CeO2 nanoparticles synthesized by a microwave-assisted hydrothermal method: evolution from nanospheres to nanorods

Ceria (CeO2) plays a vital role in emerging technologies for environmental and energy-related applications. The catalytic efficiency of ceria nanoparticles depends on its morphology. In this study, CeO2 nanoparticles were synthesized by a microwave-assisted hydrothermal method under different synthesis temperatures. The samples were characterized by X-ray diffraction, transmission electron microscopy, Raman scattering spectroscopy, electron paramagnetic resonance spectroscopy and by the Brunauer-Emmett-Teller method. The X-ray diffraction and Raman scattering results indicated that all the synthesized samples had a pure cubic CeO2 structure. Rietveld analysis and Raman scattering also revealed the presence of structural defects due to an associated reduction in the valence of the Ce4+ ions to Ce3+ ions caused by an increasing molar fraction of oxygen vacancies. The morphology of the samples was controlled by varying the synthesis temperature. The TEM images show that samples synthesized at 80 degrees C consisted of spherical particles of about 5 nm, while those synthesized at 120 degrees C presented a mix of spherical and rod-like nanoparticles and the sample synthesized at 160 degrees C consisted of nanorods with 10 nm average diameter and 70 nm length. The microwave-assisted method proved to be highly efficient for the synthesis of CeO2 nanoparticles with different morphologies.

Computational framework to support integration of biomolecular and clinical data within a translational approach

Background The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. Results We have implemented an extension of Chado – the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Conclusions Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different “omics” technologies with patient’s clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans webcite.

The β to α phase transition of tantalum coatings deposited by modulated pulsed power magnetron sputtering

Tantalum coatings are of particular interest today as promising candidates to replace potentially hazardous electrodeposited chromium coatings for tribological and corrosion resistant applications, such as the internal lining on large-caliber gun barrels. Tantalum coatings have two crystalline phases, α-Ta (body-centered-cubic) and β-Ta (metastable tetragonal) that exhibit relatively different properties. Alpha-Ta is typically preferred for wear and corrosion resistant applications and unfortunately, is very difficult to deposit without the assistance of substrate heating or post-annealing treatments. Furthermore, there is no general consensus on the mechanism which causes α or β to form or if there is a phase transition or transformation from β → α during coating deposition. In this study, modulated pulsed power (MPP) magnetron sputtering was used to deposit tantalum coatings with thicknesses between 2 and 20 μm without external substrate heating. The MPP Ta coatings showed good adhesion and low residual stress. This study shows there is an abrupt β → α phase transition when the coating is 5–7 μm thick and not a total phase transformation. Thermocouple measurements reveal substrate temperature increases as a function of deposition time until reaching a saturation temperature of ~ 388 °C. The importance of substrate temperature evolution on the β → α phase transition is also explained.

Incorporating IT & AT Convergence into Lean Thinking/Six Sigma via the Smarter Operation Transformation (SOT) Methodology

The growing demands for industrial products are imposing an increasingly intense level of competitiveness on the industrial operations. In the meantime, the convergence of information technology (IT) and automation technology (AT) is showing itself to be a tool of great potential for the modernization and improvement of industrial plants. However, for this technology fully to achieve its potential, several obstacles need to be overcome, including the demonstration of the reasoning behind estimations of benefits, investments and risks used to plan the implementation of corporative technology solutions. This article focuses on the evolutionary development of planning and adopting processes of IT & AT convergence. It proposes the incorporation of IT & AT convergence practices into Lean Thinking/Six Sigma, via the method used for planning the convergence of technological activities, known as the Smarter Operation Transformation (SOT) methodology. This article illustrates the SOT methodology through its application in a Brazilian company in the sector of consumer goods. In this application, it is shown that with IT & AT convergence is possible with low investment, in order to reduce the risk of not achieving the goals of key indicators.

Metachronic malignant transformation of small bowel and rectal endometriosis in the same patient

[ES] Background: Malignant transformation of intestinal endometriosis is a rare event with an unknown rate of incidence. Metachronous progression of endometriosis to adenocarcinoma from two distant intestinal foci happening in the same patient has not been previously reported. Case presentation: We describe a case of metachronic transformation of ileal and rectal endometriosis into an adenocarcinoma occurring in a 45-year-old female without macroscopic pelvic involvement of her endometriosis. First, a right colectomy was performed due to intestinal obstruction by an ileal mass. Pathological examination revealed an ileal endometrioid adenocarcinoma and contiguous microscopic endometriotic foci. Twenty months later, a rectal mass was discovered. An endoscopic biopsy revealed an adenocarcinoma. En bloc anterior rectum resection, hysterectomy and bilateral salpingectomy were performed. A second endometrioid adenocarcinoma arising from a focus of endometriosis within the wall of the rectum was diagnosed. Conclusion: Intestinal endometriosis should be considered a premalignant condition in premenopausal women.

Constraint handling rules. Compositional semantics and program transformation

This thesis intends to investigate two aspects of Constraint Handling Rules (CHR). It proposes a compositional semantics and a technique for program transformation. CHR is a concurrent committed-choice constraint logic programming language consisting of guarded rules, which transform multi-sets of atomic formulas (constraints) into simpler ones until exhaustion [Frü06] and it belongs to the declarative languages family. It was initially designed for writing constraint solvers but it has recently also proven to be a general purpose language, being as it is Turing equivalent [SSD05a]. Compositionality is the first CHR aspect to be considered. A trace based compositional semantics for CHR was previously defined in [DGM05]. The reference operational semantics for such a compositional model was the original operational semantics for CHR which, due to the propagation rule, admits trivial non-termination. In this thesis we extend the work of [DGM05] by introducing a more refined trace based compositional semantics which also includes the history. The use of history is a well-known technique in CHR which permits us to trace the application of propagation rules and consequently it permits trivial non-termination avoidance [Abd97, DSGdlBH04]. Naturally, the reference operational semantics, of our new compositional one, uses history to avoid trivial non-termination too. Program transformation is the second CHR aspect to be considered, with particular regard to the unfolding technique. Said technique is an appealing approach which allows us to optimize a given program and in more detail to improve run-time efficiency or spaceconsumption. Essentially it consists of a sequence of syntactic program manipulations which preserve a kind of semantic equivalence called qualified answer [Frü98], between the original program and the transformed ones. The unfolding technique is one of the basic operations which is used by most program transformation systems. It consists in the replacement of a procedure-call by its definition. In CHR every conjunction of constraints can be considered as a procedure-call, every CHR rule can be considered as a procedure and the body of said rule represents the definition of the call. While there is a large body of literature on transformation and unfolding of sequential programs, very few papers have addressed this issue for concurrent languages. We define an unfolding rule, show its correctness and discuss some conditions in which it can be used to delete an unfolded rule while preserving the meaning of the original program. Finally, confluence and termination maintenance between the original and transformed programs are shown. This thesis is organized in the following manner. Chapter 1 gives some general notion about CHR. Section 1.1 outlines the history of programming languages with particular attention to CHR and related languages. Then, Section 1.2 introduces CHR using examples. Section 1.3 gives some preliminaries which will be used during the thesis. Subsequentely, Section 1.4 introduces the syntax and the operational and declarative semantics for the first CHR language proposed. Finally, the methodologies to solve the problem of trivial non-termination related to propagation rules are discussed in Section 1.5. Chapter 2 introduces a compositional semantics for CHR where the propagation rules are considered. In particular, Section 2.1 contains the definition of the semantics. Hence, Section 2.2 presents the compositionality results. Afterwards Section 2.3 expounds upon the correctness results. Chapter 3 presents a particular program transformation known as unfolding. This transformation needs a particular syntax called annotated which is introduced in Section 3.1 and its related modified operational semantics !0t is presented in Section 3.2. Subsequently, Section 3.3 defines the unfolding rule and prove its correctness. Then, in Section 3.4 the problems related to the replacement of a rule by its unfolded version are discussed and this in turn gives a correctness condition which holds for a specific class of rules. Section 3.5 proves that confluence and termination are preserved by the program modifications introduced. Finally, Chapter 4 concludes by discussing related works and directions for future work.

Transformations of bridging ligands in diiron complexes: unconventional routes to new functionalized multisite bound organic frames

The main scope of this Ph.D. thesis has concerned the possible transformations of bridging ligands in diiron complexes, in order to explore unconventional routes to the synthesis of new functionalized multisite bound organic frames. The results achieved during the Ph.D. can be summarized in the following points: 1) We have extended the assembling between small unsaturated molecules and bridging carbyne ligands in diiron complexes to other species. In particular, we have investigated the coupling between olefins and thiocarbyne, leading to the synthesis of thioallylidene bridging diiron complexes. Then, we have extended the study to the coupling between olefins and aminocarbyne. This result shows that the coupling between activated olefins and heteroatom substituted bridging carbynes has a general character. 2) As we have shown, the coupling of bridging alkylidyne ligands with alkynes and alkenes provides excellent routes to the synthesis of bridging C3 hydrocarbyl ligands. As a possible extension of these results we have examined the synthesis of C4 bridging frames through the combination of bridging alkylidynes with allenes. Also in this case the reaction has a general character. 3) Diiron complexes bearing bridging functionalized C3 organic frames display the presence of donor atoms, such as N and S, potentially able to coordinate unsaturated metal fragments. Thus, we have studied the possibility for these systems to act as ‘organometallic ligands’, in particular towards Pd and Rh. 4) The possibility of releasing the organic frame from the bridging coordination appears particularly appealing in the direction of a metal-assisted organic synthesis. Within this field, we have investigated the possibility of involving the C3 bridging ligand in cycloaddition reactions with alkynes, with the aim of generating variously functionalized five-membered cycles. The [3+2] cyclization does not lead to the complete release of the organic fragment but rather it produces its transformation into a cyclopentadienyl ring, which remains coordinated to one Fe atom. This result introduces a new approach to the formation of polyfunctionalised ferrocenes. 5) Furthermore, I have spent a research period of about six months at the Department of Inorganic Chemistry of the Barcelona University, under the supervision of Prof. Concepción López, with the aim of studying the chemistry of polydentate ferrocenyl ligands and their use in organometallic synthesis.

A partial dependence factorial analysis to deal with selection bias in observational studis

This thesis presents a creative and practical approach to dealing with the problem of selection bias. Selection bias may be the most important vexing problem in program evaluation or in any line of research that attempts to assert causality. Some of the greatest minds in economics and statistics have scrutinized the problem of selection bias, with the resulting approaches – Rubin’s Potential Outcome Approach(Rosenbaum and Rubin,1983; Rubin, 1991,2001,2004) or Heckman’s Selection model (Heckman, 1979) – being widely accepted and used as the best fixes. These solutions to the bias that arises in particular from self selection are imperfect, and many researchers, when feasible, reserve their strongest causal inference for data from experimental rather than observational studies. The innovative aspect of this thesis is to propose a data transformation that allows measuring and testing in an automatic and multivariate way the presence of selection bias. The approach involves the construction of a multi-dimensional conditional space of the X matrix in which the bias associated with the treatment assignment has been eliminated. Specifically, we propose the use of a partial dependence analysis of the X-space as a tool for investigating the dependence relationship between a set of observable pre-treatment categorical covariates X and a treatment indicator variable T, in order to obtain a measure of bias according to their dependence structure. The measure of selection bias is then expressed in terms of inertia due to the dependence between X and T that has been eliminated. Given the measure of selection bias, we propose a multivariate test of imbalance in order to check if the detected bias is significant, by using the asymptotical distribution of inertia due to T (Estadella et al. 2005) , and by preserving the multivariate nature of data. Further, we propose the use of a clustering procedure as a tool to find groups of comparable units on which estimate local causal effects, and the use of the multivariate test of imbalance as a stopping rule in choosing the best cluster solution set. The method is non parametric, it does not call for modeling the data, based on some underlying theory or assumption about the selection process, but instead it calls for using the existing variability within the data and letting the data to speak. The idea of proposing this multivariate approach to measure selection bias and test balance comes from the consideration that in applied research all aspects of multivariate balance, not represented in the univariate variable- by-variable summaries, are ignored. The first part contains an introduction to evaluation methods as part of public and private decision process and a review of the literature of evaluation methods. The attention is focused on Rubin Potential Outcome Approach, matching methods, and briefly on Heckman’s Selection Model. The second part focuses on some resulting limitations of conventional methods, with particular attention to the problem of how testing in the correct way balancing. The third part contains the original contribution proposed , a simulation study that allows to check the performance of the method for a given dependence setting and an application to a real data set. Finally, we discuss, conclude and explain our future perspectives.

Transformation von Osteospermum ecklonis mit Konstrukten zur Induktion von Virusresistenz und Blühverfrühung

Für die Etablierung einer Transformationsmethode züchterisch relevanter Sorten von Osteospermum ecklonis (Kapmargerite) wurde zunächst ein geeignetes Protokoll für die Regeneration adventiver Sprosse aus vegetativem Gewebe entwickelt. Anschließend wurden Transformationen von Markergenen durch Kokultur mit Agrobacterium tumefaciens durchgeführt. Hierzu wurden Konstrukte verwendet, die das Gen für ß-D-Glucuronidase (GUS) enthielten und deren Expression in transgenen Pflanzen histochemisch nachgewiesen werden konnte. Kanamycinresistenz erwies sich als geeigneter Selektionsmarker für die Transformation. Es konnten von verschiedenen O. ecklonis Sorten GUS-transgene, nicht-chimäre Pflanzen regeneriert werden.Zur Erzeugung transgener Pflanzen mit dem Ziel der Resistenz gegen LMV (lettuce mosaic potyvirus, Salat Mosaik Virus) wurden drei Konstrukte verwendet. Das erste enthält die kodierende Sequenz der Virusproteine VPg, Pro und 6K2. Durch PCR-Mutation wurde die Proteinase-Schnittstelle zwischen 6K2 und VPg zerstört, sowie Start- und Stopcodon eingeführt. Die anderen LMV-abgeleiteten Konstrukte enthalten nicht translatierbare Fragmente des coat protein Gens in sense und antisense Orientierung.Außerdem wurde O. ecklonis noch mit dem Gen des mutmaßlichen Transkriptionsfaktor SPL3 aus Arabidopsis thaliana unter der Kontrolle eines konstitutiven Promotors transformiert. SPL3 ist an der Regulierung der Blüteninduktion in A. thaliana beteiligt.Regenerierte O. ecklonis wurden durch PCR mit konstruktspezifischen Primern auf Anwesenheit des Transgens und Kontamination durch A. tumefaciens überprüft.

Transformation, Progression und Zellinienspezifität der chronischen myeloischen Leukämie

Die Analyse der CML-Zellinie K562 mittels Fluoreszenz in situ Hybridisierung (FISH), Multiplex-FISH (M-FISH) und comparativer genomischer Hybridisierung (CGH) ergab einen hypotriploiden Karyotyp mit 67 Chromosomen und 21 verschiedenen Marker-Chromosomen. Das bei über 90% der CML-Patienten nachgewiesene Ph-Chromosom entsteht durch die reziproke Translokation t(9;22)(q34;q11). Bei 5 - 10% der Patienten resultiert das Ph-Chromosom aus varianten Translokation. Anhand der Untersuchung dreier varianter Translokation mittels Bruchpunkt-übergreifender FISH-Proben für die BCR- und ABL-Gene werden drei verschiedene Mechanismen der Entstehung komplexer Translokationen dargestellt. Das Auftreten sekundärer Aberrationen wurde in 15 CML-Blastenkrisen untersucht. Zudem wurde anhand der CGH-Analyse von CD34-positiven Zellen, Monozyten, Granulozyten und T-Zellen die Zellinienspezifität sekundärer Aberrationen untersucht. In einem Fall wurde eine sekundäre Aberration in allen vier Fraktionen gefunden. In zwei Fällen traten sekundäre Aberrationen in allen untersuchten Fraktionen mit Ausnahme der T-Zellen auf. Aufgrund dieser Ergebnisse lassen sich zwei alternative Modelle der Tumor-Progression der CML ableiten: 1. Sekundäre Mutatonen treten vor der Differenzierung der hämatopoetischen Stammzelle auf. 2. Sekundäre Mutationen treten in einer hämatopoetischen Vorläuferzelle nach der T-Zell-Differenzierung auf.

Bedeutung N- und C-terminaler Aminosäuren für die Monomer- und Dimerbildung von Lichtsammelproteinen des Photosystems I

Der LHCI-730 ist ein heterodimerer, Chlorophyll a/b-bindender Lichtsammelkomplex (LHC) des Photosystem I in höheren Pflanzen. Mit Hilfe rekombinanter, modifizierter Proteine wurde untersucht, welche terminalen Bereiche der Untereinheiten Lhca1 und Lhca4 für die Bildung von monomeren und dimeren Lichtsammelproteinen relevant sind. Durch PCR-Mutagenese modifizierte Apoproteine wurden in vitro mit Gesamtpigmentextrakt rekonstituiert und auf ihre Fähigkeit mono- bzw. dimere LHCs zu bilden untersucht.Für die Monomerbildung sind der extrinsische N-Terminus und die der amphipathischen vierten Helix folgenden Aminosäuren beider Proteine für die Faltung stabiler monomerer Pigmentproteinkomplexe nicht notwendig. Die Aminosäuren, mit deren Deletion die Monomerbildung an N- und C-Terminus verhindert wurde, verfügten über geladene (Glu, Asp), aromatische (Trp) oder neutrale Seitenketten (Leu).Die Untersuchungen zur Dimerbildung des LHCI-730 zeigten, daß am N-Terminus des Lhca1 nur bis zu einer Entfernung von drei Aminosäuren (Trp) eine Assemblierung der Untereinheiten möglich ist. Nur Phe (anstatt Trp) war in Substitutionsexperimenten im Vollängenprotein in der Lage, Dimere zu bilden. Das Ausbleiben der Dimerbildung der bis einschließlich zum Trp-39 und Ile-168 verkürzten Deletionsmutanten des Lhca4 ist vermutlich auf die Instabilität dieser Lhca4-Mutanten zurückzuführen. Die Deletion von Trp-185 am C-Terminus des Lhca1 führt zu einem Ausbleiben der Dimerbildung, die aber offensichtlich durch weitere, zuvor schon deletierte Aminosäuren beeinträchtigt wurde.

Application of reactive fluid transport modeling to hydrothermal systems

A one-dimensional multi-component reactive fluid transport algorithm, 1DREACT (Steefel, 1993) was used to investigate different fluid-rock interaction systems. A major short coming of mass transport calculations which include mineral reactions is that solid solutions occurring in many minerals are not treated adequately. Since many thermodynamic models of solid solutions are highly non-linear, this can seriously impact on the stability and efficiency of the solution algorithms used. Phase petrology community saw itself faced with a similar predicament 10 years ago. To improve performance and reliability, phase equilibrium calculations have been using pseudo compounds. The same approach is used here in the first, using the complex plagioclase solid solution as an example. Thermodynamic properties of a varying number of intermediate plagioclase phases were calculated using ideal molecular, Al-avoidance, and non-ideal mixing models. These different mixing models can easily be incorporated into the simulations without modification of the transport code. Simulation results show that as few as nine intermediate compositions are sufficient to characterize the diffusional profile between albite and anorthite. Hence this approach is very efficient, and can be used with little effort. A subsequent chapter reports the results of reactive fluid transport modeling designed to constrain the hydrothermal alteration of Paleoproterozoic sediments of the Southern Lake Superior region. Field observations reveal that quartz-pyrophyllite (or kaolinite) bearing assemblages have been transformed into muscovite-pyrophyllite-diaspore bearing assemblages due to action of fluids migrating along permeable flow channels. Fluid-rock interaction modeling with an initial qtz-prl assemblage and a K-rich fluid simulates the formation of observed mineralogical transformation. The bulk composition of the system evolves from an SiO2-rich one to an Al2O3+K2O-rich one. Simulations show that the fluid flow was up-temperature (e.g. recharge) and that fluid was K-rich. Pseudo compound approach to include solid solutions in reactive transport models was tested in modeling hydrothermal alteration of Icelandic basalts. Solid solutions of chlorites, amphiboles and plagioclase were included as the secondary mineral phases. Saline and fresh water compositions of geothermal fluids were used to investigate the effect of salinity on alteration. Fluid-rock interaction simulations produce the observed mineral transformations. They show that roughly the same alteration minerals are formed due to reactions with both types of fluid which is in agreement with the field observations. A final application is directed towards the remediation of nitrate rich groundwaters. Removal of excess nitrate from groundwater by pyrite oxidation was modeled using the reactive fluid transport algorithm. Model results show that, when a pyrite-bearing, permeable zone is placed in the flow path, nitrate concentration in infiltrating water can be significantly lowered, in agreement with proposals from the literature. This is due to nitrogen reduction. Several simulations investigate the efficiency of systems with different mineral reactive surface areas, reactive barrier zone widths, and flow rates to identify the optimum setup.

Charakterisierung von apoFNR, einer weiteren Form des Sauerstoffsensors FNR aus Escherichia coli und von NreB, einem potentiellen Sauerstoffsensor aus Staphylococcus carnosus

FNR (Fumarat Nitratreduktase Regulator) ist der Sauerstoffsensor aus Escherichia coli. Bisher waren zwei Formen von FNR bekannt, der aktive Zustand, ein Dimer mit je einem [4Fe4S]-Zentrum und ein inaktiver Zustand, in dem FNR als Monomer mit je einem [2Fe2S]-Zentrum vorliegt. Die Untersuchungen dieser Arbeit geben nun Hinweise, dass es mit apoFNR eine dritte physiologische Form von FNR gibt. Es wurde die Entstehung von apoFNR aus [4Fe4S]•FNR untersucht und die biochemischen Eigenschaften von apoFNR charakterisiert. ApoFNR konnte in vitro zu [4Fe4S]•FNR rekonstituiert werden, hierbei konnte die Lagphase der Rekonstitution durch Zusatz von Glutaredoxinen zum Rekonstitutionsansatz verkürzt werden. FNR, dessen Cysteinreste in vivo unter aeroben bzw. anaeroben Bedingungen mit 4-Acetamido-4´-Maleimidylstilbene-2,2´Disulfonsäure markiert wurden, zeigt auf SDS-Gelen einen Shift zu einer höheren Masse im Vergleich zu unmarkiertem FNR. Allerdings trat in aeroben Zellen eine zusätzliche Bande bei einer niedrigeren Masse auf. Es waren hier also weniger Cysteinreste markierbar. Weiterhin wurde mit NreB ein potentieller Sauerstoffsensor aus Staphylococcus carnosus untersucht. Es wurden Hinweise auf ein Eisen-Schwefel-Zentrum vom FNR-Typ als Cofaktor gefunden. Der Einbau dieses Cofaktors war abhängig von der Anwesenheit der Cysteinreste in NreB, von der Cysteindesulfurase NifSAV und von Eisenionen. Der Cofaktor war sauerstoffempfindlich und beeinflusste die Autophosphorylierung von NreB.

On the cellular stress response to Staphylococcus aureus alpha-toxin

Staphylococcus aureus alpha-hemolysin was the first bacterial toxin recognized to form pores in the plasma membrane of eukaryotic cells. It is secreted as a water-soluble monomer that upon contact with target membranes forms an amphiphatic heptameric beta-barrel which perforates the bilayer. As a consequence, red cells undergo colloidosmotic lyses, while some nucleated cells may succumb to necrosis or programmed cell death. However, most cells are capable of repairing a limited number of membrane lesions, and then respond with productive transcriptional activation of NF-kB. In the present study, by using microarray and semiquantitative reverse transcriptase polymerase chain reaction (RT-PCR), data from a previously performed serial analysis of gene expression (SAGE) were extended and verified, revealing that immediate early genes (IEGs) such as c-fos, c-jun and egr-1 are strongly induced at 2-8 h after transient toxin treatment. Activating protein 1 (AP-1: c-Fos, c-Jun) binding activity was increased accordingly. As IEGs are activated by growth factors, these findings led to the discovery that -toxin promotes cell cycle progression of perforated cells in an EGFR-dependent fashion. Although the amount of c-fos mRNA rose rapidly after toxin treatment, c-Fos protein expression was observed only after a lag of about 3 h. Since translation consumes much ATP, which transiently drops after transient membrane perforation, the suspicion arised that membrane-perforation caused global, but temporary downregulation of translation. In fact, eIF2α became heavily phosphorylated minutes after cells had been confronted with the toxin, resulting in shutdown of protein synthesis before cellular ATP levels reached the nadir. GCN2 emerged as a candidate eIF2α kinase, since its expression rapidly increased in toxin-treated cells. Two hours after toxin treatment, GADD34 transcripts, encoding a protein that targets the catalytic subunit of protein phosphatase 1 (PP1) to the endoplasmic reticulum, were overexpressed. This was followed by dephosphorylation of eIF2α and resumption of protein synthesis. Addition of tautomycetin, a specific inhibitor of PP1, led to marked hyperphosphorylation of eIF2α and significantly reduced the drop of ATP-levels in toxin-treated cells. A novel link between two major stress-induced signalling pathways emerged when it was found that both translational arrest and restart were under the control of stress-activated protein kinase (SAPK) p38. The data provide an explanation for the indispensible role of p38 for defence against the archetypal threat of membrane perforation by agents that produce small transmembrane-pores.

Structural transformations related to organic solid-state reactions: correlation studies of NMR and X-ray analysis

Eine zielgerichtete Steuerung und Durchführung von organischen Festkörperreaktionen wird unter anderem durch genaue Kenntnis von Packungseffekten ermöglicht. Im Rahmen dieser Arbeit konnte durch den kombinierten Einsatz von Einkristallröntgenanalyse und hochauf-lösender Festkörper-NMR an ausgewählten Beispielen ein tieferes Verständnis und Einblicke in die Reaktionsmechanismen von organischen Festkörperreaktionen auf molekularer Ebene gewonnen werden. So konnten bei der topotaktischen [2+2] Photodimerisierung von Zimt-säure Intermediate isoliert und strukturell charakterisiert werden. Insbesondere anhand statischer Deuteronen- und 13C-CPMAS NMR Spektren konnten eindeutig dynamische Wasserstoffbrücken nachgewiesen werden, die transient die Zentrosymmetrie des Reaktions-produkts aufheben. Ein weiterer Nachweis gelang daraufhin mittels Hochtemperatur-Röntgen-untersuchung, sodass der scheinbare Widerspruch von NMR- und Röntgenuntersuchungen gelöst werden konnte. Eine Veresterung der Zimtsäure entfernt diese Wasserstoffbrücken und erhält somit die Zentrosymmetrie des Photodimers. Weiterhin werden Ansätze zur Strukturkontrolle in Festkörpern basierend auf der molekularen Erkennung des Hydroxyl-Pyridin (OH-N) Heterosynthon in Co-Kristallen beschrieben, wobei vor allem die Stabilität des Synthons in Gegenwart funktioneller Gruppen mit Möglichkeit zu kompetetiver Wasserstoffbrückenbildung festgestellt wurde. Durch Erweiterung dieses Ansatzes wurde die molekulare Spezifität des Hydroxyl-Pyridin (OH-N) Heterosynthons bei gleichzeitiger Co-Kristallisation mit mehreren Komponenten erfolgreich aufgezeigt. Am Beispiel der Co-Kristallisation von trans--1,2-bis(4-pyridyl)ethylen (bpe) mit Resorcinol (res) in Gegenwart von trans-1,2-bis(4-pyridyl)ethan (bpet) konnten Zwischenprodukte der Fest-körperreaktionen und neuartige Polymorphe isoliert werden, wobei eine lückenlose Aufklärung des Reaktionswegs mittels Röntgenanalyse gelang. Dabei zeigte sich, dass das Templat Resorcinol aus den Zielverbindungen entfernbar ist. Ferner gelang die Durchführung einer seltenen, nicht-idealen Einkristall-Einkristall-Umlagerung von trans--1,2-bis(4-pyridyl)ethylen (bpe) mit Resorcinol (res). In allen Fällen konnten die Fragen zur Struktur und Dynamik der untersuchten Verbindungen nur durch gemeinsame Nutzung von Röntgenanalyse und NMR-Spektroskopie bei vergleichbaren Temperaturen eindeutig und umfassend geklärt werden.