A comparative study was made between two similar red algal endophytes, Audouinella porphyrae (Drew) Garbary and Audouinella vaga (Drew) Garbary, Hansen et Scagel, (Acrochaetiaceae, Acrochaetiales) and their red algal hosts Porphyra spp. and Pterosiphonia bipinnata, respectively. Both endophytes have axial, stellate chloroplasts with a central pyrenoid and reside in their host's cell walls, producing erect portions outside the host that may bear monosporangia. The endophytes were cultured "free" from their hosts and morphological and cytological features of the free-living forms were compared with field material. Although the two endophytes differ significantly in cell dimensions and branching patterns, the free-living forms do not retain these differences. Cell dimensions, branching patterns and developmental patterns are identical in the two free-living forms. Asexual reproduction with regeneration by monospores was observed. Sexual reproduction was not observed in either endophytic or free-living forms of the endophytes. Free-living forms were used for re-infection and cross-infection experiments. Under all experimental conditions, the endophytes showed only epiphytic growth. The hosts seem to have some effect on both of the endophytes. Epiphytes, Audouinella porphyrae and A. vaga were not selective and grew on both hosts, Porphyra torta and Pterosiphonia bipinnata. Both epiphtyes growing on blades of Porphyra tended to branch and have more extensive prostrate portions (3-5 cells) whereas both epiphytes on Pterosiphoni a bipinnata tend not to branch and have only 1-2 cells in the prostrate portions. Ultrastructural studies of both endophytes showed typical florideophycean features. Ultrastructural features of field material of the two endophytes were similar and free-living, cultured endophytes were similar to field material. A large vacuole was observed in sections of the field material of both prostrate and erect portions whereas this was not observed in cultured material. Based on the results of this study it is proposed that the two endophytes are conspecific. Audouinella vaga is referred to synonymy in Audouinella porphyrae (Drew) Garbary, Hansen et Scagel. / Science, Faculty of / Botany, Department of / Graduate

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Thesis (PhD)--Stellenbosch University, 2005. / ENGLISH ABSTRACT: Since their inception, biology and biochemistry have been spectacularly successful in characterising the living cell and its components. As the volume of information about cellular components continues to increase, we need to ask how we should use this information to understand the functioning of the living cell? Computational systems biology uses an integrative approach that combines theoretical exploration, computer modelling and experimental research to answer this question. Central to this approach is the development of computational models, new modelling strategies and computational tools. Against this background, this study aims to: (i) develop a new modelling package: PySCeS, (ii) use PySCeS to study discontinuous behaviour in a metabolic pathway in a way that was very difficult, if not impossible, with existing software, (iii) develop an interactive, web-based repository (JWS Online) of cellular system models. Three principles that, in our opinion, should form the basis of any new modelling software were laid down: accessibility (there should be as few barriers as possible to PySCeS use and distribution), flexibility (pySCeS should be extendable by the user, not only the developers) and usability (PySCeS should provide the tools we needed for our research). After evaluating various alternatives we decided to base PySCeS on the freely available programming language, Python, which, in combination with the large collection of science and engineering algorithms in the SciPy libraries, would give us a powerful modern, interactive development environment. / AFRIKAANSE OPSOMMING: Sedert hul totstandkoming was biologie en, meer spesifiek, biochemie uiters suksesvol in die karakterisering van die lewende sel se komponente. Steeds groei die hoeveelheid informasie oor die molekulêre bestanddele van die sel daagliks; ons moet onself dus afvra hoe ons hierdie informasie kan integreer tot 'n verstaanbare beskrywing van die lewende sel se werking. Om dié vraag te beantwoord gebruik rekenaarmatige sisteembiologie 'n geïntegreerde benadering wat teorie, rekenaarmatige modellering en eksperimenteeIe navorsing kombineer. Sentraal tot die benadering is die ontwikkeling van nuwe modelle, strategieë vir modellering, en sagteware. Teen hierdie agtergrond is die hoofdoelstelling van hierdie projek: (i) die ontwikkeling van 'n nuwe modelleringspakket, PySCeS (ii) die benutting van PySCeS om diskontinue gedrag in n metaboliese sisteem te bestudeer (iets wat met die huidiglik beskikbare sagteware redelik moeilik is), (en iii) die ontwikkeling vann interaktiewe, internet-gebaseerde databasis van sellulêre sisteem modelle, JWS Online. Ons is van mening dat nuwe sagteware op drie belangrike beginsels gebaseer behoort te wees: toeganklikheid (die sagteware moet maklik bekombaar en bruikbaar wees), buigsaamheid (die gebruiker moet self PySCeS kan verander en ontwikkel) en bruikbaarheid (al die funksionalitiet wat ons vir ons navorsing nodig moet in PySCeS ingebou wees). Ons het verskeie opsies oorweeg en besluit om die vrylik verkrygbare programmeringstaal, Python, in samehang die groot kolleksie wetenskaplike algoritmes, SciPy, te gebruik. Hierdie kombinasie verskaf n kragtige, interaktiewe ontwikkelings- en gebruikersomgewing. PySCeS is ontwikkel om onder beide die Windows en Linux bedryfstelsels te werk en, meer spesifiek, om gebruik te maak van 'n 'command line interface'. Dit beteken dat PySCeS op enige interaktiewe rekenaar-terminaal Python ondersteun sal werk. Hierdie eienskap maak ook moontlik die gebruik van PySCeS as 'n modelleringskomponent in 'n groter sagteware pakket onder enige bedryfstelsel wat Python ondersteun. PySCeS is op 'n modulere ontwerp gebaseer, wat dit moontlik vir die eindgebruiker maak om die sagteware se bronkode verder te ontwikkel. As 'n toepassing is PySCeS gebruik om die oorsaak van histeretiese gedrag van 'n lineêre, eindproduk-geïnhibeerde metaboliese pad te ondersoek. Ons het hierdie interessante gedrag in 'n vorige studie ontdek, maar kon nie, met die sagteware wat op daardie tydstip tot ons beskikking was, hierdie studie voortsit nie. Met PySCeS se ingeboude vermoë om parameter kontinuering te doen, kon ons die oorsake van hierdie diskontinuë gedrag volledig karakteriseer. Verder het ons 'n nuwe metode ontwikkel om hierdie gedrag te visualiseer as 'n interaksie tussen die volledige sisteem se subkomponente. Tydens PySCeS se ontwikkeling het ons opgemerk dat dit baie moeilik was om metaboliese modelle wat in die literature gepubliseer is te herbou en te bestudeer. Hierdie situasie is grotendeels die gevolg van die feit dat nêrens 'n sentrale databasis vir metaboliese modelle bestaan nie (soos dit wel bestaan vir genomiese data of proteïen strukture). Die JWS Online databasis is spesifiek ontwikkel om hierdie leemte te vul. JWS Online maak dit vir die gebruiker moontlik om, via die internet en sonder die installasie van enige gespesialiseerde modellerings sagteware, gepubliseerde modelle te bestudeer en ook af te laai vir gebruik met ander modelleringspakkette soos bv. PySCeS. JWS Online het alreeds 'n onmisbare hulpbron vir sisteembiologiese navorsing en onderwys geword.

Immunhistokemi (IHC) och immuncytokemi (ICC) är viktiga verktyg inom cancerdiagnostik för att fastställa diagnoser. Både histologiskt och cytologiskt material kan användas för immunokemisk analys men kräver olika förberedelser. Den preanalytiska fasen påverkar epitop och antigenens tillgänglighet samt immunoreaktivitet, vilket gör valet av pre- och postfixering och hur de påverkar cytologiskt material, viktiga att förstå. ICC tillämpas vanligen på cytologiskt material som preparerats enligt cellblockteknik (CBT) men ibland saknas extraherat material för analys. Antikroppar kan användas för att differentiera tumörursprung, tumörsubtyper och inflammatoriska tillstånd, vilket är avgörande för klinisk diagnostik och behandlingsbeslut för individen. Vid klinisk patologi och cytologi i Kalmar är ett återkommande problem bristen på cellmaterial för CBT-preparering vid punktionscytologi. Syftet med denna studie var att validera antikroppar (kalretinin, CD45, CK5, CK7, SOX-10, EpCAM och TTF-1) på cytologiskt material (pleuraexsudat från 10 patienter) som preparerats enligt ThinPrep™- metoden (TP-metoden). Studien syftade även till att undersöka effekterna av post-fixering i 4 % formalin, 96% etanol eller ingen post-fixering inför ICC-analys för att se om valet av post-fixeringsmedel påverkar antikropparnas färgningsmönster (nukleärt, cytoplasmatiskt eller membranöst). CD45, CK5, CK7 och TTF-1 kunde valideras i studien. Det fanns inte någon signifikant skillnad (p > 0,05) i bedömningskategorierna (bakgrund, inmärkning och cellantal) mellan olika post-fixeringsmedel. Det fanns heller inga indikationer som visade att en särskild post-fixering gynnande ett särskilt färgningsmönster. Fler studier behövs för att förstå den preanalytiska fasens påverkan på ICC- analys av cytologiskt material. I samband med punktionscytologi skulle preparering enligt TP-metoden säkerställa tillgången på cellmaterial för ICC-analys. / Immunohistochemistry (IHC) and immunocytochemistry (ICC) are crucial tools in cancer diagnostics for establishing diagnosis. Both histological and cytological materials can be used for immunochemical analysis, but they require different preparations. The pre-analytical phase affects the epitope and antigen availability as well as immunoreactivity, making the choice of pre- and post-fixation and their impact on cytological material important to understand. ICC is usually applied to cytological material prepared using the cell block technique (CBT), but sometimes there is a lack of extracted material for analysis. Antibodies can differentiate tumor origins, subtypes, and inflammatory conditions, which is essential for clinical diagnostics and treatment decisions. In clinical pathology and cytology in Kalmar, a recurring issue is the lack of cell material for CBT preparation in fine-needle aspiration cytology. This study aimed to validate antibodies (calretinin, CD45, CK5, CK7, SOX-10, EpCAM, and TTF-1) on cytological material (n=10 pleural effusions) prepared using the ThinPrep™ method (TP method). The study also aimed to study the effects of post-fixation in 4% formalin, 96% ethanol, or without fixation medium before ICC analysis to see if the choice of post-fixation medium affects the staining patterns of the antibodies (nuclear, cytoplasmic, or membranous). CD45, CK5, CK7, and TTF-1 were validated in the study. There was no significant difference (p > 0.05) in the assessment categories (background, staining, and cell count) between different post-fixation media. There were also no indications that a particular post-fixation medium favored a specific staining pattern. Further studies are needed to understand the pre-analytical phase's impact on ICC analysis of cytological material. In fine-needle aspiration cytology, preparation using the TP method would ensure the availability of cell material for ICC analysis.

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Call number: LD2668 .T4 1984 S326 / Master of Science

Call number: LD2668 .T4 1985 S38 / Master of Science