Promoting Portuguese exports to Germany: An export promotion plan for the machinery & equipment sector

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics

Systematic analysis of protein complexes involved in the human RNA polymerase II machinery

La transcription, la maturation d’ARN, et le remodelage de la chromatine sont tous des processus centraux dans l'interprétation de l'information contenue dans l’ADN. Bien que beaucoup de complexes de protéines formant la machinerie cellulaire de transcription aient été étudiés, plusieurs restent encore à identifier et caractériser. En utilisant une approche protéomique, notre laboratoire a purifié plusieurs composantes de la machinerie de transcription de l’ARNPII humaine par double chromatographie d’affinité "TAP". Cette procédure permet l'isolement de complexes protéiques comme ils existent vraisemblablement in vivo dans les cellules mammifères, et l'identification de partenaires d'interactions par spectrométrie de masse. Les interactions protéiques qui sont validées bioinformatiquement, sont choisies et utilisées pour cartographier un réseau connectant plusieurs composantes de la machinerie transcriptionnelle. En appliquant cette procédure, notre laboratoire a identifié, pour la première fois, un groupe de protéines, qui interagit physiquement et fonctionnellement avec l’ARNPII humaine. Les propriétés de ces protéines suggèrent un rôle dans l'assemblage de complexes à plusieurs sous-unités, comme les protéines d'échafaudage et chaperonnes. L'objectif de mon projet était de continuer la caractérisation du réseau de complexes protéiques impliquant les facteurs de transcription. Huit nouveaux partenaires de l’ARNPII (PIH1D1, GPN3, WDR92, PFDN2, KIAA0406, PDRG1, CCT4 et CCT5) ont été purifiés par la méthode TAP, et la spectrométrie de masse a permis d’identifier de nouvelles interactions. Au cours des années, l’analyse par notre laboratoire des mécanismes de la transcription a contribué à apporter de nouvelles connaissances et à mieux comprendre son fonctionnement. Cette connaissance est essentielle au développement de médicaments qui cibleront les mécanismes de la transcription.

Neuartige Verfahren für die Überwachung und Diagnose von aktiv magnetgelagerten rotierenden Maschinen

Mit aktiven Magnetlagern ist es möglich, rotierende Körper durch magnetische Felder berührungsfrei zu lagern. Systembedingt sind bei aktiv magnetgelagerten Maschinen wesentliche Signale ohne zusätzlichen Aufwand an Messtechnik für Diagnoseaufgaben verfügbar. In der Arbeit wird ein Konzept entwickelt, das durch Verwendung der systeminhärenten Signale eine Diagnose magnetgelagerter rotierender Maschinen ermöglicht und somit neben einer kontinuierlichen Anlagenüberwachung eine schnelle Bewertung des Anlagenzustandes gestattet. Fehler können rechtzeitig und ursächlich in Art und Größe erkannt und entsprechende Gegenmaßnahmen eingeleitet werden. Anhand der erfassten Signale geschieht die Gewinnung von Merkmalen mit signal- und modellgestützten Verfahren. Für den Magnetlagerregelkreis erfolgen Untersuchungen zum Einsatz modellgestützter Parameteridentifikationsverfahren, deren Verwendbarkeit wird bei der Diagnose am Regler und Leistungsverstärker nachgewiesen. Unter Nutzung von Simulationsmodellen sowie durch Experimente an Versuchsständen werden die Merkmalsverläufe im normalen Referenzzustand und bei auftretenden Fehlern aufgenommen und die Ergebnisse in einer Wissensbasis abgelegt. Diese dient als Grundlage zur Festlegung von Grenzwerten und Regeln für die Überwachung des Systems und zur Erstellung wissensbasierter Diagnosemodelle. Bei der Überwachung werden die Merkmalsausprägungen auf das Überschreiten von Grenzwerten überprüft, Informationen über erkannte Fehler und Betriebszustände gebildet sowie gegebenenfalls Alarmmeldungen ausgegeben. Sich langsam anbahnende Fehler können durch die Berechnung der Merkmalstrends mit Hilfe der Regressionsanalyse erkannt werden. Über die bisher bei aktiven Magnetlagern übliche Überwachung von Grenzwerten hinaus erfolgt bei der Fehlerdiagnose eine Verknüpfung der extrahierten Merkmale zur Identifizierung und Lokalisierung auftretender Fehler. Die Diagnose geschieht mittels regelbasierter Fuzzy-Logik, dies gestattet die Einbeziehung von linguistischen Aussagen in Form von Expertenwissen sowie die Berücksichtigung von Unbestimmtheiten und ermöglicht damit eine Diagnose komplexer Systeme. Für Aktor-, Sensor- und Reglerfehler im Magnetlagerregelkreis sowie Fehler durch externe Kräfte und Unwuchten werden Diagnosemodelle erstellt und verifiziert. Es erfolgt der Nachweis, dass das entwickelte Diagnosekonzept mit beherrschbarem Rechenaufwand korrekte Diagnoseaussagen liefert. Durch Kaskadierung von Fuzzy-Logik-Modulen wird die Transparenz des Regelwerks gewahrt und die Abarbeitung der Regeln optimiert. Endresultat ist ein neuartiges hybrides Diagnosekonzept, welches signal- und modellgestützte Verfahren der Merkmalsgewinnung mit wissensbasierten Methoden der Fehlerdiagnose kombiniert. Das entwickelte Diagnosekonzept ist für die Anpassung an unterschiedliche Anforderungen und Anwendungen bei rotierenden Maschinen konzipiert.

Unveiling the components of the signaling pathway between endosomes and the phagocytic uptake machinery in Dictyostelium discoideum

The soil amoebae Dictyostelium discoideum take up particles from their environment in order to obtain nutrition. The particle transits through the cell within a phagosome that fuses with organelles of different molecular compositions, undergoing a gradual degradation by different sets of hydrolytic enzymes. Griffiths’ concept of “phagosome individuality” predicts signaling from phagosomes into the cytoplasm, which might regulate many aspects of cell physiology. The finding that Dictyostelium cells depleted of the lysozyme AlyA or over-expressing the esterase Gp70 exhibit increased uptake of food particles, led to the postulation of a signaling cascade between endocytic compartments and the cytoskeletal uptake machinery at the plasma membrane. Assuming that Gp70 acts downstream of AlyA, gene-expression profiling of both mutants revealed different and overlapping sets of misregulated genes that might participate in this signaling cascade. Based on these results, we analyzed the effects of the artificial misregulation of six candidate genes by over-expression or negative genetic interference, in order to reconstruct at least part of the signaling pathway. SSB420 and SSL793 were chosen as candidates for the first signaling step, as they were up-regulated in AlyA-null cells and remained unaltered in the Gp70 over-expressing cells. The over-expression of SSB420 enhanced phagocytosis and raised the expression levels of Gp70, supporting its involvement in the signaling pathway between AlyA and Gp70 as a positive regulator of phagocytosis. However, this was not the case of cells over-expressing SSL793, as this mutation had no effects on phagocytosis. For the signaling downstream of Gp70, we studied four commonly misregulated genes in AlyA-depleted and Gp70 over-expressing cells. The expression levels of SLB350, SSB389 and TipD were lower in both mutants and therefore these were assumed as possible candidates for the negative regulation of phagocytosis. Cells depleted of SLB350 exhibited an increased phagocytic activity and no effect on Gp70 expression, proving its participation in the signaling pathway downstream of Gp70. Unlike SLB350, the disruption of the genes coding for SSB389 and TipD had no effects on particle uptake, excluding them from the pathway. The fourth candidate was Yipf1, the only gene that was commonly up-regulated in both mutants. Yet, the artificial over-expression of this protein had no effects on phagocytosis, so this candidate is also not included in the signaling pathway. Furthermore, localizing the products of the candidate genes within the cell helped unveiling several cellular organelles that receive signals from the phagosome and transduce them towards the uptake machinery.

Targeting the cell cycle machinery for the treatment of cardiovascular disease

Cardiovascular disease represents a major clinical problem affecting a significant proportion of the world's population and remains the main cause of death in the UK. The majority of therapies currently available for the treatment of cardiovascular disease do not cure the problem but merely treat the symptoms. Furthermore, many cardioactive drugs have serious side effects and have narrow therapeutic windows that can limit their usefulness in the clinic. Thus, the development of more selective and highly effective therapeutic strategies that could cure specific cardiovascular diseases would be of enormous benefit both to the patient and to those countries where healthcare systems are responsible for an increasing number of patients. In this review, we discuss the evidence that suggests that targeting the cell cycle machinery in cardiovascular cells provides a novel strategy for the treatment of certain cardiovascular diseases. Those cell cycle molecules that are important for regulating terminal differentiation of cardiac myocytes and whether they can be targeted to reinitiate cell division and myocardial repair will be discussed as will the molecules that control vascular smooth muscle cell (VSMC) and endothelial cell proliferation in disorders such as atherosclerosis and restenosis. The main approaches currently used to target the cell cycle machinery in cardiovascular disease have employed gene therapy techniques. We will overview the different methods and routes of gene delivery to the cardiovascular system and describe possible future drug therapies for these disorders. Although the majority of the published data comes from animal studies, there are several instances where potential therapies have moved into the clinical setting with promising results.

Reprogramming the cell cycle machinery to treat cardiovascular disease

Coronary artery disease is one of the most common heart pathologies. Restriction of blood flow to the heart by atherosclerotic lesions, leading to angina pectoris and myocardial infarction, damages the heart, resulting in impaired cardiac function. Damaged myocardium is replaced by scar tissue since surviving cardiomyocytes are unable to proliferate to replace lost heart tissue. Although narrowing of the coronary arteries can be treated successfully using coronary revascularisation procedures, re-occlusion of the treated vessels remains a significant clinical problem. Cell cycle control mechanisms are key in both the impaired cardiac repair by surviving cardiomyocytes and re-narrowing of treated vessels by maladaptive proliferation of vascular smooth muscle cells. Strategies targeting the cell cycle machinery in the heart and vasculature offer promise both for the improvement of cardiac repair following MI and the prevention of restenosis and bypass graft failure following revascularisation procedures.

Multivariable cluster analysis for high-speed industrial machinery

The overall operation and internal complexity of a particular production machinery can be depicted in terms of clusters of multidimensional points which describe the process states, the value in each point dimension representing a measured variable from the machinery. The paper describes a new cluster analysis technique for use with manufacturing processes, to illustrate how machine behaviour can be categorised and how regions of good and poor machine behaviour can be identified. The cluster algorithm presented is the novel mean-tracking algorithm, capable of locating N-dimensional clusters in a large data space in which a considerable amount of noise is present. Implementation of the algorithm on a real-world high-speed machinery application is described, with clusters being formed from machinery data to indicate machinery error regions and error-free regions. This analysis is seen to provide a promising step ahead in the field of multivariable control of manufacturing systems.

Trypanosome Prereplication Machinery Contains a Single Functional Orc1/Cdc6 Protein, Which Is Typical of Archaea

In unicellular eukaryotes, such as Saccharomyces cerevisiae, and in multicellular organisms, the replication origin is recognized by the heterohexamer origin recognition complex (ORC) containing six proteins, Orc1 to Orc6, while in members of the domain Archaea, the replication origin is recognized by just one protein, Orc1/Cdc6; the sequence of Orc1/Cdc6 is highly related to those of Orc1 and Cdc6. Similar to Archaea, trypanosomatid genomes contain only one gene encoding a protein named Orc1. Since trypanosome Orc1 is also homologous to Cdc6, in this study we named the Orc1 protein from trypanosomes Orc1/Cdc6. Here we show that the recombinant Orc1/Cdc6 from Trypanosoma cruzi (TcOrc1/Cdc6) and from Trypanosoma brucei (TbOrc1/Cdc6) present ATPase activity, typical of prereplication machinery components. Also, TcOrc1/Cdc6 and TbOrc1/Cdc6 replaced yeast Cdc6 but not Orc1 in a phenotypic complementation assay. The induction of Orc1/Cdc6 silencing by RNA interference in T. brucei resulted in enucleated cells, strongly suggesting the involvement of Orc1/Cdc6 in DNA replication. Orc1/Cdc6 is expressed during the entire cell cycle in the nuclei of trypanosomes, remaining associated with chromatin in all stages of the cell cycle. These results allowed us to conclude that Orc1/Cdc6 is indeed a member of the trypanosome prereplication machinery and point out that trypanosomes carry a prereplication machinery that is less complex than other eukaryotes and closer to archaea.

Changes in the Australian Commonwealth departmental machinery of government 1928-1982

The Commonwealth departmental machinery of government is changed by using Orders in Council to create, abolish or change the name of departments. Since 1906 governments have utilised a particular form of Order in Council, the Administrative Arrangements Order (AAO), as the means to reallocate functions between departments for administration. After 1928 successive governments from Scullin to Fraser gradually streamlined and increasingly used the formal processes for the executive to change departmental arrangements and the practical role of Parliament, in the process of change, virtually disappeared. From 1929 to 1982, 105 separate departments were brought into being, as new departments or through merger, and 91 were abolished, following the merger of their functions in one way or another with other departments. These figures exclude 6 situations where the change was simply that of name alone. Several hundred less substantial transfers of responsibilities were also made between departments. This dissertation describes, documents and analyses all these changes. The above changes can be distilled down to 79 events termed primary decisions. Measures of the magnitude of change arising from the decisions are developed with 157.25 units of change identified as occurring during the period, most being in the Whitlam and Fraser periods. The reasons for the changes were assessed and classified as occurring for reasons of policy, administrative logic or cabinet comfort. 47.2% of the units of change were attributed to policy, 34.9% to administrative logic, 17% to cabinet comfort. Further conclusions are drawn from more detailed analysis of the change and the reasons for the changes.