Polymerase Chain Reaction (PCR) detection paves the way to reliable and rapid diagnosis of diseases and has been used extensively since its introduction. Many miniaturized PCR systems were presented by microfluidics and lab-on-a-chip community. However, most of the developed systems did not employ real-time detection and thus required post-PCR processes to obtain results. Among the few real-time PCR systems, almost all of them aimed for medical applications and those for plant pathogen diagnosis systems are almost non-existent in the literature. In this work, we are presenting a portable system that employs microfluidics PCR system with integrated optical systems to accomplish real-time quantitative PCR for plant pathogen diagnosis. The system is comprised of a PCR chip that has a chamber for PCR sample with integrated metal heaters fabricated by standard microfabrication procedures, an optical system that includes lenses, filters, a dichroic mirror and a photomultiplier tube (PMT) to achieve sensitive fluorescence measurement capability and a computer control system for Proportional Integral Derivative (PID) control and data acquisition. The optical detection system employs portable components and has a size of 3.9 x 5.9 x 11.9 cm which makes it possible to be used in field settings. On the device side, two different designs are used. The first design includes a single chamber in a 25.4 x 25.4 mm device and the capacity of the chamber is 9 micro-liters which is sufficient to do gel electrophoresis verification. The second design has three 2.2 micro-liter chambers squeezed in the same size device while having smaller volume to increase high throughput of the system. The operation of the system was demonstrated using Fusarium oxysporum spf. lycopersici which is a fungal plant pathogen that affects crops in the USA. In the presence of the plant pathogen, noticeable increases in the photomultiplier tube output were observed which means successful amplifications and detections occurred. The results were confirmed using gel electrophoresis which is a conventional post-PCR process to determine the existence and length of the amplified DNA. Clear bands located in the expected position were observed following the gel electrophoresis. Overall, we have presented a portable PCR system that has the capability of detecting plant pathogens.

This thesis examines a broad spectrum of physiological and silvicultural features of the highly valued woody angiosperm hemi-parasite Santalurn album L. (Indian sandalwood) in relation to its culture in plantations in northern Western Australia. Topics covered include allometry of host and Santalum when grown as single plant pairings in both field and pot culture, nutritional interactions between Santalum and beneficial and non-beneficial hosts, deleterious influences of parasitism on plantation productivity and heartwood induction in young trees. In Western Australia sandalwood is grown in the nursery for 8 months before establishment in the field and during this time a pot host is introduced. Survival of Santalurn after field establishment and its subsequent growth were significantly affected by the time of introduction of the pot host, Alternanthera nana. Increasing the period of the Santalum : Alternanthera association in the nursery to 109 days prior to field establishment markedly increased early growth of Salztalum plantations. Introduction at 134 days prior to field establishment was detrimental to the parasite as the Alternanthera was too vigorous for the small Santalum seedlings. Santalurn plants had a lower root : shoot ratio lower when cultured with Alternanthera in the nursery prior to field establishment compared with seedlings grown without Alternanthera. Alterrzantlzera survival in the field was high when it had been grown with Santalum for 12 weeks or more in the nursery prior to field establishment. After 1 1 weeks in the field a strong negative linear relationship was shown between Santalunz root : shoot ratio and Alternarzthera dry weight, and a positive linear relationship between Salztalum DW and Alternanthera DW. In Western Australia Santalu~n is established in the field with an intermediate host which nourishes the parasite for 3-5 years before Santalum becomes dependent on its long-term host and the intermediate host dies. The relationship between Santalum and several species tested as intermediate hosts was examined by pairing Santalum seedlings with intermediate host seedlings in 25 litre pots over a 10 month period. Growth of Santalum in pot culture with three N2-fixing woody intermediate hosts (Sesbania forrnosa, Acacia traclzycarpa and A. ampliceps), the woody non N2-fixing Eucalyptus camaldulensis or without a host varied considerably between host treatments. Santalum growth was greater and root : shoot ratio lower for seedlings grown with N2-fixing hosts compared with seedlings grown with E. carnaldulensis or with no host. The root : shoot ratio of unattached Santalum increased exponentially over time, whereas for all other treatments it remained relatively constant. An assessment of the value of the hosts, termed host use efficiency, was computed as Santalum shoot DW / host shoot DW. The host use efficiency of A. trachycalpa was greater than that of the other hosts. The xylem sap of hosts and Sarztalum, and ethanolic extracts of endophytic tissue of haustoria of Santalzkm were analysed for amino acids, organic acids and sugars to determine which solutes were available in the host and which were extracted by the Santalum haustoria from different hosts. There were similarities between Santalum and legume hosts in concentration and composition of xylem sap amino acids, and in the amino acid spectra of the corresponding Santalum endophytic tissue, whereas there were low N levels in xylem sap of E. camaldulensis and dissimilarities between its amino acid composition and that of Santalum. This indicated substantial direct intake of xylem N by Santalum from legume hosts but little N from the xylem sap of E. canzaldulensis. There were high concentrations of asparagine, glutamate, aspartate and y-amino glutamate in the xylem sap of the legume hosts, while in the non-legume the most common amino acids were glutamate, aspartate, glutamine and arginine. Proline, the predominant amino acid in the xylem sap of Santalum acurninatum growing in natural vegetation (Tennakoon et al. 1997) was not detected or present in very low concentrations in Santalurn album under these conditions. in the non-legume. Xylem sap of hosts contained variable amounts of sugars (sucrose, glucose and fructose) and organic acids (fumaric, citric and malic acid), whereas that of the parasitic Santalum was dominated by fructose and malic acid. Dissimilarities in the proportional amounts of xylem-borne sugars and organic acids were particularly evident for the E. camaldulensis : Santalum partnership. Diurnal profiles of photosynthesis and transpiration of Santalum were closely similar to those for corresponding hosts, whereas the midday leaf water potential of Santalum was consistently more negative than that of corresponding hosts. Net photosynthesis and water use efficiency was lower, but transpiration rates were similar to that of corresponding hosts. Nitrogen concentrations of foliage of Santalum were higher than their hosts, and higher when on legume hosts than on E. camaldulensis, or without a host. Nitrogen concentrations of Santalum foliage was strongly correlated with net photosynthesis and water use efficiency of Santalum. 813C values of shoot dry matter of Santalum were poorly correlated with instantaneous water use efficiency of Santalum. Tissue water relations of Santalum were similar to that of water-stress tolerant species. S. formosa proved the best host followed by Acacia ampliceps and A. traclzycarpa based on dry matter gains of Santalum. Estimates of heterotrophic gain of C of Santalum when grown in association with the legume hosts over a nine week period indicate 57.9% of C was derived from A. ampliceps, 45.5% from A. trachycarpa and 34.6% fiom S. fomosa. Abundance of haustorial attachments on roots of hosts was poorly correlated to Santalum shoot DW. Root nodules of legume hosts were parasitised by a small proportion of Santalum haustoria. Sodium and phosphorus concentrations of foliage of Santalum were generally higher than that of corresponding hosts. Net gains of calcium, potassium, phosphorus and sodium in Santalum was greatest when grown in association with hosts richest in the corresponding element. Net losses or only small gains of calcium, potassium, phosphorus and sodium were recorded when Santalum was grown with E. camaldulensis or without a host suggesting that Santalum has limited ability for uptake of those minerals through its own root system. To understand the effect of hosts on the productivity of a Santalum plantation a young plantation of Santalum with three host species Cathormion umbellatum, Sesbania formosa and Acacia anuera was selected to study the relationship between host quality and distance of hosts from Santalunz on Santalum health. The selected plantation showed marked decline in health and vigour of both Santalum and hosts between years 3 and 5. Parameters of the host plants were assessed to select the best predictor of Santalunz crown health. The height and diameter growth increment of Santalum between years 3 and 5 was strongly correlated to Santalum crown health. Santaluin crown health and growth increased as host quality increased, and the distance of host fiom Santalum decreased. An index, which combined host quality and the distance of the host from that of Santalum, was a better predictor of Santalum crown health than host distance or quality alone. The age at which heartwood is initiated in Santalum album under plantation conditions in Western Australia in unknown, but in natural stands in India it occurs between 10-13 years of age (Rai 1990). A field experiment was conducted to determine the efficacy of stem injections of paraquat andlor ethrel in initiating heartwood formation in five year old Santalum trees in a plantation. Trees injected with paraquat alone had a significantly greater extension of induced heartwood, both radially and vertically, than those trees injected with ethrel alone or distilled water. Eight months after treatment with paraquat or ethrel or a combination of these chemicals induced heartwood was formed, which had high lipid, and low starch and polysaccharide concentrations compared to the sapwood. Induced heartwood from both chemical treatments and their combinations contained total volatile oil and santalol oil (alpha and beta santalol) concentrations that were equal to or greater than that of naturally formed heartwood and greater than that of sapwood. Moisture content, and concentrations of K and Mg, and in some treatments Ca of induced heartwood were significantly lower than that of sapwood. The thesis concludes with a synthesis of the findings and suggestions for future research, with special reference to mid-rotation aspects of Santaltrm plantation silviculture.

Thesis (Ph. D.)--University of Melbourne, 1994. / Typescript (photocopy). Includes bibliographical references (leaves 235-246).

Thesis (Ph. D.)--Ohio State University, 2004. / Title from first page of PDF file. Document formatted into pages; contains xvii, 232 p.; also includes graphics (some col.). Includes bibliographical references (p. 206-232).

Thesis (Ph. D.)--University of Chicago, Dept. of Ecology and Evolution, December 2002. / Includes bibliographical references. Also available on the Internet.

M.Sc. / Barley (Hordeum vulgare) production is a vital constituent of the South African economy. Many pathogens reside on barley, which lead to low quality and yield. One of the most prominent barley pathogens, Fusarium graminearum, is the causal agent of small grain scab. F. graminearum resistance to barley is regulated by multiple genes referred to as quantitative trait loci (QTL), which makes it difficult to breed for resistance in new cultivars. Each of these genes contributes to a specific defence area and collectively counteracts Fusarium infection and spread in the barley plant. The aim of this project was to isolate and identify induced genes after infection of three leave stage barley with F. graminearum. These genes were isolated through the use of Suppression subtractive hybridisation (SSH), cloned and then sequenced. From this data set three transcript derived fragments (TDFs) sharing homology to known genes were selected and their expression profiles were studied through Northern blot analysis. Three TDFs shared homology with known genes namely a putative protease inhibitor-related protein, a senescence associated gene, and a manganese superoxide dismutase (MnSOD). These TDFs were previously also recognised for their function in host pathogen interactions. The expression analysis done using Northern blots showed up-regulation of the three fragments after inoculation. These results indicated that all the TDFs studied may play a role in the defence reaction of barley infected with F. graminearum, where both senescence and proteinase inhibitors could limit infection as well as spread and MnSODs might be a protective enzyme against oxidative stress. The results of this study indicated that all of the identified TDFs had database matches to proteins identified during stress responses. Furthermore, the Northern blot results indicated that all the TDFs studied could play a role in the defence reaction of F. graminearum infected barley. These TDFs will form the basis of further studies into the interaction between barley and F. graminearum. The results form this study will add to our knowledge of the interaction between barley and a necrotrophic pathogen. This will aid in understanding how cereal pathogens deal with pathogen attack and will aid in development of new more tolerant barley cultivars.

Phytopathogenic fungi parasitise plants for survival. Knowledge of the interactions between plants and these fungi is of importance in designing control strategies. In this thesis the interactions of Eucalyptus polygalacturonase-inhibiting proteins (PGIPs) and fungal polygalacturonases (PGs) were characterised. About thirty years of research on the interaction between PGIPs and PGs was reviewed in Chapter 1. The gene sequences of the mature PGIP peptides from selected Eucalyptus species were determined in Chapter 2. The PGIP genes have very high similarities among themselves, signifying conservation of the function of PGIPs in this genus. Molecular characterisation of the endoPG gene of C. cubensis was presented in Chapter 3. This endoPG gene occurs more than two times in the genome of C. cubensis. The gene sequences of the other endoPGs remain to be determined. EndoPG production by C. cubensis, a Eucalyptus canker pathogen, was presented in Chapter 4. It was found that polygalactw:onases probably have a minor role in determining the levels of pathogenicity in different C. cubensis isolates. However, the hypovirus CHVl-173 has a role in reducing polygalacturonase production in infected hypovirulent C. cubensis isolates. Chapter 5 dealt with the interaction between Eucalyptus PGIPs and endoPGs from different fungal pathogens. Coniothyrium zuluense and Botryosphaeria dothidea produced more PGs than C. cubensis and Phytophthora cinnamomi in liquid culture. Disease tolerant Eucalyptus TAG5 clones produced PGIPs that are more effective in inhibiting endoPGs from C. zuluense than the susceptible Eucalyptus ZG14 clones. In Chapter 6 the gene sequence of the endoPG of Fusarium circinatum was detennined. This :fungus causes the . pitch canker disease in pine trees. This endoPG gene occurs as a single copy and is related to those of other Fusarium spp. The results presented in this thesis add to the current scientific knowledge pertaining to the role of PGIPs and PGs in pathogenic interactions, especially, between Eucalyptus PGIPs and fungal endoPGs. Interaction of Eucalyptus PGIPs and fungal endoPGs was demonstrated; therefore it is possible to genetically engineer Eucalyptus for more disease tolerant Eucalyptus plants using PGIP genes, especially, against Coniothyrium zuluense. This means that more research is needed to identity genes that will give a more global protection against many fungal pathogens. / Thesis (PhD (Plant Biotechnology))--University of Pretoria, 2006. / Genetics / unrestricted

Thesis (Ph. D.)--Ohio State University, 2007. / Full text release at OhioLINK's ETD Center delayed at author's request

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Invasive plants may leave enemies behind when they colonize a new habitat, allowing selection to favor increased investment in growth and/or reproduction over defensive traits. Previous studies have identified reduced diversity of potential bacterial pathogens and evolutionary increases in growth and reproduction in invading populations of yellow starthistle (Centaurea solstitialis). This study leverages a recently developed high-throughput assay of immune function to test for evidence of a trade-off between increased growth and defense against bacterial pathogens in yellow starthistle's invasion of California (USA). Seven bacterial strains were cultured from infected leaf tissue in the native range. Healthy leaf tissue from five native European collections and six invading collections were exposed to these native bacterial strains. A standardized assay of peroxidase activity was used measure the oxidative burst immune response to pathogen recognition by the leaf. Immune responses were compared to plant growth within and between ranges to assess evidence for a trade-off. Plant genotypes from the native range demonstrated a higher immune response to bacterial strains than did invading genotypes, consistent with a trade-off with plant growth across regions. The same trade-off was also apparent across genotypes from the native range, but not across genotypes from the invaded range. Our results provide evidence that increased growth in a highly invasive plant species may come at a cost to immune function, consistent with the hypothesis that escape from enemies can provide opportunities for shifts in resource allocation that favor the proliferation of non-native species.