Sels d’imidazolium avec des anions catalytiques : vers le développement de nouveaux catalyseurs bio-hybrides actifs en milieu liquide ionique

Les liquides ioniques connaissent depuis quelques décennies un essor particulier en raison de leurs nombreuses propriétés physico-chimiques intéressantes, telles qu’une faible pression de vapeur saturante, une viscosité limitée, une faible miscibilité avec la plupart des solvants communs, ou encore des propriétés d’agencement supramoléculaire, qui en font des outils puissants dans de nombreux domaines de la chimie. Les sels d’imidazolium représentent la plus grande famille de liquides ioniques à ce jour. Leur modulabilité leur permet d’être dérivés pour de nombreuses applications spécifiques, notamment en synthèse organique, où ils sont utilisés majoritairement comme solvants, et plus récemment comme catalyseurs. Les travaux présentés dans cette thèse se concentrent sur leur utilisation en synthèse organique, à la fois comme solvants et principalement comme catalyseurs chiraux, catalyseurs pour lesquels l’anion du sel est l’espèce catalytique, permettant d’ajouter de la flexibilité et de la mobilité au système. En tirant parti de la tolérance des liquides ioniques envers la majorité des macromolécules naturelles, l’objectif principal des travaux présentés dans cette thèse est le développement d’un nouveau type de catalyseur bio-hybride reposant sur l’encapsulation d’un sel d’imidazolium dans une protéine. Par le biais de la technologie biotine-avidine, l’inclusion supramoléculaire de sels d’imidazolium biotinylés portant des contre-anions catalytiques dans l’avidine a été réalisée et exploitée en catalyse. Dans un premier temps, le développement et l’étude de deux sels de 1-butyl-3-méthylimidazolium possédant des anions chiraux dérivés de la trans-4-hydroxy-L-proline sont rapportés, ainsi que leur comportement dans des réactions énantiosélectives d’aldol et d’addition de Michael. Ces types de composés se sont révélés actifs et performants en milieu liquide ionique. Dans un second temps, la préparation de sels d’imidazolium dont le cation est biotinylé et portant un contre-anion achiral, a été réalisée. Le comportement de l’avidine en milieu liquide ionique et son apport en termes de chiralité sur le système bio-hybride ont été étudiés. Les résultats montrent le rôle crucial des liquides ioniques sur la conformation de la protéine et l’efficacité du catalyseur pour des réactions d’aldol. Dans un dernier temps, l’influence de la structure du cation et de l’anion sur le système a été étudiée. Différents espaceurs ont été introduits successivement dans les squelettes cationiques et anioniques des sels d’imidazolium biotinylés. Dans le cas du cation, les résultats ne révèlent aucune influence majeure sur l’efficacité du catalyseur. La structure de l’anion se montre cependant beaucoup plus importante : la préparation de différents catalyseurs bio-hybrides possédant des anions aux propriétés physico-chimiques différentes a permis d’obtenir de plus amples informations sur le mode de fonctionnement du système bio-hybride et de la coopérativité entre l’avidine et l’anion du sel d’imidazolium.La nature ionique de la liaison cation-anion offrant une liberté de mouvement accrue à l’anion dans la protéine, la tolérance à différents substrats a également été abordée après optimisation du système.

DNA methylation in Dictyostelium discoideum

DNA methyltransferases of type Dnmt2 are a highly conserved protein family with enigmatic function. The aim of this work was to characterize DnmA, the Dnmt2 methyltransferase in Dictyostelium discoideum, and further to investigate its implication in DNA methylation and transcriptional gene silencing. The genome of the social amoeba Dictyostelium encodes DnmA as the sole DNA methyltransferase. The enzyme bears all ten characteristic DNA methyltransferase motifs in its catalytic domain. The DnmA mRNA was found by RT-PCR to be expressed during vegetative growth and down regulated during development. Investigations using fluorescence microscopy showed that both DnmA-myc and DnmA-GFP fusions predominantly localised to the nucleus. The function of DnmA remained initially unclear, but later experiment revealed that the enzyme is an active DNA methyltransferase responsible for all DNA (cytosine) methylation in Dictyostelium. Neither in gel retardation assays, nor by the yeast two hybrid system, clues on the functionality of DnmA could be obtained. However, immunological detection of the methylation mark with an α - 5mC antibody gave initial evidence that the DNA of Dictyostelium was methylated. Furthermore, addition of 5-aza-cytidine as demethylating agent to the Dictyostelium medium and subsequent in vitro incubation of the DNA isolated from these cells with recombinant DnmA showed that the enzyme binds slightly better to this target DNA. In order to investigate further the function of the protein, a gene knock-out for dnmA was generated. The gene was successfully disrupted by homologous recombination, the knock-out strain, however, did not show any obvious phenotype under normal laboratory conditions. To identify specific target sequences for DNA methylation, a microarray analysis was carried out. Setting a threshold of at least 1.5 fold for differences in the strength of gene expression, several such genes in the knock-out strain were chosen for further investigation. Among the up-regulated genes were the ESTs representing the gag and the RT genes respectively of the retrotransposon skipper. In addition Northern blot analysis confirmed the up-regulation of skipper in the DnmA knock-out strain. Bisufite treatment and sequencing of specific DNA stretches from skipper revealed that DnmA is responsible for methylation of mostly asymmetric cytosines. Together with skipper, DIRS-1 retrotransposon was found later also to be methylated but was not present on the microarray. Furthermore, skipper transcription was also up-regulated in strains that had genes disrupted encoding components of the RNA interference pathway. In contrast, DIRS 1 expression was not affected by a loss of DnmA but was strongly increased in the strain that had the RNA directed RNA polymerase gene rrpC disrupted. Strains generated by propagating the usual wild type Ax2 and the DnmA knock-out cells over 16 rounds in development were analyzed for transposon activity. Northern blot analysis revealed activation for skipper expression, but not for DIRS-1. A large number of siRNAs were found to be correspondent to the DIRS-1 sequence, suggesting concerted regulation of DIRS-1 expression by RNAi and DNA methylation. In contrast, no siRNAs corresponding to the standard skipper element were found. The data show that DNA methylation plays a crucial role in epigenetic gene regulation in Dictyostelium and that different, partially overlapping mechanisms control transposon silencing for skipper and DIRS-1. To elucidate the mechanism of targeting the protein to particular genes in the Dictyostelium genome, some more genes which were up-regulated in the DnmA knock-out strain were analyzed by bisulfite sequencing. The chosen genes are involved in the multidrug response in other species, but their function in Dictyostelium is uncertain. Bisulfite data showed that two of these genes were methylated at asymmetrical C-residues in the wild type, but not in DnmA knock-out cells. This suggested that DNA methylation in Dictyostelium is involved not only in transposon regulation but also in transcriptional silencing of specific genes.

Das ER-lokalisierte Protein Farinelli und seine möglichen Interaktionspartner in der Spermatogenese von Drosophila melanogaster

Dem Farinelli-Protein wird eine Funktion als hodenspezifisches VAP-Protein zugesprochen (Renner, 2001). Mit Hilfe des ER-Markers PDI konnte Fan eindeutig dem ER zugeordnet werden. Fan stellt dabei ein integrales Membranprotein dar, welches nur durch Detergenz- Behandlung in Lösung zu bringen war. Durch den Einsatz zweier Fragment-Konstrukte (fan∆MSP-GFP und fanMSP-GFP) von Fan wurde die Relevanz der MSP-Domäne für die männliche Fertilität dokumentiert. Das Fusionsprotein Fan∆MSP-GFP lag aufgrund der verbliebenen Transmembrandomäne weiterhin im ER vor. Dennoch konnte der sterile Phänotyp der fanJo-Männchen, die keinerlei Fan-Protein enthalten, durch das Einbringen des Fusionskonstrukts nicht gerettet werden. MSP-GFP für sich allein konnte keine Verbindung mit dem ER eingehen und zeigte eine diffuse Fluoreszenz. Im Rahmen der Dissertation wurden mehrere, durch das yeast two hybrid-System ermittelte, mögliche Interaktionspartner von Fan analysiert. Das Protein CG5194 konnte als einziges wie Fan dem ER zugeordnet werden. Seine Expression beschränkte sich aber auf die Spermatocytenphase und ist somit kürzer als die von Farinelli. Nach Einkreuzen der GFP-Fusionskonstrukte in die fan-Nullmutante konnte CG5194 nicht mehr am ER der Spermatocyten beobachtet werden, sondern lag innerhalb des Cytoplasmas diffus verteilt vor. Auch bei der Western Blot-Analyse konnte das Protein von CG5194 nur noch in der Überstand-Fraktion mit den ungebundenen Proteinen nachgewiesen werden. Lag in der fan-Nullmutante ausschließlich das Fan∆MSP-GFP-Fusionsprotein vor, konnte die ER-Lokalisation von CG5194 ebenfalls nicht beibehalten werden. Mit Hilfe einer Fragment-Analyse konnte gezeigt werden, dass in den männlichen Gonaden das erste Exon von CG5194 für die Interaktion mit Fan entscheidend ist. Innerhalb der Ovarien dagegen ist das zweite Exon für die Lokalisation im ER notwendig. Demzufolge ist neben einem anderen Interaktionspartner als Fan auch eine andere Domäne im Protein für die ER-Lokalisation in der weiblichen Keimbahn entscheidend. Durch den Einsatz von antisense- und RNAi-Konstrukten konnte ein steriler Phänotyp bei den Männchen erzeugt werden. Überraschenderweise zeigten die Tiere erst einen Defekt während der Spermatiden-Differenzierung. Bereits während der Diplomarbeit wurde 98A im Kopfbereich der elongierten Spermatiden nachgewiesen. Mittels einer DNA-Färbung sowie durch die Colokalisation mit dem Akrosom-Protein Sneaky wurde 98A dem Bereich des Akrosoms zugeordnet. Sneaky taucht jedoch bereits früher als 98A in den Keimzellen auf. Die Erzeugung eines sterilen Phänotyps durch den Einfluss eines RNAi-Konstrukts gelang nicht. Entweder ist 98A für die Fertilität von Drosophila nicht relevant oder aber seine Funktion kann von anderen Proteinen übernommen werden.

Untersuchungen zur Rolle von Isoformen katalytischer Untereinheiten der PKA

ZUSAMMENFASSUNG: Proteinkinasen übernehmen zentrale Aufgaben in der Signaltransduktion höherer Zellen. Dabei ist die cAMP-abhängige Proteinkinase (PKA) bezüglich ihrer Struktur und Funktion eine der am besten charakterisierten Proteinkinasen. Trotzdem ist wenig über direkte Interaktionspartner der katalytischen Untereinheiten (PKA-C) bekannt. In einem Split-Ubiquitin basiertem Yeast Two Hybrid- (Y2H-)System wurden potenzielle Interaktionspartner der PKA-C identifiziert. Als Bait wurden sowohl die humane Hauptisoform Cα (hCα) als auch die Proteinkinase X (PrKX) eingesetzt. Nach der Bestätigung der Funktionalität der PKA-C-Baitproteine, dem Nachweis der Expression und der Interaktion mit dem bekannten Interaktionspartner PKI wurde ein Y2H-Screen gegen eine Mausembryo-cDNA-Expressionsbibliothek durchgeführt. Von 2*10^6 Klonen wurden 76 Kolonien isoliert, die ein mit PrKX interagierendes Preyprotein exprimierten. Über die Sequenzierung der enthaltenen Prey-Vektoren wurden 25 unterschiedliche, potenzielle Interaktionspartner identifiziert. Für hCα wurden über 2*10^6 S. cerevisiae-Kolonien untersucht, von denen 1.959 positiv waren (1.663 unter erhöhter Stringenz). Über die Sequenzierung von ca. 10% der Klone (168) konnten Sequenzen für 67 verschiedene, potenzielle Interaktionspartner der hCα identifiziert werden. 15 der Preyproteine wurden in beiden Screens identifiziert. Die PKA-C-spezifische Wechselwirkung der insgesamt 77 Preyproteine wurde im Bait Dependency Test gegen largeT, ein Protein ohne Bezug zum PKA-System, untersucht. Aus den PKA-C-spezifischen Bindern wurden die löslichen Preyproteine AMY-1, Bax72-192, Fabp3, Gng11, MiF, Nm23-M1, Nm23-M2, Sssca1 und VASP256-375 für die weitere in vitro-Validierung ausgewählt. Die Interaktion von FLAG-Strep-Strep-hCα (FSS-hCα) mit den über Strep-Tactin aus der rekombinanten Expression in E. coli gereinigten One-STrEP-HA-Proteinen (SSHA-Proteine) wurde über Koimmunpräzipitation für SSHA-Fabp3, -Nm23-M1, -Nm23-M2, -Sssca1 und -VASP256-375 bestätigt. In SPR-Untersuchungen, für die hCα kovalent an die Oberfläche eines CM5-Sensorchips gekoppelt wurde, wurden die ATP/Mg2+-Abhängigkeit der Bindungen sowie differentielle Effekte der ATP-kompetitiven Inhibitoren H89 und HA-1077 untersucht. Freie hCα, die vor der Injektion zu den SSHA-Proteinen gegeben wurde, kompetierte im Gegensatz zu FSS-PrKX die Bindung an die hCα-Oberfläche. Erste kinetische Analysen lieferten Gleichgewichtsdissoziationskonstanten im µM- (SSHA-Fabp3, -Sssca1), nM- (SSHA-Nm23-M1, –M2) bzw. pM- (SSHA-VASP256-375) Bereich. In funktionellen Analysen konnte eine Phosphorylierung von SSHA-Sssca1 und VASP256-375 durch hCα und FSS-PrKX im Autoradiogramm nachgewiesen werden. SSHA-VASP256-375 zeigte zudem eine starke Inhibition von hCα im Mobility Shift-Assay. Dieser inhibitorische Effekt sowie die hohe Affinität konnten jedoch auf eine Kombination aus der Linkersequenz des Vektors und dem N-Terminus von VASP256-375 zurückgeführt werden. Über die Wechselwirkungen der hier identifizierten Interaktionspartner Fabp3, Nm23-M1 und Nm23-M2 mit hCα können in Folgeuntersuchungen neue PKA-Funktionen insbesondere im Herzen sowie während der Zellmigration aufgedeckt werden. Sssca1 stellt dagegen ein neues, näher zu charakterisierendes PKA-Substrat dar.

The Logical Problem of Language Change

This paper considers the problem of language change. Linguists must explain not only how languages are learned but also how and why they have evolved along certain trajectories and not others. While the language learning problem has focused on the behavior of individuals and how they acquire a particular grammar from a class of grammars ${cal G}$, here we consider a population of such learners and investigate the emergent, global population characteristics of linguistic communities over several generations. We argue that language change follows logically from specific assumptions about grammatical theories and learning paradigms. In particular, we are able to transform parameterized theories and memoryless acquisition algorithms into grammatical dynamical systems, whose evolution depicts a population's evolving linguistic composition. We investigate the linguistic and computational consequences of this model, showing that the formalization allows one to ask questions about diachronic that one otherwise could not ask, such as the effect of varying initial conditions on the resulting diachronic trajectories. From a more programmatic perspective, we give an example of how the dynamical system model for language change can serve as a way to distinguish among alternative grammatical theories, introducing a formal diachronic adequacy criterion for linguistic theories.

Lower Bounds for Achieving Synchronous Early Stopping Consensus with Orderly Crash Failures

In this paper, we discuss the consensus problem for synchronous distributed systems with orderly crash failures. For a synchronous distributed system of n processes with up to t crash failures and f failures actually occur, first, we present a bivalency argument proof to solve the open problem of proving the lower bound, min (t + 1, f + 2) rounds, for early-stopping synchronous consensus with orderly crash failures, where t < n - 1. Then, we extend the system model with orderly crash failures to a new model in which a process is allowed to send multiple messages to the same destination process in a round and the failing processes still respect the order specified by the protocol in sending messages. For this new model, we present a uniform consensus protocol, in which all non-faulty processes always decide and stop immediately by the end of f + 1 rounds. We prove that the lower bound of early stopping protocols for both consensus and uniform consensus are f + 1 rounds under the new model, and our proposed protocol is optimal.

Robust fault detection using consistency techniques for uncertainty handling

Often practical performance of analytical redundancy for fault detection and diagnosis is decreased by uncertainties prevailing not only in the system model, but also in the measurements. In this paper, the problem of fault detection is stated as a constraint satisfaction problem over continuous domains with a big number of variables and constraints. This problem can be solved using modal interval analysis and consistency techniques. Consistency techniques are then shown to be particularly efficient to check the consistency of the analytical redundancy relations (ARRs), dealing with uncertain measurements and parameters. Through the work presented in this paper, it can be observed that consistency techniques can be used to increase the performance of a robust fault detection tool, which is based on interval arithmetic. The proposed method is illustrated using a nonlinear dynamic model of a hydraulic system

Diagnosing Patients Combining Principal Components Analysis and Case Based Reasoning

This paper addresses the application of a PCA analysis on categorical data prior to diagnose a patients data set using a Case-Based Reasoning (CBR) system. The particularity is that the standard PCA techniques are designed to deal with numerical attributes, but our medical data set contains many categorical data and alternative methods as RS-PCA are required. Thus, we propose to hybridize RS-PCA (Regular Simplex PCA) and a simple CBR. Results show how the hybrid system produces similar results when diagnosing a medical data set, that the ones obtained when using the original attributes. These results are quite promising since they allow to diagnose with less computation effort and memory storage

Modelación de los sectores estudiados para definir el perfil logístico de Colombia

Colombia siempre ha velado por tener una mejor infraestructura del país, haciendo que se mantenga preocupado por su posición competitiva frente a su desarrollo como hub logístico de Latinoamérica. Esto se ve fundamentado a través de la política nacional logística escrita en el COMPES 3547. Sin embargo, hay un desconocimiento por los empresarios grandes y pequeños del país acerca de las pretensiones que el gobierno quiere llevar a cabo sobre los distintos sectores económicos. La simulación de estructuras como sistemas es de vital importancia para el desarrollo y mejoramiento de cadenas de suministro. La administración de la cadena como sistema que integra procesos permite producir constantemente, mantener niveles adecuados de inventario y cumplir con los requerimientos del cliente final. Lo anterior teniendo en cuenta que los principales actores de la cadena son proveedores, fabricantes, clientes, detallistas, transportadores y distribuidores, En un entorno en el que la globalización constituye quizá el motor más importante para el desempeño de la cadena de suministros, pues rompe barreras geográficas. En síntesis la simulación es un aporte importante para la correcta planeación y operación de la cadena de suministros y esto a la vez permite prestar un buen servicio al cliente mientras se reducen costos y tiempos.

Architecture for Living Neuronal Network Control of a mobile robot

The intelligent controlling mechanism of a typical mobile robot is usually a computer system. Research is however now ongoing in which biological neural networks are being cultured and trained to act as the brain of an interactive real world robot – thereby either completely replacing or operating in a cooperative fashion with a computer system. Studying such neural systems can give a distinct insight into biological neural structures and therefore such research has immediate medical implications. The principal aims of the present research are to assess the computational and learning capacity of dissociated cultured neuronal networks with a view to advancing network level processing of artificial neural networks. This will be approached by the creation of an artificial hybrid system (animat) involving closed loop control of a mobile robot by a dissociated culture of rat neurons. This paper details the components of the overall animat closed loop system architecture and reports on the evaluation of the results from preliminary real-life and simulated robot experiments.

Normal coordinates for the planar vibrations of benzene

Force constants and normal coordinates have been recalculated for all of the in-plane vibrations of benzene, making use of the recently observed data on one of the Coriolis constants in the E2g species from the work of Callomon et al. The extent to which the force field is uniquely determined by the data is reviewed for each symmetry species in turn, and the results of a force constant refinement calculation are reported in which a modified valency force field was used based on the hybrid orbital model. The results show considerable differences from Whiffen's normal coordinates for benzene, but somewhat smaller differences from Scherer's recent calculations.

Controlling a mobile robot with a biological brain

The intelligent controlling mechanism of a typical mobile robot is usually a computer system. Some recent research is ongoing in which biological neurons are being cultured and trained to act as the brain of an interactive real world robot�thereby either completely replacing, or operating in a cooperative fashion with, a computer system. Studying such hybrid systems can provide distinct insights into the operation of biological neural structures, and therefore, such research has immediate medical implications as well as enormous potential in robotics. The main aim of the research is to assess the computational and learning capacity of dissociated cultured neuronal networks. A hybrid system incorporating closed-loop control of a mobile robot by a dissociated culture of neurons has been created. The system is flexible and allows for closed-loop operation, either with hardware robot or its software simulation. The paper provides an overview of the problem area, gives an idea of the breadth of present ongoing research, establises a new system architecture and, as an example, reports on the results of conducted experiments with real-life robots.

Architecture for neuronal cell control of a mobile robot

It is usually expected that the intelligent controlling mechanism of a robot is a computer system. Research is however now ongoing in which biological neural networks are being cultured and trained to act as the brain of an interactive real world robot - thereby either completely replacing or operating in a cooperative fashion with a computer system. Studying such neural systems can give a distinct insight into biological neural structures and therefore such research has immediate medical implications. In particular, the use of rodent primary dissociated cultured neuronal networks for the control of mobile `animals' (artificial animals, a contraction of animal and materials) is a novel approach to discovering the computational capabilities of networks of biological neurones. A dissociated culture of this nature requires appropriate embodiment in some form, to enable appropriate development in a controlled environment within which appropriate stimuli may be received via sensory data but ultimate influence over motor actions retained. The principal aims of the present research are to assess the computational and learning capacity of dissociated cultured neuronal networks with a view to advancing network level processing of artificial neural networks. This will be approached by the creation of an artificial hybrid system (animal) involving closed loop control of a mobile robot by a dissociated culture of rat neurons. This 'closed loop' interaction with the environment through both sensing and effecting will enable investigation of its learning capacity This paper details the components of the overall animat closed loop system and reports on the evaluation of the results from the experiments being carried out with regard to robot behaviour.

A stable one-step-ahead predictive control of non-linear systems

In this paper stability of one-step ahead predictive controllers based on non-linear models is established. It is shown that, under conditions which can be fulfilled by most industrial plants, the closed-loop system is robustly stable in the presence of plant uncertainties and input–output constraints. There is no requirement that the plant should be open-loop stable and the analysis is valid for general forms of non-linear system representation including the case out when the problem is constraint-free. The effectiveness of controllers designed according to the algorithm analyzed in this paper is demonstrated on a recognized benchmark problem and on a simulation of a continuous-stirred tank reactor (CSTR). In both examples a radial basis function neural network is employed as the non-linear system model.

A mixture of experts network structure construction algorithm for modelling and control

This paper introduces a new fast, effective and practical model structure construction algorithm for a mixture of experts network system utilising only process data. The algorithm is based on a novel forward constrained regression procedure. Given a full set of the experts as potential model bases, the structure construction algorithm, formed on the forward constrained regression procedure, selects the most significant model base one by one so as to minimise the overall system approximation error at each iteration, while the gate parameters in the mixture of experts network system are accordingly adjusted so as to satisfy the convex constraints required in the derivation of the forward constrained regression procedure. The procedure continues until a proper system model is constructed that utilises some or all of the experts. A pruning algorithm of the consequent mixture of experts network system is also derived to generate an overall parsimonious construction algorithm. Numerical examples are provided to demonstrate the effectiveness of the new algorithms. The mixture of experts network framework can be applied to a wide variety of applications ranging from multiple model controller synthesis to multi-sensor data fusion.