Miracle-dz/UniFAR-FTUs huggingface dataset:
Botryosphaeria diseases of proteaceae

The Proteaceae cut-flower industry is an important agricultural industry in South Africa, accounting for 70% of the local cut-flower industry. Species of Botryosphaeria are serious pathogens of Proteaceae, severely restricting commercial production thereof. Not much is known about these pathogens on Proteaceae, and the aim of this study was to summarise essential information pertaining to the taxonomy, pathology, epidemiology and control of Botryosphaeria spp. associated with this crop. The taxonomy of Botryosphaeria requires thorough review, and molecular techniques need to be employed to resolve species identification. Thus, many of the species previously assigned to Botryosphaeria are arbitrary. Definitive taxonomic studies are required to establish which species of Botryosphaeria are associated with Proteaceae. Several pathogenic Botryosphaeria spp. reside endophytically within their hosts, waiting for specific stimuli to incite disease development. Aspects such as seasonal effects, stress and carbohydrate status of host tissue are associated with disease development. By implementing an integrated control programme incorporating sanitation pruning, specific cultural practices and fungicides, disease can be combated.
Ecology and control of ticks as disease vectors in wildlife of the Ngorongoro Crater, Tanzania

Wild mammals in Africa mostly have high levels of innate resistance to haemoparasites and the tick vectors that transmit them. Occasionally though, biotic and abiotic factors combine to alter this relationship and tick-borne disease is diagnosed in wildlife. We postulate an inter-relationship between anthropogenic and natural factors that resulted in wildlife mortality, attributable to disease transmission associated with a gradual build-up of large numbers of ticks. Suppression of grassland fire for 27 years in a distinct ecological unit promoted a gradual expansion of areas covered by tall grass. Changes in composition of the pasture led to improved tick survival, which was further boosted by the availability of increasing numbers of a coarse-grazing species and preferred tick host, African buffalo. Alternating climatic cycles then appeared to precipitate an outbreak of tick-borne haemolytic disease by subjecting ticks and their herbivore hosts to ideal conditions (in wet years) followed by starvation and immune suppression (in dry years). Evidence supporting the hypothesis was gathered retrospectively in the present study through systematic sampling of tick density and correlating life stages of ticks to season, grass species and height of the grass sward. Tick host preference was noted by collection from immobilized wild animals and sympatric livestock. A long series of census data confirmed the changing composition of resident wild herbivores in the Ngorongoro Crater. To reduce the tick challenge, prescribed burning of the crater grassland was reintroduced; tick numbers fell rapidly and three years of subsequent monitoring confirmed the success of this strategy.
Investigating fatty acid composition in the diet to determine biomarkers indicative of obesity-related disease.

This research investigated the role that dietary fatty acids have in the detection of obesity-related diseases. While studies have focused on whether fatty acid composition changes due to various obesity-related diseases, e.g. Cardiovascular, metabolic syndrome, very few have investigated whether fatty acids can be used as biomarkers to detect the predilection towards obesity. In response this project investigated a range of animal and plant oils, as well as liver and adipose tissue samples to determine whether the composition of fatty acids is similar between a low fat diet and a high carbohydrate high fat diet, simulating the unhealthy diet eaten by many. Through the use of fatty acid methyl esters (FAME) which were derivitized using two different methods using either H2SO4 or BF3 as catalysts, samples were analysed by GC-MS. While both methods were viable, BF3 proved to be the more reliable method. Previous research completed by this laboratory was extended using tissue samples not previously examined. Results indicated that supplementation of the diet by EPA (C20:5) possibly attenuates the impact of obesity-related inflammation (p<0.05). Increased levels of n-3 PUFA in tissues from a diet supplemented with EPA indicates that preferential metabolism of anti-inflammatory eicosanoids may occur. The outcome of this research indicates that the composition of fatty acids produced by varying diets does differ and therefore may have an impact on obesity-related diseases. This research has contributed to current knowledge by extending previous findings (Poudyal et al., 2012b) from other tissues and provides further indication that study should continue in examining what role eicosanoids play in attenuating obesity-related diseases.
MECHANISMS LEADING TO CHROMOSOMAL INSTABILITY IN ORAL CANCER CELLS

In the United States, cancer is a leading cause of death, second only to heart disease (MOKDAD et al. 2004). Although it is estimated that in 2005, cancer of the oral cavity will account for only 2.1% of cancer cases and 1.3% of overall cancer deaths in the U. S. (JEMAL et al. 2005), high-risk behaviors such as smoking cigarettes, using smokeless tobacco, and consuming excessive alcohol have been shown to play a major role in OSCC development. Exposure to environmental agents, including tobacco products, alcoholic beverages, and/or viruses, such as human papillomavirus (FORASTIERE et al. 2001; HO and CALIFANO 2004; MORK et al. 2001) have a profound influence on cells within the oral cavity. These factors have been shown to induce genetic alterations including chromosomal alterations, DNA changes, and/or epigenetic alterations, such as changes in DNA methylation that affect genetic regulation. Genetic alterations in cells are useful biological markers that assist in early detection of cancer and response to therapy (SIDRANSKY 1995). Currently, however, there are no useful biomarkers to identify early changes involved in OSCC development. One genetic alteration observed in 45% of OSCC is amplification of chromosomal band, 11q13. This event has been shown to follow dysplastic cellular changes, but occur prior to development of carcinoma in situ (FORASTIERE et al. 2001). Therefore, 11q13 amplification may be a useful biomarker for detecting OSCC. In addition, understanding the molecular mechanisms that promote 11q13 gene amplification may provide valuable information for devising novel prevention measures and therapies. In the current study, we show that the primary mechanism promoting 11q13 gene amplification is BFB cycles. Furthermore, we suggest that breakage at the common fragile site, FRA11F, may be responsible for initiating 11q13 gene amplification. By determining the primary mechanism that leads to 11q13 amplification in OSCC, additional investigations focusing on the biological basis of this process may provide important information for developing successful measures and treatments that will increase the survival rate for individuals afflicted with oral cancer.
Production of trivalent influenza vaccines: disposable technology and insect cell lines

The overall production for the entire process is 22 million doses per year. This production capacity is approximately the same as a medium sized facility. Using a baculovirus insect cell expression system can reduce the production time of influenza vaccines from 6 months to 4 months. The other cell line considered, Chinese Hamster Ovaries, was determined to be unfavorable due to safety concerns. It was determined that disposable technology would be ideal for the process, as it allows production scale up with minimal capital investment. The disposable technology employed in the facility was found to be more economically viable than conventional multi-use technology. The facility still requires the use of some multi-use components, such as chromatography and diafiltration, but single use technology is employed where possible. Examining the project, a lifespan of 23 years was determined to be appropriate for demonstrating the economic feasibility of the project. It was found that the minimum IRR at current prices was 33.36%. With a 12% discrete interest rate, the net present value of the facility is $278 million, for a total capital investment of $149 million. At this rate, it was also determined that the payback period was 2.83 years with a return on investment of 34.42%. From this data, it was concluded that the project should proceed as planned.
A 2D-difference gel electrophoresis strategy for redox proteomics.

Post-genomic biomedical science requires quantitative proteomics. In most cases this involves differential protein expression analysis using matched pairs of simultaneously detectable labelling reagents for specific protein amino acids. In this thesis the development and optimisation of a novel cysteine labelling strategy, that is based on the use of iodoacetyl derivatives of Cy3 and Cy5 (ICy3/5) and 2D-difference gel electrophoresis (2D-DIGE) is described. The differentially labelled samples are separated on a single 2D gel and detected by multi-wavelength fluorescence scanning. The method is used to analyse standard proteins and then cell lysates to define the stoichiometry, sensitivity and specificity of this labelling technique. A comparative study of this new proteomic ICy dye protocol with the current NHS-Cy dye labelling system and methods that employ commonly used protein staining methods is described. The method is then used for cysteine labelling of proteins in non-reduced, denatured biological samples allowing accurate monitoring and sensitive detection of redox-dependent thiol modifications and expression level changes. The method is shown to be compatible with the use of MALDI mass spectrometry to identify proteins by analysis of trypsinised ICy labelled peptide digests. Using parallel sample analysis within single gels, the ICy-dye reagents were used to detect redox-, ErbB-2- and growth factor-dependent changes in a human mammary luminal epithelial cell system which was exposed to hydrogen peroxide or to growth factor stimulation. The conventional lysine labelling 2D-DIGE technique was also used in parallel to assess the new ICy labelling strategy for determination of the effects of oxidative stress on protein isoform levels. This study has revealed the identity of proteins involved in the response to oxidative stress and growth factor stimulation in the context of ErbB-2 growth factor receptor over-expression. In addition, this labelling strategy was also used to detect changes in thiol reactivity that follow the UV irradiation of plasma proteins as part of a study designed to evaluate the effect of UV disinfection on plasma product safety for clinical use.
Development of a non-radioactive probe generated by RAPD-PCR for the detection of Theileria annulata

A highly reproducible, dominant and monomorphic fragment of 963 base pair (bp) was amplified from the genome of Theileria annulata by random amplified polymorphic DNA - polymerase chain reaction (RAPD-PCR) using a arbitrarily selected primer AP17 (5’-GGTGACGCAG-3’). This fragment was reamplified using the same random primer (AP17), gel purified and labeled with digoxigenin (DIG). Dot-blot hybridization of total genomic DNA with the probe detected Parbhani and Izatnagar strains of T. annulata with a threshold detection level of 10 pg of parasite template DNA. No cross-hybridization was observed with Babesia bigemina, Trypanosoma evansi and the bovine host DNA. The sensitivity of the DIG labeled probe developed in this study is at least 6 to 65 times higher than the other DIG labeled probes developed in India and therefore considered highly suitable for diagnosis of carrier animals especially when they are imported or exported from the country.
Characterization of putative regulators of the small GTPase, Rac, in Drosophila

The Rho s ubfamily G TPases (Rho, R ac, C dc42) are small G TP-binding proteins that act as switches, controlling many cellular functions. These GTPases fluctuate between a GTP-bound 'on' state and a GDP-bound 'off state, this being catalyzed by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPS). Rac, a possible oncogene, has diverse roles including regulation of cell adhesion, the release of arachidonic acid, formation of F-actin based membrane ruffles/lamellipodia, assembly of multi-molecular focal complexes, apoptosis, and regulation of the JNK MAP kinase pathway. Model systems such as Drosophila have furthered the understanding of the functional roles of Rac in neuronal development, epithelial morphogenesis, and apoptosis. The use of model systems allows the study of molecular processes at levels not possible in cell culture. These include genetic approaches and the study of gene function at the level of tissue morphogenesis. Three putative interactors of Rac, originally identified in mammals, were studied in Drosophila. Sra-1, a cytoskeletal effector, was found to interact with Rac and had roles in neuronal development and F-actin regulation. POSH, a modulator of JNK signaling in mammals, was found to indirectly modulate Rac in Drosophila but was not required for JNK signaling during embryonic development. Drosophila POSH also had a role in apoptosis during development. RhoGAP68F, a GAP protein, was found to preferentially negatively regulate activated Rho rather than Rac in Drosophila and was therefore not investigated further. DEDICATION To Mom, Dad and Deanna. ACKNOWLEDGEMENTS Thanks for help from Dr. Esther Verheyen, Dr. Bruce Brandhorst, Ryan Conder, Justina Sanny, Barton Xu, Bari Zahedi, Kai-Ping Sem, Darrell Bessette, Marina 'Hoss' Kanjer, Jobi 'wan Kinobi' McKenzie, Krista 'Krispy' Ryz, Daniel 'Han Solo' Han, Claire Hou, Richard 'Oh, Heck! ' Heck, Micheal 'The Sleeper' Sha, Miles 'Dr. Lean' Chu, Ricky 'Martin' Choi. Also thank you to the Esther Verheyen Laboratory and the Susan Parkhurst Laboratory. Finally thank you to Dr. Nick Harden for being an extremely supportive supervisor.
Prevention of Complications of Incisional Hernia Repair: Current Problem State (Review)

The review covers the important aspects of complications in incisional hernia repair. The paper specifies the most relevant issues of modern herniology, its social and economical aspects, considers the preventive techniques for preoperative, intraoperative and postoperative complications. When describing the preoperative predictive and preventive methods in complications, the authors analyzed the existent classifications and integral grading scales for patients’ state indicators, showed the benefits and drawbacks of current techniques of preoperative preparation. The part devoted to an intraoperative period presents the main current hernia repair techniques, mesh implants, and their characteristics. Much attention is given to the description of surgical options depending on mesh arrangement in relation to anatomical abdominal wall layers, and the assessment of mesh implant types, their selection for a specific clinical setting. The review considers the principles of component separation as one of the most promising directions of abdominal surgery. When studying the postoperative preventive methods, the emphasis was made on the description of fast-track principles. Currently, a fast-track technique is being widely used in surgery, and gaining popularity in herniology.
Genetic patchwork of network-building wood ant populations.

Genetic organization of colonies and populations of the ant Formica aquilonia were studied at the edge of the urban area of the city of Helsinki within an area of about 400 km 2 . Over six thousand old queens and workers were sampled from a total of 288 nest mounds from 14 populations (patches of forest) for an allozyme study, and workers from 13-15 nests in each of three populations were also characterized by microsatellite genotyping. Genetic relatedness among nest mates within populations was close to zero for both queens (estimates ranging from 0.02 to 0.13) and workers (from 0.01 to 0.22), with some of the estimates being significantly greater than zero. These results supported the view of a high level of polygyny within the nests. The populations showed significant genetic differences both at the allozyme loci (overall F S T = 0.17) and at the microsatellites (F S T = 0.24). The estimates of F S T between pairs of populations varied from 0.01 to 0.61, the largest values being associated to reduced genetic variation and an apparent bottleneck within one population. The results showed that the local populations of this highly polygynous (multiple queens in a nest) and polydomous (multiple nests in a colony) ant can be differentiated genetically within potential dispersal distances, suggesting restricted dispersal and possible bottlenecks when colonizing new patches of forest.
Cibles moléculaires de la myostatine impliquées dans l'hypertrophie musculaire chez la souris et le bovin

La myostatine, un facteur de croissance de la superfamille des TGF-beta, regule negativement la croissance et la masse du muscle squelettique en controlant le nombre de fibres par son action anti-proliferative, et la croissance individuelle de chacune d'entre elles. Dans le but de completer les connaissances sur ces mecanismes d'action, cette these (2006-2009) avait pour objectif d'identifier de nouvelles cibles moleculaires de la myostatine impliquees dans l'hypertrophie musculaire. Ce travail de these a revele de nouvelles cibles de la myostatine, notamment une activation de la cascade PI3K/Akt, une expression differentielle des genes et des proteines impliquees dans la regulation de la survie cellulaire. L'inhibition de l'apoptose des noyaux musculaires en l'absence de myostatins fonctionnelle, et par consequent , l'augmentation du nombre de noyaux et de la taille du domaine nucleo-cytoplasmique pourraient ainsi contribuer au phenomene d'hypertrophie
Understanding the role of perivascular macrophages in Parkinson's disease pathophysiology

Parkinson’s disease (PD) is characterized by the progressive loss of dopaminergic neurons in the substantia nigra (SN) associated to the aggregation of α-synuclein (α-Syn) that forms intraneuronal inclusions. In addition, mounting evidence suggest that neuro-immune interactions, favoured by cerebrovascular alterations, are involved in the pathomechanisms of PD. In this work, we focus on a myeloid population that surrounds blood vessels: perivascular macrophages (PVMs). We show that both in PD patients and in a mouse model of degenerative synucleinopathy, there is an increased proliferative recruitment of PVMs within the SN. We also found that specific ablation of PVMs aggravates the degenerative phenotype in synucleinopathic mice. PVMs-mediated neuroprotection is not likely linked to regulatory mechanisms of microglial cell response. Interestingly, the absence of PVMs is associated with higher vascular expression of VCAM-1 and enhanced infiltration of CD4+ and CD8+ T-cells, whose pathogenic role remains to be determined. We also observe that PVMs deficiency leads to an increased spreading of α-Syn pathology following striatal injections of α-Syn fibrils. We hypothesize that PVMs might be essential for the clearance of toxic α-Syn species due to their phagocytic activity, but also to their importance in regulating interstitial and cerebrospinal fluid (CSF) circulation, as shown by analysing CSF movement via the infusion of fluorescent tracers in PVMs-deficient conditions. Overall, our data highlight the importance of PVMs in regulating the toxicity and propagation of synucleinopathy and provide a rationale for therapeutic strategies aimed at boosting PVMs functions in PD.
Registration of NFLT12, a Tissue Culture–Responsive Lolium temulentum (Darnel Ryegrass) Line

Lolium temulentum L. (Darnel ryegrass) is closely related to major forage and turf species, is self-pollinated, diploid, and has a short life cycle. These traits make it suitable to serve as a model species for testing gene functions in grasses. A new L. temulentum line, NFLT12 (Reg. No. GS-7, PI 655941), was developed using anther culture on an F 2 population derived from a cross of two parental L. temulentum lines. Haploid and doubled haploid plants were obtained and their tissue culture responsiveness and amiability to genetic transformation were tested. NFLT12 is highly responsive to tissue culture, is readily transformable and is expected to provide a resource for those using L. temulentum as a model species for functional genomics studies.
Candida spp. and Oxidative Stress Response in Innate Immune Cells

In dieser Arbeit wurde der „Oxidative Burst“ des angeborenen Immunsystems in der Interaktion mit Candida albicans untersucht. Das klinische Spektrum des opportunistischen Pathogens C. albicans reicht von mucokutanen Infektionen bis hin zu lebensbedrohlichen, systemischen Krankheiten in immunsupprimierten Patienten. Eine der ersten Reaktionen der Zellen des angeborenen Immunsystems, sogenannte Phagozyten, ist die Produktion von Reaktiven Oxygen Spezies (ROS) wenn sie auf Pathogene stosen. ROS spielen eine wichtige Rolle bei Entzundungsreaktionen, zum Beispiel zerstoren sie eindringende Krankheitserreger. Durch eine Uberproduktion von ROS kann aber auch das Endothel beschadigt werden. Fruhere Studien haben gezeigt, dass Zymosan, eine Zellwand Aufbereitung von Saccharomyces cerevisiae, und C. albicans die ROS Produktion in Makrophagen aktivieren. Das C. albicans Genom codiert sechs Superoxid Dismutasen (SOD1 bis SOD6), die an der Zersetzung von ROS beteiligt sind, SOD1 bis SOD3 sind intrazellular und SOD4 bis SOD6 sind wahrscheinlich an der Zellwand von C. albicans lokalisiert. Diese Arbeit zeigt, dass die Co-Kultur von Makrophagen oder myeloischen dendritischen Zellen mit C. albicans denen Sod5 genetisch entfernt wurde zu einer massiven extrazellularen Anhaufung von ROS in vitro fuhrt. Diese ROS Akkumulierung ist in der Interaktion mit Makrophagen noch hoher wenn C. albicans weder Sod4 noch Sod5 haben. Weiteres werden C. albicans Sod5 und Sod4 Mutanten von Makrophagen in vitro besser getotet als Wildtyp C. albicans. Makrophagen, die einen Defekt im Oxidativen Burst haben weil ihnen das gp91Phox Gen fehlt, konnen diese Mutanten nicht mehr toten, dies zeigt eine ROS-abhangige Eliminierung von pathogenen Pilzen durch Makrophagen. Diese Daten zeigen die physiologische Rolle der C. albicans Zellwand SODs bei der Entgiftung von ROS und weisen auf einen Mechanismus, mit dem C. albicans das Immunsystems in vivo uberlistet, hin. Im zweiten Teil dieser Arbeit wurden potentielle Rezeptor(en) untersucht, durch die Makrophagen C. albicans erkennen, um den oxidative Burst zu induzieren. Die Toll Like Rezeptor-Familie und das intrazellulare MyD88 Adapter-Protein sind nicht an der ROS-Produktion durch Zymosan oder C. albicans Stimulation beteiligt. Wenn der C-Typ-Lectin-Rezeptor Dectin-1 mit Zymosan oder Hitze-getoteter C. albicans stimuliert wird, induziert Dectin-1 die ROS Antwort indem die Src und Syk-Kinase aktiviert wird. Daruber hinaus aktiviert Zymosan auch die ERK1/2 MAP-Kinasen via Dectin-1. Im Gegensatz dazu ist Dectin-1 nur masig an der Aktivierung von ROS und ERK1 beteiligt wenn die Makrophagen mit lebenden C. albicans stimuliert werden. Interessanterweise ist die Aktivierung der Src und Syk-Kinasen auch wichtig fur ROS Induktion durch Stimulierung mit lebender C. albicans. Dies fuhrt zu dem Schluss, dass ein Rezeptor oder Adapter-Protein mit einem ITAM Motif an der Induktion von ROS beteiligt ist. Ein siRNA-basierendes knock-down-Experiment zeigt, dass das ITAM Adapter-Protein DAP12 fur die ROS Produktion durch C. albicans und Zymosan mitverantwortlich ist.