an effective manifestation of SU(2) pure gauge dynamics of Yang-Mills scale Lambda ~ 10^-4 eV. Results for the pressure and the energy density in the deconfining phase of this theory, obtained in a nonperturbative and analytical way, support this connection in view of large-angle features inherent in the map of the CMB temperature fluctuations and temperature-polarization cross correlations.
We study optimal investment in self-protection of insured individuals when they face interdependencies in the form of potential contamination from others. If individuals cannot coordinate their actions, then the positive externality of investing in self-protection implies that, in equilibrium, individuals underinvest in self-protection. Limiting insurance coverage through deductibles or selling “at-fault” insurance can partially internalize this externality and thereby improve individual and social welfare. JEL Classification: C72, D62, D80
Effects of BPA in snails
(2006)
It is an ethical requirement that new findings be presented in light of and in conjunction with a balanced evaluation of the current knowledge and published literature. We believe that Oehlmann et al. (2006) violated this general principle in several ways. For example, the authors inferred that prosobranch snails have a functional estrogen receptor and therefore a much higher sensitivity to estrogens and endocrine-disrupting compounds (EDCs) than other species previously reported in the literature. We found several other problems in their article...
We welcome critical appraisals that help to provide balance; however, Dietrich et al. gave an unjustified reproach. We feel that Dietrich’s position is severely compromised because he serves as an expert for the bisphenol A (BPA) Industry Group (Brussels, Belgium). We would like to respond to the issues raised by Dietrich et al., as well as to their oversights and inappropriate interpretations of our findings...
There is a growing body of evidence that indicates common environmental pollutants are capable of disrupting reproductive and developmental processes by interfering with the actions of endogenous hormones. Many reports of endocrine disruption describe changes in the normal development of organs and tissues that are consistent with genetic damage, and recent studies confirm that many chemicals classified to have hormone-modulating effects also possess carcinogenic and mutagenic potential. To date, however, there have been no conclusive examples linking genetic damage with perturbation of endocrine function and adverse effects in vivo. Here, we provide the first evidence of DNA damage associated with the development of imposex (the masculinization of female gastropods considered to be the result of alterations to endocrine-mediated pathways) in the dog-whelk Nucella lapillus. Animals (n = 257) that displayed various stages of tributyltin (TBT)-induced imposex were collected from sites in southwest England, and their imposex status was determined by physical examination. Linear regression analysis revealed a very strong relationship (correlation coefficient of 0.935, p < 0.0001) between the degree of imposex and the extent of DNA damage (micronucleus formation) in hemocytes. Moreover, histological examination of a larger number of dog-whelks collected from sites throughout Europe confirmed the presence of hyperplastic growths, primarily on the vas deferens and penis in both TBT-exposed male snails and in females that exhibited imposex. A strong association was found between TBT body burden and the prevalence of abnormal growths, thereby providing compelling evidence to support the hypothesis that environmental chemicals that affect reproductive processes do so partly through DNA damage pathways.
Previous investigations have shown that bisphenol A (BPA) induces a superfeminization syndrome in the freshwater snail Marisa cornuarietis at concentrations as low as 1 μg/L. Superfemales are characterized by the formation of additional female organs, enlarged accessory sex glands, gross malformations of the pallial oviduct, and a stimulation of egg and clutch production, resulting in increased female mortality. However, these studies were challenged on the basis of incomplete experimentation. Therefore, the objective of the current approach was to bridge several gaps in knowledge by conducting additional experiments. In an initial series of experiments, study results from the reproductive phase of the snails were evaluated in the sub-micrograms per liter range. Before and after the spawning season, superfemale responses were observed [NOEC (no observed effect concentration) 7.9 ng/L, EC10 (effective concentration at 10%) 13.9 ng/L], which were absent during the spawning season. A further experiment investigated the temperature dependence of BPA responses by exposing snails at two temperatures in parallel. The adverse effect of BPA was at least partially masked at 27°C (EC10 998 ng/L) when compared with 20°C (EC10 14.8 ng/L). In M. cornuarietis, BPA acts as an estrogen receptor (ER) agonist, because effects were completely antagonized by a co-exposure to tamoxifen and Faslodex. Antiandrogenic effects of BPA, such as a significant decrease in penis length at 20°C, were also observed. Competitive receptor displacement experiments indicate the presence of androgen- and estrogen-specific binding sites. The affinity for BPA of the estrogen binding sites in M. cornuarietis is higher than that of the ER in aquatic vertebrates. The results emphasize that prosobranchs are affected by BPA at lower concentrations than are other wildlife groups, and the findings also highlight the importance of exposure conditions.
Tens of thousands of man-made chemicals are in regular use and discharged into the environment. Many of them are known to interfere with the hormonal systems in humans and wildlife. Given the complexity of endocrine systems, there are many ways in which endocrine-disrupting chemicals (EDCs) can affect the body’s signaling system, and this makes unraveling the mechanisms of action of these chemicals difficult. A major concern is that some of these EDCs appear to be biologically active at extremely low concentrations. There is growing evidence to indicate that the guiding principle of traditional toxicology that “the dose makes the poison” may not always be the case because some EDCs do not induce the classical dose–response relationships. The European Union project COMPRENDO (Comparative Research on Endocrine Disrupters—Phylogenetic Approach and Common Principles focussing on Androgenic/Antiandrogenic Compounds) therefore aims to develop an understanding of potential health problems posed by androgenic and antiandrogenic compounds (AACs) to wildlife and humans by focusing on the commonalities and differences in responses to AACs across the animal kingdom (from invertebrates to vertebrates).
Polyploidy is common in higher eukaryotes, especially in plants, but it is generally assumed that most prokaryotes contain a single copy of a circular chromosome and are therefore monoploid. We have used two independent methods to determine the genome copy number in halophilic archaea, 1) cell lysis in agarose blocks and Southern blot analysis, and 2) Real-Time quantitative PCR. Fast growing H. salinarum cells contain on average about 25 copies of the chromosome in exponential phase, and their ploidy is downregulated to 15 copies in early stationary phase. The chromosome copy number is identical in cultures with a twofold lower growth rate, in contrast to the results reported for several other prokaryotic species. Of three additional replicons of H. salinarum, two have a low copy number that is not growth-phase regulated, while one replicon even shows a higher degree of growth phase-dependent regulation than the main replicon. The genome copy number of H. volcanii is similarly high during exponential phase (on average 18 copies/cell), and it is also downregulated (to 10 copies) as the cells enter stationary phase. The variation of genome copy numbers in the population was addressed by fluorescence microscopy and by FACS analysis. These methods allowed us to verify the growth phase-dependent regulation of ploidy in H. salinarum, and they revealed that there is a wide variation in genome copy numbers in individual cells that is much larger in exponential than in stationary phase. Our results indicate that polyploidy might be more widespread in archaea (or even prokaryotes in general) than previously assumed. Moreover, the presence of so many genome copies in a prokaryote raises questions about the evolutionary significance of this strategy.