Hierarchical Bayesian modelling of plant pest invasions with human-mediated dispersal

Hierarchical Bayesian models can assimilate surveillance and ecological information to estimate both invasion extent and model parameters for invading plant pests spread by people. A reliability analysis framework that can accommodate multiple dispersal modes is developed to estimate human-mediated dispersal parameters for an invasive species. Uncertainty in the observation process is modelled by accounting for local natural spread and population growth within spatial units. Broad scale incursion dynamics are based on a mechanistic gravity model with a Weibull distribution modification to incorporate a local pest build-up phase. The model uses Markov chain Monte Carlo simulations to infer the probability of colonisation times for discrete spatial units and to estimate connectivity parameters between these units. The hierarchical Bayesian model with observational and ecological components is applied to a surveillance dataset for a spiralling whitefly (Aleurodicus dispersus) invasion in Queensland, Australia. The model structure provides a useful application that draws on surveillance data and ecological knowledge that can be used to manage the risk of pest movement.

Studies of the genetic epidemiology of cardiovascular disease: focus on inflammatory candidate genes

Cardiovascular disease (CVD) is a complex disease with multifactorial aetiology. Both genetic and environmental factors contribute to the disease risk. The lifetime risk for CVD differs markedly between men and women, men being at increased risk. Inflammatory reaction contributes to the development of the disease by promoting atherosclerosis in artery walls. In the first part of this thesis, we identified several inflammatory related CVD risk factors associating with the amount of DNA from whole blood samples, indicating a potential source of bias if a genetic study selects the participants based on the available amount of DNA. In the following studies, this observation was taken into account by applying whole genome amplification to samples otherwise subjected to exclusion due to very low DNA yield. We continued by investigating the contribution of inflammatory genes to the risk for CVD separately in men and women, and looked for sex-genotype interaction. In the second part, we explored a new candidate gene and its role in the risk for CVD. Selenoprotein S (SEPS1) is a membrane protein residing in the endoplasmic reticulum where it participates in retro-translocation of unfolded proteins to cytosolic protein degradation. Previous studies have indicated that SEPS1 protects cells from oxidative stress and that variations in the gene are associated with circulating levels of inflammatory cytokines. In our study, we identified two variants in the SEPS1 gene, which associated with coronary heart disease and ischemic stroke in women. This is, to our knowledge, the first study suggesting a role of SEPS1 in the risk for CVD after extensively examining the variation within the gene region. In the third part of this thesis, we focused on a set of seven genes (angiotensin converting enzyme, angiotensin II receptor type I, C-reactive protein (CRP), and fibrinogen alpha-, beta-, and gamma-chains (FGA, FGB, FGG)) related to inflammatory cytokine interleukin 6 (IL6) and their association with the risk for CVD. We identified one variant in the IL6 gene conferring risk for CVD in men and a variant pair from IL6 and FGA genes associated with decreased risk. Moreover, we identified and confirmed an association between a rare variant in the CRP gene and lower CRP levels, and found two variants in the FGA and FGG genes associating with fibrinogen. The results from this third study suggest a role for the interleukin 6 pathway genes in the pathogenesis of CVD and warrant further studies in other populations. In addition to the IL6 -related genes, we describe in this thesis several sex-specific associations in other genes included in this study. The majority of the findings were evident only in women encouraging other studies of cardiovascular disease to include and analyse women separately from men.

Genetics of Cardiovascular Disease: A Candidate Gene Study of USF1

Cardiovascular diseases (CVD) are major contributors to morbidity and mortality worldwide. Several interacting environmental, biochemical, and genetic risk factors can increase disease susceptibility. While some of the genes involved in the etiology of CVD are known, many are yet to be discovered. During the last few decades, scientists have searched for these genes with genome-wide linkage and association methods, and with more targeted candidate gene studies. This thesis investigates variation within the upstream transcription factor 1 (USF1) gene locus in relation to CVD risk factors, atherosclerosis, and incidence and prevalence of CVD. This candidate gene was first identified in Finnish families ascertained for familial combined hyperlipidemia, a common dyslipidemia predisposing to coronary heart disease. The gene is a ubiquitously expressed transcription factor regulating expression of several genes from lipid and glucose metabolism, inflammation, and endothelial function. First, we examined association between USF1 variants and several CVD risk factors, such as lipid phenotypes, body composition measures, and metabolic syndrome, in two prospective population cohorts. Our data suggested that USF1 contributes to these CVD risk factors at the population level. Notably, the associations with quantitative measurements were mostly detected among study subjects with CVD or metabolic syndrome, suggesting complex interactions between USF1 effects and the pathophysiological state of an individual. Second, we investigated how variation at the USF1 locus contributes to atherosclerotic lesions of the coronary arteries and abdominal aorta. For this, we used two study samples of middle-aged men with detailed measurements of atherosclerosis obtained in autopsy. USF1 variation significantly associated with areas of several types of lesions, especially with calcification of the arteries. Next, we tested what effect the USF1 risk variants have on sudden cardiac death and incidence of CVD. The atherosclerosis-associated risk variant increased the risk of sudden cardiac death of the same study subjects. Furthermore, USF1 alleles associated with incidence of CVD in the Finnish population follow-up cohorts. These associations were especially prominent among women, suggesting a sex specific effect, which has also been detected in subsequent studies. Finally, as some of the low-yield DNA samples of the Finnish follow-up study cohort needed to be whole-genome amplified (WGA) prior to genotyping, we evaluated whether the produced WGA genotypes were of good quality. Although the samples giving genotype discrepancies could not be detected before genotyping with standard laboratory quality control methods, our results suggested that enhanced quality control at the time of the genotyping could identify such samples. In addition, combining two WGA reactions into one pooled DNA sample for genotyping markedly reduced the number of discrepancies and samples showing them. In conclusion, USF1 seems to have a role in the etiology of CVD. Additional studies are warranted to identify functional variants and to study interactions between USF1 and other genetic or environmental factors. This USF1 study, and other studies with low DNA yield of some samples, can benefit from whole genome amplification of the low-yield samples prior to genotyping. Careful quality control procedures are, however, needed in WGA genotyping.

Influence of plant traits on production costs and profitability of strawberry in southeast Queensland.

In Queensland the subtropical strawberry ( Fragaria * ananassa) breeding program aims to combine traits into novel genotypes that increase production efficiency. The contribution of individual plant traits to cost and income under subtropical Queensland conditions was investigated, with the overall goal of improving the profitability of the industry through the release of new strawberry cultivars. The study involved specifying the production and marketing system using three cultivars of strawberry that are currently widely grown annually in southeast Queensland, developing methods to assess the economic impact of changes to the system, and identifying plant traits that influence outcomes from the system. From May through September P (price; $ punnet -1), V (monthly mass; tonne of fruit on the market) and M (calendar month; i.e. May=5) were found to be related ( r2=0.92) by the function (SE) P=4.741(0.469)-0.001630(0.0005) V-0.226(0.102) M using data from 2006 to 2010 for the Brisbane central market. Both income and cost elements in the gross margin were subject to sensitivity analysis. 'Harvesting' and 'Handling/Packing' 'Groups' of 'Activities' were the major contributors to variable costs (each >20%) in the gross margin analysis. Within the 'Harvesting Group', the 'Picking Activity' contributed most (>80%) with the trait 'display of fruit' having the greatest (33%) influence on the cost of the 'Picking Activity'. Within the 'Handling/Packing Group', the 'Packing Activity' contributed 50% of costs with the traits 'fruit shape', 'fruit size variation' and 'resistance to bruising' having the greatest (12-62%) influence on the cost of the 'Packing Activity'. Non-plant items (e.g. carton purchases) made up the other 50% of the costs within the 'Handling/Packing Group'. When any of the individual traits in the 'Harvesting' and 'Handling/Packing' groups were changed by one unit (on a 1-9 scale) the gross margin changed by up to 1%. Increasing yield increased the gross margin to a maximum (15% above present) at 1320 g plant -1 (94% above present). A 10% redistribution of total yield from September to May increased the gross margin by 23%. Increasing fruit size increased gross margin: a 75% increase in fruit size (to ~30 g) produced a 22% increase in the gross margin. The modified gross margin analysis developed in this study allowed simultaneous estimation of the gross margin for the producer and gross value of the industry. These parameters sometimes move in opposite directions.

Patterns of seed bank and size asymmetry of plant growth across varying sites in the invasive Lantana camara L. (Verbenaceae)

Lantana camara L. (Verbenaceae) is a weed of great significance in Australia and worldwide, but little is known about connections among components of its life history. We document over a 3-year period, the links between L. camara seed-bank dynamics and its above-ground growth, including size asymmetry in four land-use types (a farm, a hoop pine plantation and two open eucalypt forests) invaded by the weed near Brisbane, Queensland Australia. Seed-bank populations varied appreciably across sites and in response to rainfall and control measures, and they were higher (~1,000 seeds/m2) when annual rainfall was 15-30 % below the long-term yearly average. Fire reduced seed-bank populations but not the proportion germinating (6-8 %). Nearly a quarter of fresh seeds remain germinable after 3 years of soil burial. For small seedlings (<10 cm high), the expected trade-offs in two life-history traits-survival and growth-did not apply; rather the observed positive association between these two traits, coupled with a persistent seed-bank population could contribute to the invasiveness of the plant. Relationships between absolute growth rate and initial plant size (crown volume) were positively linear, suggesting that most populations are still at varying stages of the exponential phase of the sigmoid growth; this trend also suggests that at most sites and despite increasing stand density and limiting environmental resources of light and soil moisture, lantana growth is inversely size asymmetric. From the observed changes in measures of plant size inequality, asymmetric competition appeared limited in all the infestations surveyed. © 2013 Crown Copyright as represented by: Department of Agriculture, Fisheries and Forestry, Australia.

Host selection and parasitism behavior of lysiphlebus testaceipes: Role of plant, aphid species and instar

The aphid parasitoid Lysiphlebus testaceipes is a potentially valuable biological control agent of Aphis gossypii a major worldwide pest of cotton. One means of increasing the abundance of a biological control agent is to provide an alternative host habitat adjacent to cropping, from which they can provide pest control services in the crop. Host selection and parasitism rate of an alternative host aphid, Aphis craccivora by L. testaceipes were studied in a series of experiments that tested its host suitability relative to A. gossypii on cotton, hibiscus and mungbean. Host acceptance, as measured by number of ovipositions was much greater in A. craccivora compared to A. gossypii, while more host aphids were accepted on mungbean than cotton. When given a choice L. testaceipes attacks more 4th instar and adult stages (63% and 70%, respectively) of both hosts than 2nd instar nymphs (47%). In a switching (host choice) experiment, L. testaceipes preferentially attacked A. craccivora on mungbean over A. gossypii on cotton. Observations of parasitoid contact with A. gossypii cornicle secretion suggest it provides a useful deterrent against parasitoid attack. From these experiments it appears L. testaceipes has a preference for A. craccivora and mungbean compared to A. gossypii and cotton, in this respect using A. craccivora and mungbean as alternative habitat may not work as the parasitoid is unlikely to switch away from its preferred host. © 2012.

HPLC analysis of plant sterol oxidation products

Increased interest in the cholesterol-lowering effect of plant sterols has led to development of plant sterol-enriched foods. When products are enriched, the safety of the added components must be evaluated. In the case of plant sterols, oxidation is the reaction of main concern. In vitro studies have indicated that cholesterol oxides may have harmful effects. Due their structural similarity, plant sterol oxidation products may have similar health implications. This study concentrated on developing high-performance liquid chromatography (HPLC) methods that enable the investigation of formation of both primary and secondary oxidation products and thus can be used for oxidation mechanism studies of plant sterols. The applicability of the methods for following the oxidation reactions of plant sterols was evaluated by using oxidized stigmasterol and sterol mixture as model samples. An HPLC method with ultraviolet and fluorescence detection (HPLC-UV-FL) was developed. It allowed the specific detection of hydroperoxides with FL detection after post-column reagent addition. The formation of primary and secondary oxidation products and amount of unoxidized sterol could be followed by using UV detection. With the HPLC-UV-FL method, separation between oxides was essential and oxides of only one plant sterol could be quantified in one run. Quantification with UV can lead to inaccuracy of the results since the number of double bonds had effect on the UV absorbance. In the case of liquid chromatography-mass spectrometry (LC-MS), separation of oxides with different functionalities was important because some oxides of the same sterol have similar molecular weight and moreover epimers have similar fragmentation behaviour. On the other hand, coelution of different plant sterol oxides with the same functional group was acceptable since they differ in molecular weights. Results revealed that all studied plant sterols and cholesterol seem to have similar fragmentation behaviour, with only relative ion abundances being slightly different. The major advantage of MS detection coupled with LC separation is the capability to analyse totally or partly coeluting analytes if these have different molecular weights. The HPLC-UV-FL and LC-MS methods were demonstrated to be suitable for studying the photo-oxidation and thermo-oxidation reactions of plant sterols. The HPLC-UV-FL method was able to show different formation rates of hydroperoxides during photo-oxidation. The method also confirmed that plant sterols have similar photo-oxidation behaviour to cholesterol. When thermo-oxidation of plant sterols was investigated by HPLC-UV-FL and LC-MS, the results revealed that the formation and decomposition of individual hydroperoxides and secondary oxidation products could be studied. The methods used revealed that all of the plant sterols had similar thermo-oxidation behaviour when compared with each other, and the predominant reactions and oxidation rates were temperature dependent. Overall, these findings showed that with these LC methods the oxidation mechanisms of plant sterols can be examined in detail, including the formation and degradation of individual hydroperoxides and secondary oxidation products, with less sample pretreatment and without derivatization.

Modelling the effect of plant water use traits on yield and stay-green expression in sorghum

Post-rainy sorghum (Sorghum bicolor (L.) Moench) production underpins the livelihood of millions in the semiarid tropics, where the crop is affected by drought. Drought scenarios have been classified and quantified using crop simulation. In this report, variation in traits that hypothetically contribute to drought adaptation (plant growth dynamics, canopy and root water conducting capacity, drought stress responses) were virtually introgressed into the most common post-rainy sorghum genotype, and the influence of these traits on plant growth, development, and grain and stover yield were simulated across different scenarios. Limited transpiration rates under high vapour pressure deficit had the highest positive effect on production, especially combined with enhanced water extraction capacity at the root level. Variability in leaf development (smaller canopy size, later plant vigour or increased leaf appearance rate) also increased grain yield under severe drought, although it caused a stover yield trade-off under milder stress. Although the leaf development response to soil drying varied, this trait had only a modest benefit on crop production across all stress scenarios. Closer dissection of the model outputs showed that under water limitation, grain yield was largely determined by the amount of water availability after anthesis, and this relationship became closer with stress severity. All traits investigated increased water availability after anthesis and caused a delay in leaf senescence and led to a ‘stay-green’ phenotype. In conclusion, we showed that breeding success remained highly probabilistic; maximum resilience and economic benefits depended on drought frequency. Maximum potential could be explored by specific combinations of traits.

Studies on "Sappe" disease of the silkworm, Bombyx mori : II. Effect of age of larvae on the manifestation of the disease

The effect of age of the larvae on the manifestation of the "Sappe" disease of the silkworm by oral inoculation of different pathogens, viz., Aerobacter cloacae, Pseudomonas boreopolis, Escherichia freundii, Achromobacter delmarvae, A. Superficialis, Pseudomonas ovalis, and Staphylococcus albus was tested. It was found that the reaction of the larva to the pathogen was influenced by its age. Some, e.g., Escherichia freundii, were more lethal when introduced at early stages whereas certain others, e.g., Aerobacter cloacae and Staphylococcus albus, caused maximum damage when invading older larvae. Irrespective of the age of infection, death of the worms mainly occurred during molting and before spinning. The studies also indicated that growth and mortality of the larvae were affected differentially by the pathogens.

Combinations of plant-derived compounds against Campylobacter in vitro

Campylobacter occur in fresh retail poultry products as a result of their colonization of the gastro-intestinal tract of chickens during growth. Feed additives could be used for suppression of Campylobacter levels in the chickens prior to slaughter. To address this opportunity, feed manufacturers are targeting natural antimicrobials from plant material as new forms of consumer-accepted feed additives. However, to be practical, these natural antimicrobials must be effective at low concentrations. The current study has validated an improved laboratory method to study minimal inhibitory concentrations of plant compounds and their combinations against Campylobacter. The assay was shown to be valid for testing lipid-soluble and water-soluble plant extracts and byproducts from the food industry. The study screened 29 extracts or plant-derived compounds and their mixtures for anti-Campylobacter activity using a laboratory assay. Combinations of oregano, lactic acid, and sorghum byproduct showed effective synergy in anti-Campylobacter activity. The synergies allowed a large reduction in the concentration of the individual compounds needed to kill the bacteria with an 80% reduction in concentration being achieved for oregano essential oil. The assay gives rise to further opportunities for the testing of a greater range of combinations of plant-derived compounds and other natural antimicrobials. The method is robust, simple, and easily automated, and it could be used to adjust the cost of feed formulations by reducing costs associated with antimicrobial feed additives.

Endoplasmic reticulum stress and cell death mechanisms in the cell model of Huntington’s disease

This thesis clarifies important molecular pathways that are activated during the cell death observed in Huntington’s disease. Huntington’s disease is one of the most common inherited neurodegenerative diseases, which is primarily inherited in an autosomal dominant manner. HD is caused by an expansion of CAG repeats in the first exon of the IT15 gene. IT15 encodes the production of a Huntington’s disease protein huntingtin. Mutation of the IT15 gene results in a long stretch of polyQ residues close to the amino-terminal region of huntingtin. Huntington’s disease is a fatal autosomal neurodegenerative disorder. Despite the current knowledge of HD, the precise mechanism behind the selective neuronal death, and how the disease propagates, still remains an enigma. The studies mainly focused on the control of endoplasmic reticulum (ER) stress triggered by the mutant huntingtin proteins. The ER is a delicate organelle having essential roles in protein folding and calcium regulation. Even the slightest perturbations on ER homeostasis are effective enough to trigger ER stress and its adaptation pathways, called unfolded protein response (UPR). UPR is essential for cellular homeostasis and it adapts ER to the changing environment and decreases ER stress. If adaptation processes fail and stress is excessive and prolonged; irreversible cell death pathways are engaged. The results showed that inhibition of ER stress with chemical agents are able to decrease cell death and formation of toxic cell aggregates caused by mutant huntingtin proteins. The study concentrated also to the NF-κB (nuclear factor-kappaB) pathway, which is activated during ER stress. NF-κB pathway is capable to regulate the levels of important cellular antioxidants. Cellular antioxidants provide a first line of defence against excess reactive oxygen species. Excess accumulation of reactive oxygen species and subsequent activation of oxidative stress damages motley of vital cellular processes and induce cell degeneration. Data showed that mutant huntingtin proteins downregulate the expression levels of NF-κB and vital antioxidants, which was followed by increased oxidative stress and cell death. Treatment with antioxidants and inhibition of oxidative stress were able to counteract these adverse effects. In addition, thesis connects ER stress caused by mutant huntingtin to the cytoprotective autophagy. Autophagy sustains cellular balance by degrading potentially toxic cell proteins and components observed in Huntington’s disease. The results revealed that cytoprotective autophagy is active at the early points (24h) of ER stress after expression of mutant huntingtin proteins. GADD34 (growth arrest and DNA damage-inducible gene 34), which is previously connected to the regulation of translation during cell stress, was shown to control the stimulation of autophagy. However, GADD34 and autophagy were downregulated at later time points (48h) during mutant huntingtin proteins induced ER stress, and subsequently cell survival decreased. Overexpression GADD34 enhanced autophagy and decreased cell death, indicating that GADD34 plays a critical role in cell protection. The thesis reveales new interesting data about the neuronal cell death pathways seen in Huntington’s disease, and how cell degeneration is partly counteracted by various therapeutic agents. Expression of mutant huntingtin proteins is shown to alter signaling events that control ER stress, oxidative stress and autophagy. Despite that Huntington’s disease is mainly an untreatable disorder; these findings offer potential targets and neuroprotective strategies in designing novel therapies for Huntington’s disease.