Η άθροιση μεγάλων αριθμών είναι μια χρονοβόρα και ενεργοβόρα διαδικασία. Πολλές μέθοδοι έχουν αναπτυχθεί για να μειωθεί η καθυστέρηση υπολογισμού του αθροίσματος λόγω της μετάδοσης κρατουμένου. Τέτοιες είναι η πρόβλεψη κρατουμένου (carry look ahead) και η επιλογή κρατουμένου (carry select). Αυτές οι αρχιτεκτονικές δεν είναι επαρκώς επεκτάσιμες για μεγάλους αριθμούς (με πολλά bits) ή πολλούς αριθμούς, διότι παράγονται μεγάλα και ενεργοβόρα κυκλώματα. Στην παρούσα εργασία μελετάται η μέθοδος υπολοίπου (RNS), η οποία χρησιμοποιεί συστήματα αριθμών μεγαλύτερα από το δυαδικό. Ορίζεται μια βάση τριών αριθμών και οι αριθμοί αναπαρίστανται στα εκάστοτε τρία συστήματα της βάσης. Η άθροιση γίνεται παράλληλα σε κάθε σύστημα και τέλος οι αριθμοί μετατρέπονται πάλι στο δυαδικό. Τα πλεονεκτήματα αυτής της προσέγγισης είναι η παραλληλία και η απουσία μεγάλων κυκλωμάτων διάδοσης κρατουμένου. Το μειονέκτημα είναι ότι χρειάζονται κυκλώματα μετατροπής από και προς το δυαδικό σύστημα. Αυτού του είδους οι αθροιστές συγκρίνονται για κατανάλωση ενέργειας με τους γνωστούς carry look ahead και carry select. Διαπιστώθηκε ότι οι RNS αθροιστές καταναλώνουν λιγότερη ενέργεια. / The addition of many-bits numbers is a time and power consuming task. Many methods are developed to reduce the sum calculation delay due to carry propagation. Such techniques are Carry Look Ahead and Carry Select, Those techniques are not scalable to many bits numbers or a set of many numbers: the circuits needed are big and power consuming. In this thesis, the the RNS technique is investigated. This technique uses radix bigger than binary. A 3-numbers base is defined and the numbers that participate in the sum are represented uniquely in each element radix. The addition is performed in parallel in each radix. Finally the result is transformed back to the binary numbers system. The advantages of this technique are the parallelization of the process and the lack of carry propagation circuits. The disadvantage is that transformation circuits are need from/to binary system. The RNS adders are compared to CLA and CS for power. Such adders are compared to CLA and CS for power consumption. It is found that RNS adders consume less energy.

It is currently believed that the splicing of most pre-mRNAs occurs, at least in part, co-transcriptionally. In order to validate this principle in yeast and establish an experimental system for monitoring spliceosome assembly in vivo, I have employed the chromatin immunoprecipitation (ChIP) assay to study co-transcriptional splicing events. Here, I use ChIP to examine key questions with respect to the recent proposal that RNA polymerase II (Pol II) recruits pre-mRNA splicing factors to active genes. In my thesis, I address: 1) whether the U1 snRNP, which binds to the 5¡¦ splice site of each intron, is recruited co-transcriptionally in vivo and 2) if so, where along the length of active genes the U1 snRNP is concentrated. U1 snRNP accumulates on downstream positions of genes containing introns but not within promoter regions or along intronless genes. More specifically, accumulation correlated with the presence and position of the intron, indicating that the intron is necessary for co-transcriptional U1 snRNP recruitment and/or retention (Kotovic et al., 2003). In contrast to capping enzymes, which bind directly to Pol II (Komarnitsky et al., 2000; Schroeder et al., 2000), the U1 snRNP is poorly detected in promoter regions, except in genes harboring promoter-proximal introns. Detection of the U1 snRNP is dependent on RNA synthesis and is abolished by intron removal. Microarray data reveals that intron-containing genes are preferentially selected by ChIP with the U1 snRNP furthermore indicating recruitment specificity to introns. Because U1 snRNP levels decrease on downstream regions of intron-containing genes with long second exons, our lab is expanding the study to 3¡¦ splice site factors in hopes to address co-transcriptional splicing. In my thesis, I also focus on questions pertaining to the requirements for recruitment of the U1 snRNP to sites of transcription. To test the proposal that the cap-binding complex (CBC) promotes U1 snRNP recognition of the 5¡¦ splice site (Colot et al., 1996), I use a ?´CBC mutant strain and determine U1 snRNP accumulation by ChIP. Surprisingly, lack of the CBC has no effect on U1 snRNP recruitment. The U1 snRNP component Prp40p has been identified as playing a pivotal role in not only cross-intron bridging (Abovich and Rosbash, 1997), but also as a link between Pol II transcription and splicing factor recruitment (Morris and Greenleaf, 2000). My data shows that Prp40p recruitment mirrors that of other U1 snRNP proteins, in that it is not detected on promoter regions, suggesting that Prp40p does not constitutively bind the phosphorylated C-terminal domain (CTD) of Pol II as previously proposed. This physical link between Pol II transcription and splicing factor recruitment is further tested in Prp40p mutant strains, in which U1 snRNP is detected at normal levels. Therefore, U1 snRNP recruitment to transcription units is not dependent on Prp40p activity. My data indicates that co-transcriptional U1 snRNP recruitment is not dependent on the CBC or Prp40p and that any effects of these players on spliceosome assembly must be reflected in later spliceosome events. My data contrasts the proposed transcription factory model in which Pol II plays a central role in the recruitment of mRNA processing factors to TUs. According to my data, splicing factor recruitment acts differently than capping enzyme and 3¡¦ end processing factor recruitment; U1 snRNP does not accumulate at promoter regions of intron-containing genes or on intronless genes rather, accumulation is based on the synthesis of the intron. These experiments have lead me to propose a kinetic model with respect to the recruitment of splicing factors to active genes. In this model, U1 snRNP accumulation at the 5¡¦ splice site requires a highly dynamic web of protein-protein and protein-RNA interactions to occur, ultimately leading to the recruitment and/or stabilization of the U1 snRNP.

Phosducin-like Protein existiert in zwei Splicevarianten: PhLPLONG (PhLPL) und PhLPSHORT (PhLPS). Sie unterscheiden sich in der Länge ihres N-Terminus und in ihrem Expressionsmusters: Die lange Form (PhLPL) wird ubiquitär exprimiert und bindet G-Protein-betagamma-Untereinheiten (Gbetagama), was zur Hemmung von Gbetagamma-abhängigen Funktionen führt. Der um 83 Aminosäuren verlängerte N-Terminus besitzt ein hoch konserviertes Motiv, welches für die Gbetagamma-Bindung und Regulation von entscheidender Bedeutung ist. Im Gegensatz hierzu besitzt die kurzen Spliceform PhLPS, deren Expression in verschiedenen Gewebetypen deutlich geringer ist, diese hoch konservierte Region nicht. In der vorliegenden Arbeit wurde nun erstmals die Rolle von PhLPL und PhLPS bei der Gbetagamma-Regulation in intakten Zellen untersucht. Hierbei konnte überraschenderweise gefunden werden, dass PhLPS der potentere und effizientere Regulator für Gbetagamma-abhängige Signale war. PhLPL hingegen schien in seiner Gbetagamma-regulierenden Fähigkeit limitiert zu werden. Die Ursache dieser Limitierung von PhLPL in intakten Zellen wurde auf eine konstitutive Phosphorylierung seines verlängerten N-Terminus durch die ubiquitäre Casein Kinase 2 (CK2) zurückgeführt. Die verantwortlichen Phosphorylierungsstellen (S18, T19, S20) wurde identifiziert und die Mutation der CK2-Phosphorylierungsstellen (PhLPLA18-20) führte zu einer Verbesserung der hemmenden Funktion von PhLPL in Zellen. In vitro-Assays zur Bindungsfähigkeit von rekombinantem PhLPL (vor und nach CK2-Phosphorylierung) zeigten allerdings: die Phosphorylierung beeinflusste die Affinität nicht. Eine genaue Analyse der N-terminalen Strukuren von PhLPL zeigte indes, dass die Regulationsfähigkeit von PhLPL in intakten Zellen vor allem in dem konservierten Gbetagamma-Bindungsmotiv zu suchen war. Die Mutation einer einzigen Aminosäure (W66V) war ausreichend, um sowohl die Gbetagamma-Bindungsfähigkeit, als auch die Fähigkeit zur funktionellen Hemmung in intakten Zellen zu verlieren. Was war also der Mechanismus der Hemmung von Gbetagamma durch PhLPS und die phophorylierungsdefiziente Mutante von PhLPL? Ein erster Hinweis hierauf kam von der Beobachtung, dass die Gbeta- und Ggamma-Untereinheiten in Anwesenheit von PhLPS in ihrem Proteingehalt deutlich reduziert vorlagen (wie in Western Blots gezeigt). Dieser Mechanismus schien von proteasomalen Abbauwegen abzuhängen (gezeigt durch Effekte des spezifischen Proteasominhibitors Lactazystin). Allerdings schien eine Stabilisierung der Gbeta- und Ggamma-Untereinheiten (durch N-terminale Fusion mit einem Protein zur vitalen Proteinfärbung) nicht die Funktionsfähigkeit von Gbetagamma in Anwesenheit von PhLPS bewahren zu können. Ganz im Gegenteil, es wurde gezeigt, dass Gbeta und Ggamma hierbei nicht mehr zu einem funktionellen Dimer assoziierten. Dies war ein Hinweis darauf, dass möglicherweise Proteinfaltungsmechanismen bei der Regulation essentiell sein könnten. Eine postulierte Rolle bei der Faltung von WD40-Repeatproteinen wie der Gbeta-Untereinheit wurde dem Chaperonin-Komplex CCT (chaperonin containing TCP) zugedacht. Folgerichtig konnte PhLPS mit seinen funktionell aktiven Domänen an endogenes TCP-1alpha (einer Untereinheit von CCT) binden. Ferner konnte gezeigt werden, dass die Hemmung des CCT-Komplexes durch RNA-Interferenz mit TCP-1alpha ebenso wie PhLPS zur spezifischen Reduktion von Gbetagamma führte. In dieser Arbeit wurde also ein neuartiger Mechanismus der G-Protein-Regulation durch Hemmung der Proteinfaltung von Gbetagamma beschrieben. Ein Schaltmechanismus zwischen direkter Gbetagamma-Bindung (induziert durch CK2-Phosphorylierung von PhLPL) und Hemmung der Proteinfaltung von Gbetagamma (induziert durch alternatives Splicen oder durch Dephosphorylierung von PhLP) wird postuliert. / Phosducin-like protein (PhLP) exists in two splice variants PhLPLONG (PhLPL) and PhLPSHORT (PhLPS): They differ in the length of their N-termini and their expression pattern: The long form (PhLPL) is a ubiquitously expressed protein and binds G-protein betagamma-subunits (Gbetagamma) and thereby inhibits Gbetagamma-mediated function. The extended N-terminus of PhLPL (83 amino acids) contains a highly conserved Gbetagamma-binding motif which plays the crucial role in binding and regulating Gbetagamma-subunits. In contrast, the short splice variant PhLPS, which has a more restricted expression, lacks this motif and did not seem to exert a major Gbetagamma-inhibition, when tested with purified proteins. In the present work, for the first time, we investigated the Gbetagamma-inhibiting properties of PhLPL and PhLPS in intact cells. Surprisingly, PhLPS was the more potent and effective Gbetagamma inhibitor, while PhLPL was limited in this respect. The reason for the limited ability to inhibit Gbetagamma in intact cells was found in a constitutive phosphorylation by the ubiquitious kinase casein kinase 2 (CK2). The responsible phosphorylation sites could be identified (S18, T19, S20) and mutation of those sites into alanines could ameliorate the function of PhLPL. We therefore hypothesised that CK2 dependent phosphorylation of PhLPL should reduce binding affinity towards Gbetagamma subunits. But instead, direct phosphorylation of recombinant PhLPL by CK2 did not reduce its binding affinites. A thorough analysis of the N terminus of PhLPL revealed that a single mutation of the conserved N terminal binding motif (W66V) was sufficient to ablate Gbetagamma binding and Gbetagamma inhibition in intact cells. A first hint to an alternative mechanism came from the observation that - in the presence of PhLPS - the protein content of Gbeta and Ggamma subunits was dramatically reduced (as determined by Western blotting). This phenomenon seemed to be dependent on a proteasomal pathway (which was shown by effects of the specific proteasome inhibitor lactacystine). But a stabilization of the Gbeta and Ggamma subunits through N terminal fusion of a dye-labeling protein could not restore the function of Gbetagamma in the presence of PhLPS. Instead, it could be demonstrated that under these conditions Gbeta and Ggamma did not form functional dimers any more. This finding led to the conclusion that a protein folding mechanism was possibly involved. A postulated role in the folding of WD40 repeat proteins (like the Gbeta subunit) was assumed for the cytosolic chaperonin complex CCT in the literature. PhLPS was able to bind to TCP-1alpha, a subunit of CCT, as were the functionally active domains of PhLPS. We further demonstrated that the inhibition of CCT by RNA interference with TCP-1alpha also led to down-regulation of Gbeta and Ggamma subunits. So, in this thesis, a novel mechanism of G-protein regulation through inhibition of Gbetagamma protein folding was described. Further, a switch mechanism between direct Gbetagamm binding (induced by phosphorylation of PhLPL) and inhibition of Gbetagamm folding (induced by alternative splicing or dephosphorylation of PhLP) is postulated.

Der internal transcribed spacer 2 (ITS2) des ribosomalen Genrepeats ist ein zunehmend wichtiger phylogenetischer Marker, dessen RNA-Sekundärstruktur innerhalb vieler eukaryontischer Organismen konserviert ist. Die ITS2-Datenbank hat zum Ziel, eine umfangreiche Ressource für ITS2-Sequenzen und -Sekundärstrukturen auf Basis direkter thermodynamischer als auch homologiemodellierter RNA-Faltung zu sein. Ergebnisse: (a) Eine komplette Neufassung der ursprünglichen die ITS2-Datenbank generierenden Skripte, angewandt auf einen aktuellen NCBI-Datensatz, deckte mehr als 65.000 ITS2-Strukturen auf. Dies verdoppelt den Inhalt der ursprünglichen Datenbank und verdreifacht ihn, wenn partielle Strukturen mit einbezogen werden. (b) Die Endbenutzer-Schnittstelle wurde neu geschrieben, erweitert und ist jetzt in der Lage, benutzerdefinierte Homologiemodellierungen durchzuführen. (c) Andere möglichen RNA-Strukturaufklärungsmethoden (suboptimales und formenbasiertes Falten) sind hilfreich, können aber Homologiemodellierung nicht ersetzen. (d) Ein Anwendungsfall der ITS2-Datenbank in Zusammenhang mit anderen am Lehrstuhl entwickelten Werkzeugen gab Einblick in die Verwendung von ITS2 für molekulare Phylogenie. / The internal transcribed spacer 2 (ITS2) of the ribosomal gene repeat is an increasingly important phylogenetic marker whose RNA secondary structure is widely conserved across eukaryotic organisms. The ITS2 database aims to be a comprehensive resource on ITS2 sequence and secondary structure, based on direct thermodynamic as well as homology modelled RNA folds. Results: (a) A rebuild of the original ITS2 database generation scripts applied to a current NCBI dataset reveal more than 60,000 ITS2 structures. This more than doubles the contents of the original database and triples it when including partial structures. (b) The end-user interface was rewritten, extended and now features user-defined homology modelling. (c) Other possible RNA structure discovery methods (namely suboptimal and shape folding) prove helpful but are not able to replace homology modelling. (d) A use case of the ITS2 database in conjunction with other tools developed at the department gave insight into molecular phylogenetic analysis with ITS2.

The eukaryotic cell cycle orchestrates the precise duplication and distribution of the genetic material, cytoplasm and membranes to daughter cells. In multicellular eukaryotes, cell cycle regulation also governs various organisatorial processes ranging from gametogenesis over multicellular development to tissue formation and repair. Consequently, defects in cell cycle regulation provoke a variety of human cancers. A global view of genes and pathways governing the human cell cycle would advance many research areas and may also deliver novel cancer targets. Therefore this work aimed on the genome-wide identification and systematic characterisation of genes required for cell cycle progression in human cells. I developed a highly specific and efficient RNA interference (RNAi) technology to realize the potential of RNAi for genome-wide screening of the genes essential for cell cycle progression in human tissue culture cells. This approach is based on the large-scale enzymatic digestion of long dsRNAs for the rapid and cost-efficient generation of libraries of highly complex pools of endoribonuclease-prepared siRNAs (esiRNAs). The analysis of the silencing efficiency and specificity of esiRNAs and siRNAs revealed that esiRNAs are as efficient for mRNA degradation as chemically synthesized siRNA designed with state-of-the-art design algorithms, while exhibiting a markedly reduced number of off-target effects. After demonstrating the effectiveness of this approach in a proof-of-concept study, I screened a genome-wide esiRNA library and used three assays to generate a quantitative and reproducible multi-parameter profile for the 1389 identified genes. The resulting phenotypic signatures were used to assign novel cell cycle functions to genes by combining hierarchical clustering, bioinformatics and proteomic data mining. This global perspective on gene functions in the human cell cycle presents a framework for the systematic documentation necessary for the understanding of cell cycle progression and its misregulation in diseases. The identification of novel genes with a role in human cell cycle progression is a starting point for an in-depth analysis of their specific functions, which requires the validation of the observed RNAi phenotype by genetic rescue, the study of the subcellular localisation and the identification of interaction partners of the expressed protein. One strategy to achieve these experimental goals is the expression of RNAi resistant and/or tagged transgenes. A major obstacle for transgenesis in mammalian tissue culture cells is the lack of efficient homologous recombination limiting the use of cultured mammalian cells as a real genetic system like yeast. I developed a technology circumventing this problem by expressing an orthologous gene from a closely related species including its regulatory sequences carried on a bacterial artificial chromosome (BAC). This technology allows physiological expression of the transgene, which cannot be achieved with conventional cDNA expression constructs. The use of the orthologous gene from a closely related species confers RNAi resistance to the transgene allowing the depletion of the endogenous gene by RNAi. Thus, this technology mimics homologous recombination by replacing an endogenous gene with a transgene while maintaining normal gene expression. In combination with recombineering strategies this technology is useful for RNAi rescue experiments, protein localisation and the identification of protein interaction partners in mammalian tissue culture cells. In summary, this thesis presents a major technical advance for large-scale functional genomic studies in mammalian tissue culture cells and provides novel insights into various aspects of cell cycle progression. (Die Druckexemplare enthalten jeweils eine CD-ROM als Anlagenteil: 217 MB: Movies, Rohdaten - Nutzung: Referat Informationsvermittlung der SLUB)

No description available.

Universiẗat, Diss., 2000--Kiel.

Cette thèse se situe à l'intersection de la cryptographie et de l'arithmétique des ordinateurs. Elle traite de l'amélioration de primitives cryptographiques asymétriques en termes d'accélération des calculs et de protection face aux attaques par fautes par le biais particulier de l'utilisation des systèmes de représentation des nombres par les restes (RNS). Afin de contribuer à la sécurisation de la multiplication modulaire, opération centrale en cryptographie asymétrique, un nouvel algorithme de réduction modulaire doté d'une capacité de détection de faute est présenté. Une preuve formelle garantit la détection des fautes sur un ou plusieurs résidus pouvant apparaître au cours d'une réduction. De plus, le principe de cet algorithme est généralisé au cas d'une arithmétique dans un corps fini non premier. Ensuite, les RNS sont exploités dans le domaine de la cryptographie sur les réseaux euclidiens. L'objectif est d'importer dans ce domaine certains avantages des systèmes de représentation par les restes dont l'intérêt a déjà été montré pour une arithmétique sur GF(p) notamment. Le premier résultat obtenu est une version en représentation hybride RNS-MRS de l'algorithme du « round-off » de Babai. Puis une technique d'accélération est introduite, permettant d'aboutir dans certains cas à un algorithme entièrement RNS pour le calcul d'un vecteur proche. / This thesis is at the crossroads between cryptography and computer arithmetic. It deals with enhancement of cryptographic primitives with regard to computation acceleration and protection against fault injections through the use of residue number systems (RNS) and their associated arithmetic. So as to contribute to secure the modular multiplication, which is a core operation for many asymmetric cryptographic primitives, a new modular reduction algorithm supplied with fault detection capability is presented. A formal proof guarantees that faults affecting one or more residues during a modular reduction are well detected. Furthermore, this approach is generalized to an arithmetic dedicated to non-prime finite fields Fps . Afterwards, RNS are used in lattice-based cryptography area. The aim is to exploit acceleration properties enabled by RNS, as it is widely done for finite field arithmetic. As first result, a new version of Babai’s round-off algorithm based on hybrid RNS-MRS representation is presented. Then, a new and specific acceleration technique enables to create a full RNS algorithm computing a close lattice vector.

No description available.

No / Nonsegmental vitiligo (NSV) is characterized by loss of inherited skin color. The cause of the disease is still unknown despite accumulating in vivo and in vitro evidence of massive epidermal oxidative stress via H2O2 and peroxynitrite (ONOO−) in affected individuals. The most favored hypothesis is based on autoimmune mechanisms. Strictly segmental vitiligo (SSV) with dermatomal distribution is a rare entity, often associated with stable outcome. Recently, it was documented that this form can be associated with NSV (mixed vitiligo). We here asked the question whether ROS and possibly ONOO− could be players in the pathogenesis of SSV. Our in situ results demonstrate for the first time epidermal biopterin accumulation together with significantly decreased epidermal catalase, thioredoxin/thioreoxin reductase, and MSRA/MSRB expression. Moreover, we show epidermal ONOO− accumulation. In vivo FT-Raman spectroscopy reveals the presence of H2O2, methionine sulfoxide, and tryptophan metabolites; i.e., N-formylkynurenine and kynurenine, implying Fenton chemistry in the cascade (n=10). Validation of the basic data stems from successful repigmentation of skin and eyelashes in affected individuals, regardless of SSV or segmental vitiligo in association with NSV after reduction of epidermal H2O2 (n=5). Taken together, our contribution strongly supports H2O2/ONOO-mediated stress in the pathogenesis of SSV. Our findings offer new treatment intervention for lost skin and hair color.—Schallreuter, K. U., Salem, M. A. E. L., Holtz, S., Panske, A. Basic evidence for epidermal H2O2/ONOO−-mediated oxidation/nitration in segmental vitiligo is supported by repigmentation of skin and eyelashes after reduction of epidermal H2O2 with topical NB-UVB-activated pseudocatalase PC-KUS.