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Publication Restricted An investigation of systematic camera trap monitoring for kiwi (Apteryx spp.) : A thesis submitted in partial fulfillment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2023) Tansell, A Jane SIntroduction: Kiwi (Apteryx spp.) are one of New Zealand’s national taonga/taoka (treasures) that are our responsibility and privilege to protect. To inform protective management, we need to monitor kiwi population responses to management, for which a non-invasive method that can detect all age classes has been lacking. Camera traps are non-invasive monitoring devices, which are increasingly used with recently developed analyses to monitor cryptic terrestrial species around the world. To apply these methods to kiwi, standardized methods need to be developed and benchmarked against existing methods. Aims: The aims of this study were to 1) summarise previous monitoring work on kiwi to develop a draft systematic camera trap monitoring method for kiwi, 2) determine optimal site selection and camera trap set-up, 3) determine optimal survey length and camera trap spacing for use with spatial presence-absence (SPA) analysis and identify whether realistic population estimates are obtained, 4) compare camera traps with a current noninvasive method using acoustic recorders to determine if they give realistic and comparable estimates when used with SPA, 5) compare camera traps with dog survey and an observer listening survey to assess kiwi population health, 6) trial alternative analyses for use with camera traps in high density sites, 7) investigate stereo cameras for their potential to add value to camera trap surveys. Materials and methods: We summarised the current literature on monitoring kiwi and the use of camera trap surveys. We deployed 34 camera traps over six seasons in Orokonui Ecosanctuary. We deployed 29 acoustic recorders and carried out detector dog surveys to compare the number of juveniles detected. We deployed 17 camera traps in Rotokare Scenic Reserve and 18 camera traps in the Cape Sanctuary to examine their effectiveness in high kiwi density areas. We constructed a stereo camera by chaining two off-the-shelf trail cameras together to trigger from one PIR sensor and briefly trialled the stereo camera at Orokonui. Results: Cameras were able to detect kiwi of all age groups and to provide credible population densities and trends. Kiwi detections can be maximised by using a detector dog team to select camera sites and through camera orientation. Comparable population estimates were obtained using spatial presence-absence (SPA) analysis with an optimal survey length of four months, during peak incubation, and optimal camera spacing of 350 m. Cameras and acoustic recorders gave comparable population estimates using SPA. Estimates were realistic based on matrix population model projection. Camera traps and detector dog surveys found a similar number of juvenile kiwi. Estimates obtained using Royle-Nichols analysis likely underestimated population size but correctly indicated population trend direction and magnitude, while the index-manipuation-index method did not give a biologically possible estimate of population density. The stereo camera method using two trail cameras was capable of giving surprisingly accurate bill measurements, but further work in necessary to achieve repeatability. Discussion and conclusions: Systematic camera trapping is capable of monitoring the whole kiwi population, including female and young kiwi that are usually under-recorded by other methods. Systematic camera trapping paired with spatial presence-absence analysis performed well in a low density population. Camera monitoring shows much promise as another useful noninvasive tool in the kiwi monitoring toolbox.Publication Open Access Ryegrass endophyte mixtures for improved animal health : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2024) Milsom, AndrewIn New Zealand, perennial ryegrass (Lolium perenne) with endophyte (Epichloë festucae var. lolii) is a standard ingredient of pastures where insect pests challenge the persistence of the ryegrass. Farmers currently have multiple ryegrass cultivar x endophyte strain combinations from which to choose the best match for their requirements. However, no single cultivar x strain combination provides both the highest insect protection and lowest occurrence of ryegrass staggers and heat stress in animals grazing pasture with endophyte. Furthermore, the current industry protocol for testing the safety of animals grazing a grass x endophyte combination involves exposing the animals to a simulated worst- case scenario and needs reassessment. This research aimed to examine the effects of endophyte diversity in perennial ryegrass on the health and performance of sheep using a modelling approach so that an animal response of any mixture could be predicted as a function of the mixture’s endophyte proportions, thus minimising the need for animal testing in the future. At Barenbrug Plant Breeding Station, Courtenay, Canterbury, eight pasture treatments of Maxsyn perennial ryegrass – seven that varied widely in sown proportions of three endophyte strains – nea3, nea12, and standard endophyte (SE) – and an endophyte-free control (nil), were tested over four experimental runs from February 2020 to December 2021. There were three monocultures (100% of each strain), three binary mixtures (50% of each of two strains) and one ternary mixture (33.3% of each strain) of endophyte based on a simplex centroid design. The eight treatments were randomised in three blocks of 0.156-ha plots. The animal responses of interest were ryegrass staggers, liveweight gain, heat stress, and diet selection of grazing sheep. The first experiment run was a test for ryegrass staggers in February 2020. Endophyte toxicity in late summer is typically near its annual maximum in Canterbury, so the timing of this run created a ‘worst-case scenario’ for ryegrass staggers. The pastures were managed in the previous spring so as to accumulate a large herbage dry matter (DM) mass (about 3700 kg DM/ha above a cutting height of 40–50 mm) of low nutritive quality feed (metabolisable energy (ME) = 8.7 MJ/kg DM and crude protein (CP) = 4.9%). The pasture available (kg DM/ha) was high enough for lambs to remain in the same plots for a 4-week testing period at a stocking rate of 64.1 lambs/ha. Ryegrass staggers was severe (score 4–5) in the lambs grazing the SE pasture after 8 days and in all other endophyte monocultures and mixtures after 22 days. Mixture models fitted to the staggers response data predicted the staggers score for any combination of sown endophyte proportions and identified an optimum of 65% nea3 and 35% nea12 which delayed severe staggers by 1 week. Ryegrass staggers was associated with tremorgenic alkaloids in the herbage above 40–50 mm: epoxy-janthitrem I of nea12 (1 ppm), paxilline and terpendole C of nea3 (0.1 and 1.2 ppm), and lolitrem B, paxilline and terpendole C of SE (2.2, 0.2, and 1.1 ppm). The second experimental run was a study of liveweight gain and ryegrass staggers under low toxicity conditions from September to December 2020. The spring pastures provided optimal conditions for liveweight gain and the stocking rate was kept consistent at 44.9 hoggets/ha. Pre-grazing pasture mass was ca. 1600 kg DM/ha, ME was 12 MJ/kg DM and CP was 20% above 40–50 mm. The average daily gain for all mixtures was 271 g/day over the first 4 weeks, and 20 g/day for weeks 4–8. The mixture models fitted to the liveweight gain data identified the optimum endophyte formulation that maximised liveweight gain to be a monoculture of nea12 so that the responses were equal to the monoculture performance in the first and second 4 weeks of grazing (292 and 25 g/day). Ergovaline, the alkaloid linked to suppressed liveweight, was present in nea3 and SE pastures at 0.32 and 0.16 ppm. Staggers scoring at the onset of symptoms after 10 weeks of grazing revealed mild staggers (score <2) in SE that persisted until the experiment ended at 12 weeks. The model analysis showed that any mixture containing at least 60% nea3 and up to 40% nea12 and/or SE would result in no staggers (score 0). Alkaloids associated with staggers were in lower concentrations compared to the summer test: 0.8 ppm of epoxy-janthitrem I was present in nea12 pastures while lolitrem B, paxilline, and Terpendole C were present in SE pastures at 1, 0.1, and 0.3 ppm. The third experimental run tested the assumption that endophyte strain proportions in the diet were equal to the sown proportions. Plot fences within replicates were removed, 51–56 hoggets were allocated to each replicate (40.9–44.9 hoggets/ha), and sward height decrease was measured 15 times between 15 February and 16 March 2021. Herbage mass, ME, and CP values at the beginning of grazing were circa 1400 kg DM/ha, 11.5 MJ/kg DM, and 11%. Analysis of variance showed no differences (P>0.05) in sward height decrease between sown treatments, including nil, over the whole grazing period. Mixture models of each measurement date and the average of all dates only showed differences (P<0.05) between linear terms (monocultures) on day 2 and further analysis confirmed the sward height decrease of SE was greater than nea12 (P<0.05), but not nea3. Quadratic terms (binary mixtures) were not different on any date. The mixture model analysis for the whole period predicted that a mixture containing 39% nea3 and 61% SE would maximise sward height decline despite lolitrem B concentrations of SE pastures being sufficient to cause ryegrass staggers (1.4 ppm) and ergovaline levels in nea3 pastures of 0.37 ppm. The lack of deterrence to these alkaloids indicates that animals were unable to differentiate between endophyte strains. The fourth experimental run was a repeat liveweight gain test followed by a heat stress study from October to December 2021. Pasture conditions were similar to the previous liveweight gain test at the start of grazing (ca. 2400 kg DM/ha, 12 MJ ME/kg DM, 15% CP). The same number of hoggets were used as in the previous liveweight gain study, but a higher starting liveweight and greater pre- grazing pasture mass resulted in greater liveweight gain across mixtures in the first and second 4 weeks (397 and 67 g/day) compared to the previous spring. The model analysis predicted an optimum mixture containing 16% nea3, 65% nea12, and 20% SE would result in maximum liveweight gains of 402 and 85 g/day in the first and second 4 weeks of the test. Data loggers attached to controlled internal drug release (CIDR) devices recorded vaginal temperatures in selected mixtures (nea3, nea12, nea3–nea12, and nil) during the final 8 days of the 8-week grazing period. Average temperature for the three mixtures was 39.07°C compared to 38.96°C in the nil endophyte control. Hoggets grazing nea12 had the lowest temperature of the three mixtures (38.94°C; P<0.05). Consequently, the mixture model predicted the optimum mixture would only contain nea12. Ergovaline concentrations were 0.7 and 0.5 ppm in nea3 and SE. An endophyte diversity model that included ryegrass staggers and liveweight gain responses from experimental runs 1, 2, and 4 as multivariates, predicted a mixture containing 77% nea12 and 23% nea3 would give the best overall combination of responses. Although temperature was not included in the model, the vaginal temperature response of this optimal mixture was predicted to be 39.02°C, just 0.06°C higher than the nil endophyte control. This thesis showed that endophyte mixtures can improve the health of grazing sheep and provides the industry with a new option for mitigating health issues associated with endophyte without searching for novel strains. Such mixtures would be best suited to scenarios where insect pest pressure requires the use of endophyte strains that can increase the risk of ryegrass staggers and/or suppressed liveweight gain. The endophyte diversity modelling approach can predict responses to sown strain proportions beyond those included in the experiment, reducing the number of animal entries required for testing.Publication Open Access The effects of corporate governance on firm performance in the Association of Southeast Asian Nations (ASEAN): A comparative analysis : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2023) Fernando, ChavikaIncreasing dependence on corporate governance (CG) raises questions about whether corporate governance positively impacts firm performance and whether other variables can change the relationship between corporate governance and firm performance. We investigate the relationship between corporate governance features, including board effectiveness, block ownership, and national governance, on the firm performance of ASEAN-6 non-financial listed firms. We use the fundamental features of CG, such as board size, board independence, gender diversity, CEO duality, institution ownership, foreign ownership, insider ownership, government effectiveness, the rule of law and regulatory quality to analyse their impact on firm performance as measured by return on equity and Tobin’s Q. We use 265 ASEAN-6 non-financial listed firms (2385 firm-year observations) from 2010-2019 and uses OLS estimation and System-GMM estimator to control for the endogeneity issue. The results show that, except for CEO duality and insider ownership, that have no significant impact on performance, the other governance mechanisms significantly influence the performance of ASEAN-6 non-financial listed firms. Specifically, board independence, board gender diversity, governance effectiveness, the rule of law, and regulatory quality significantly positively influence ASEAN-6 non-financial listed firms. The results show a significant negative relationship between block ownership variables and the performance of ASEAN-6 non-financial listed firms. From a theoretical perspective, we emphasise how CG impacts firm performance and uncover the importance of CG systems in ASEAN-6 non-financial listed firms. From a practical perspective, we not only explain the optimal structure of CG that can enhance performance but also identify the moderating impact on board effectiveness, block ownership, national governance and the performance of ASEAN-6 non-financial listed firms.Publication Embargo Exploring the nutritional quality and bioactivity of different rice crackers and the influence of oyster/mussel protein fortification on potential health benefits : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2024) Sui, LiminIn New Zealand, a quarter of the population faces multiple chronic health conditions (Ministry of Health, 2023). Nutrient-dense foods containing essential constituents such as protein, fibre, vitamins, and minerals are pivotal for enhancing immunity, maintaining health, and preventing chronic diseases. Rice crackers, a popular modern convenience snack, are favoured for their ease of preparation, extended shelf-life, and appealing texture (Patil, Brennan, Mason, & Brennan, 2016). However, these crackers primarily utilise refined white rice flour obtained by removing the bran layer from brown rice, leading to low levels of protein, dietary fibre, and bioactive compounds, alongside high levels of rapidly digestible carbohydrates. This nutritional profile raises concerns about their potential high glycaemic index and potential implications for chronic health problems (Lafiandra, Riccardi, & Shewry, 2014). As a result, ongoing research is directed toward innovative reformulations of rice-based products to address these nutrient deficiencies. To comprehensively evaluate the quality of white rice crackers, this study examined and compared rice crackers produced from different rice varieties: white rice, brown rice, and black rice. Brown rice and black rice, being whole grain foods, retain their bran layer and offer higher protein, fibre content, and bioactive compounds such as polyphenols and anthocyanins, associated with reduced risks of hypercholesterolemia, cardiovascular diseases, and type 2 diabetes (Ali, Wani, Wani, & Masoodi, 2016; D. Zhu et al., 2023). The investigation encompassed assessments of physical characteristics, nutritional composition, in vitro starch digestion, and glycaemic response. Results showed that brown and black rice crackers exhibited significantly higher essential nutrient levels, including protein, ash, fat, dietary fibre, and resistant starch, compared to white rice crackers (p < 0.05). In contrast, white rice crackers exhibited a higher glycaemic response, characterised by a higher reduced sugar release and a greater content of rapidly digestible starch, along with a lower content of resistant starch during the in vitro starch digestion process. Regarding quality evaluation, white rice crackers exhibited the highest values for brightness (L* = 73.00) and yellowness (b* = 30.89), while black rice crackers demonstrated the lowest brightness (L* = 25.12) and the highest redness (a* = 6.31). Furthermore, black rice crackers displayed the greatest hardness (1022.46 g), whereas brown rice crackers showcased the highest fracturability (18.27 mm). To future examine phenolic compounds in rice crackers and establish links between in vitro digestion, antioxidative properties, and enzyme inhibition, this study extended its investigation to evaluate total phenolic content (TPC), total anthocyanin content (TAC), and antioxidant activities of white, brown, and black rice crackers. Additionally, the study evaluated changes in these parameters following simulated in vitro digestion. The identification of specific phenolic compounds within the rice crackers was carried out using high-performance liquid chromatography (HPLC). Moreover, the study explored the inhibitory effects of these phenolic compounds on the enzymatic activities of α-amylase and α-glucosidase. The findings revealed that black and brown rice crackers consistently displayed higher TPC, TAC, DPPH, and FRAP values compared to white rice crackers. In vitro digestion led to substantial TPC release, approximately 3.81-4.95 times higher, significantly increased DPPH values by 14.96-24.14 times, and elevated FRAP values by 4.25-4.90 times (p < 0.05). However, there was a reduction of TAC values following digestion. HPLC analysis indicated the presence of various phenolic compounds, including gallic acid, 2,5-dihydroxybenzoic acid, catechin, vanillic acid, rutin, p-coumaric acid, p-hydroxybenzoic acid, ferulic acid, and quercetin, in brown and black rice crackers, while white rice crackers primarily contained gallic acid and 2,5-dihydroxybenzoic acid. Furthermore, brown and black rice crackers exhibited stronger inhibitory effects on α-amylase and α-glucosidase compared to white rice crackers, with lower IC50 values. These findings highlight substantial variations among the different rice varieties, indicating the potential of brown and black rice for the production of rice crackers with lower glycaemic responses, higher nutritional value and the potential health benefits associated with enhanced phenolic composition and strong inhibitory effect on carbohydrate-digesting enzymes. Protein is essential for tissue growth, repair, and maintenance, as well as the production of enzymes, hormones, and antibodies, contributing to metabolic processes, bodily functions, and immune system function (Wu, Gao, Yu, & Wang, 2022). In response to the prevalent protein insufficiency in white rice crackers, a novel research avenue involves the formulation and advancement of protein-fortified rice crackers. Oysters (Crassostrea gigas) and mussels (Perna canaliculus) are valuable seafood resources consumed widely in New Zealand and contain higher levels of easily digestible protein and iron compared to traditional fish and red meats (Yaghubi et al., 2021). Oyster and mussel proteins are explored for functional foods and supplements, providing essential amino acids and potential health gains. Mussel proteins aid tissue engineering and drug delivery via biocompatibility and adhesion. Oyster proteins offer nutraceutical potential, aiding heart health, immunity, and antioxidants (Harnedy & FitzGerald, 2012; Ulagesan, Krishnan, Nam, & Choi, 2022). Fortifying white rice crackers with oyster and mussel proteins presents an opportunity to boost their nutritional content, lower glycaemic impact, and introduce potential bioactivity, including noteworthy antioxidant capacity and functional effects on inflammatory responses. This study evaluated the overall enhancement in the quality of crackers fortified with oyster and mussel powder at concentrations of 5%, 10%, and 20%, and assessed their impact on glycaemic response and protein bioaccessibility using in vitro starch and protein digestion assays. Additionally, antioxidative capacity was examined using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay and the Ferric Reducing Antioxidant Power (FRAP) assay. Results indicated that oyster and mussel powders inclusion led to a substantial reduction in starch content, resulting in a decrease of approximately 30% in glucose release and area under the curve (AUC) values during starch digestion compared to the control sample (white rice crackers). Furthermore, the addition of oyster and mussel powders significantly (p < 0.05) increased TPC, with values ranging from 16.74 mg GAE/100g sample to 104.90 mg GAE/100g sample in 20% oyster enriched sample and 77.65 mg GAE/100g sample in 20% mussel enriched sample. Moreover, the release of phenolic compounds during gastric and intestinal digestion was enhanced by nearly 150% and 50%, respectively, compared to the control sample. Antioxidant activity (DPPH and FRAP value) of enriched crackers also exhibited a significant increase corresponding to higher oyster and mussel powder incorporation. However, despite the increase in protein levels from 6.36% to 12.60%, protein digestibility declined from 77.64% to 63.05%. This reduction could be attributed to interactions between phenols and proteins in the samples, potentially affecting overall protein digestion. Furthermore, to evaluate protein availability and bioaccessibility, the research examined alterations in soluble protein content and amino acid composition after in vitro digestion and assessed the protein quality using the Digestible Indispensable Amino Acid Score (DIAAS). Additionally, the study evaluated bioactive peptides by measuring ACE inhibition and anti-inflammatory effects using LPS-stimulated RAW264.7 macrophages. Outcomes revealed heightened protein content and soluble protein content following digestion in oyster and mussel-enriched samples (oyster20, mussel20) compared to the control. Amino acid analysis showcased the increased release of essential and non-essential amino acids during digestion in enriched samples. DIAAS analysis underscored enhanced amino acid bioavailability in enriched rice crackers. Notably, molecular weight distribution exhibited the formation of smaller peptides during digestion. ACE inhibitory activity displayed significantly elevated values in enriched samples, suggesting potential cardiovascular benefits. Anti-inflammatory assessments demonstrated decreased NO production and pro-inflammatory cytokine levels in enriched samples compared to LPS-induced RAW 264.7 macrophages. Overall, this study underscores the significant variations among rice varieties and emphasizes the potential of brown and black rice for producing crackers with enhanced nutritional value, lower glycaemic responses, and health-promoting phenolic compounds. The exploration of marine-based protein fortification further offers a promising avenue for improving rice cracker quality and bioactivity. Through comprehensive analyses, this research contributes to a better understanding of the potential benefits and quality improvements that can be achieved through innovative approaches in rice cracker production.Publication Open Access Formulation of pasture seed mixtures with emphasis on the effect of nitrogen fertilisation : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2023) Myint, Thinzar SoeThe aim of this study was to determine the optimal proportions of pasture mixtures and amounts of seed and nitrogen fertiliser (N) to maximize yield and quality. Three monocultures and seven species mixtures, that differed widely in their proportions (0 to 1) of perennial ryegrass, white clover and plantain were sown at 1,000 and 2,000 viable seeds/m2 and with either 0 or 225 kg N/ha/year. Plots were drilled in 2.1 x 6 m plots on 31 March 2017 and measured for four years. The plots were grazed in common by sheep eight times annually (except the first defoliation after sowing when they were cut) and irrigated when required. Herbage accumulation and its proportions of sown species and weeds were determined at each harvest over four years (2017/2018–2020/2021); nutritive value (metabolisable energy (ME), crude protein (CP) and neutral detergent fibre (NDF)) over three years (2018/2019–2020/2021), and light interception and radiation use efficiency (RUE) over two years (2018/2019–2019/2020). To quantify the fractional intercepted radiation of pastures, an accurate method of measuring light interception was investigated. Fractional intercepted radiation was measured or predicted using a SunScan plant canopy analyser, GreenSeeker handheld sensor, rising plate meter (RPM), destructive harvests, and the combinations of SunScan and GreenSeeker, and SunScan and RPM. A hybrid method of SunScan and RPM (fractional light interception values ≤0.3 of SunScan were replaced with the predicted values using RPM) was chosen as an accurate method based on the parameters of extinction coefficient, critical LAI, R2 values, standard errors of regression. Response variables were quantified using diversity-interaction modelling to quantify effects of species ‘identity’ (monoculture performance or average monoculture performance of species in the mixtures) and ‘diversity’ (the excess of mixture performance over that expected from average performance of species in the mixtures). Seed density did not influence species identity and diversity effects on pasture yield and quality in any year. The annual total dry matter yields of ryegrass and plantain averaged over four years were 16.8 and 16.6 t DM/ha/year without N fertiliser, and 19.1 and 18.9 t DM/ha/year with N. White clover had the same production (14.9 t DM/ha/year) ± N. Mixtures produced diversity effects (additional dry matter yield). The highest extra dry matter yield (4.32 t DM/ha/year) among binary mixtures was obtained from the ryegrass-white clover mixture at the average of two N treatments. Three-species mixtures needed N to produce higher extra yield than binary mixtures. The extra benefit produced by the equal-proportional mixture of three species with N was 5.20 t DM/ha/year. The annual weed yield was lowest in perennial ryegrass (1.68 t DM/ha/year) at average N (average of 0 and 225 kg N/ha/year). The weed yield of ryegrass reduced from 2.16 at the –N level to 1.2 t DM/ha/year at the +N level. There was no N effect on weed yields of white clover and plantain. Mixtures reduced weed yield, and the highest amount of weed reduction was found in the even three-species mixtures (3.28 t/ha/year). Nutritive values were likely to be a function of identity effects and there was no effect of N. At average N, ME was higher in perennial ryegrass (11.0 MJ kg/DM) and white clover (11.0 MJ kg/DM) than in plantain (10.7 MJ kg/DM). CP was higher in white clover (25.7%) than plantain (20.5%) and perennial ryegrass (19.2%). Higher neutral detergent fibre (NDF) was found in perennial ryegrass (47.8%) than plantain (36.3%) and white clover (35.0%). After four years, an equi-proportional mixture of perennial ryegrass and white clover, based on seed count and equivalent to 12 kg PR and 7 kg WC (19 kg total coated seed)/ha at the low seed density (1000 seeds/m2), produced an optimal balance of increased total yield (20.6 t DM/ha/year), weed suppression (3% of total yield), ME (11 MJ/kg DM), CP (21.7%) and NDF (44%) at the –N level. The optimal mixture at the +N level was the three-species mixture with the proportion of 0.4 PR: 0.3 WC: 0.3 P equivalent to 9.60 kg PR, 4.20 kg WC, and 6.0 kg P (19.8 kg total coated seeds/ha) at the low seed density. It produced 23.0 t DM/ha/year with no weed, 10.8 MJ ME kg/DM, 19.5% CP, and 46.1% NDF. The equi-proportional seed mixture of perennial ryegrass and white clover changed to a mixture of 71% ryegrass, 26% white clover, and 3% weed as the actual proportions in the sward averaged over four years, yielding 20 t DM/ha/year. At the +N level, all three species mixtures, which changed to ryegrass-dominant mixtures in a four-year period, remained the highest-yielding mixtures, producing 20.8–22.4 t DM/ha/year. Differences in dry matter yield among mixtures were fully explained by the combined effect of light interception and radiation use efficiency (RUE). The optimal mixtures ±N that maximised intercepted light and RUE simultaneously were the same mixtures that produced maximum dry matter yield. They provided 188 and 170 MJ/m2/year more intercepted photosynthetically active radiation (PAR) and 0.23 g DM/MJ PAR more RUE. This study provided the two optimal seed mixtures for ±N level that maximised total dry matter yield with high quality and minimised weed yield under irrigated conditions. The dry matter yield differences among monocultures and mixtures were explained by the accumulated intercepted PAR and RUE. Moreover, there was an observation that accumulated intercepted PAR and RUE values changed depending on the methods used to measure light interception.Publication Embargo Livelihood goals, livelihood strategy selection and household welfare in rural China: A utility maximization perspective : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2023) Chen, ChenChina has the world’s second largest rural population and dramatic development in the rural economy. Rural households’ livelihoods have changed with economic transformation and face challenges from income equality, relative poverty, climate change and the continuing influence of COVID-19. In this situation, how to realize inclusive, sustainable and resilient livelihoods for rural residents is an urgent problem. Rural households’ livelihood decision largely results from unobserved heterogeneous goals and intentions and directly observable, different rural household characteristics. Previous studies explored the factors influencing rural households’ choice of a livelihood strategy and livelihood outcome but mainly focused on the impacts of external macro factors. However, livelihood goals are emphasized as the main base for rural households to allocate livelihood assets and are the critical orientations of livelihood strategy selection. To date, it is still poorly understood how rural households’ livelihood goals influence their livelihood strategy selection and whether different livelihood goals and their potential interaction effect with livelihood strategy selection influence rural household welfare. Using the panel data from the 2010-2018 China Family Panel Studies, this study explores the relationship between livelihood goals, livelihood strategy selection and rural household welfare. After deleting cases with missing values in the main and control variables, 23,967 rural cases are used for analysis in the study. To explore the linkages between livelihood goals and livelihood strategy selection, this study constructs measurements of three livelihood goals (the survival, security and self-respect goals) and then calculates an index for each goal. Livelihood strategies are divided into three groups (agricultural, non-agricultural, and diversification) based on rural households’ income sources. The multinomial logit model with fixed effects empirically estimates the relationship between livelihood goal indices and livelihood strategy selection. The random effects and the correlated random effects models are used to check the robustness. The two-step instrumental probit regression model is used to address the endogeneity problem. The results show that rural households with a survival goal are more likely to choose the diversification and agricultural strategies but less likely to select the non-agricultural strategy. In contrast, the non-agricultural strategy is the priority when rural households pursue security or self-respect maximization. To address potential endogeneity in the dynamic panel model, the generalized method of moments model is used to investigate the impact of livelihood goals and strategy selection on rural household welfare. The unconditional quantile regression with fixed effects model is employed to analyse the heterogeneous effects on household welfare. The results show that rural households with a higher livelihood goal do not obtain higher welfare. Rural households adopting the non-agricultural and diversification strategies have higher welfare than other strategies. The interaction effects show that rural households can get higher welfare if their livelihood goals and livelihood strategy selection match. The unconditional quantile regression result shows that households’ livelihood goals and livelihood strategy selection affect household welfare across different quantiles.Publication Open Access The biological control of the red clover casebearer in New Zealand : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2024) Faulkner, JoelBiocontrol of insect pests represents an important aspect of sustainable crop management that has potential to reduce the current reliance on chemical control measures. However, often the potential of all forms of biocontrol is undermined in contemporary productive systems and their resulting landscapes. In New Zealand seed three species of clover feeding moths of the Coleophora genus have seriously hindered red and white clover seed production during the last 100 years in New Zealand. From the 1920s until the 1960s two species of white clover casebearer (Coleophora mayrella and C. alcyonipennella) caused varying levels of seed yield reduction in white clover seed crops. During the 1960s efforts were made by government science agencies to establish parasitoid wasps of these species. This programme was highly successful, resulting in the total suppression of clover casebearer seed pests in New Zealand, until the arrival of the red clover casebearer (C. deauratella) during 2016. This pest quickly spread throughout the country’s clover growing regions, leading to yield reductions. This thesis explores the arthropod community of red clover seed crops under a main theme of ‘the biocontrol of the red clover casebearer’. The experiments employed are varied, although typically with a major aim being exploring the function of species within the red clover seed crop ecosystem. Three species of parasitoid wasp were able to successfully use C. deauratella as a host; Bracon variegator, Pteramalus puparum and Eupelmus (Macroneura) messene. The red clover casebearer was clearly undergoing remission as a pest and only two damaging populations of this pest could be located. The predominant parasitoid, B. variegator, had a field parasitism incidence of up to 75% on C. deauratella, but despite this these two populations of the pest persisted. Over the course of these experiments it was noted that a fungal growth was leading to mortality of C. deauratella larvae. From infected C. deauratella cases a potentially entomopathogenic strain of Fusarium pseudograminearum was isolated and identified through PCR sequencing. It is still uncertain how C. deauratella is being regulated in New Zealand red clover seed crops. The role of parasitoid wasps, a potential fungal pathogen and other unknown biocontrol agents is yet to be determined.Publication Open Access Understanding the growth and development of maize (Zea mays L.) : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2024) Mwayawa, AnnetteA main constraint to maize production in New Zealand is yield variability due to the low rainfall supply and also the erratic distribution of rain in the summer which consequently affects crop N uptake and utilization. The aim of this study was to understand the influence of N and water on canopy development, crop growth, phenological development and yield formation. Crops with different yield potentials were created using different levels of N and water availability. Two experiments were carried out, marking the growing season, Experiment 1 in 2015/16 and Experiment 2 in 2016/17. The two experiments were carried out at two different locations at Lincoln University, Canterbury, New Zealand. Experiment 1 was arranged in a split-plot design with four nitrogen (N) levels under different water regimes. The N levels were N1- nil, N2 -75 kg N/ha, N3 – 150 kg N/ha and N4 – 300 kg N/ha, and water levels at Irr1- Irr4 as defined by the accumulated potential soil moisture deficit as 443 (rainfed), 367, 301 and 226 mm, respectively. These created grain yields that were not different in all the treatments which averaged 12.4 t/ha and only varied in total dry matter (DM) accumulated. To create more distinct differences in grain yield, this experiment was repeated at another location with a higher dose of N. Experiment 2 used two levels of water and N in a randomised block design. The treatments were for N1 –nil N and N2 - 500 kg N/ha, rainfed and irrigation (accumulated potential soil moisture deficit at 536 and 296 mm respectively). In Experiment 1, grain yield was not different across the crops and average 12.4 t/ha. The total DM was 19.1 t/ha for the rainfed crop (Irr1) and averaged 22.4 t/ha for the irrigated crops. Grain yield and total DM as explained by intercepted photosynthetic radiation (iPAR) accumulated to 570 MJ/m2 for Irr1 and was higher at 1082 MJ/m2 for Irr2. All crops GAI reached a maximum at 3.7 m2/m2 at a rate of 0.01 m2/m2/°Cd in the duration of 677 °Cd which justified the similarities in grain yield. After the linear phase, the intercepted light in Irr1 immediately reached an asymptote as the leaves withered quickly due to water stress. The radiation use efficiency (RUE) was 2.21 g/MJ for N1 and 2.49 g/MJ for N4 and mainly because of the specific leaf N (SLN). The SLN was highest at 2.1 g N/m2 for the irrigated crop with N and lower at 1.66 g N/m2 without N. The contribution of SLN to yield was reflected in total DM. In Experiment 2, grain yield increased progressively from 0.98 t/ha under rainfed to 9.0 t/ha when irrigated and further to 16.3 t/ha with N. Total DM followed a similar response with rainfed accumulating only 4.10 t/ha and 14.3 t/ha under irrigation and doubling with N, creating total DM of 28.9 t/ha. The difference in total DM was explained by the differences in the total amount of iPAR. Under rainfed the total iPAR was 448 MJ/m2 and increased to 551 MJ/m2 with N, and when irrigated was 816 MJ/m2 and further increased to 1005 MJ/m2 with N. The rate and duration changed, indicating the capacity of the crop to capture light depended on the changes in pigment protein complexes, directly linked to development of the GAI as a process of leaf development and expansion. The maximum GAI was affected by the main effects of water and N where GAI increased from 2.14 to 3.49 m2/m2 with water and from 2.48 to 3.14 m2/m2 with N application. In the contribution of RUE to grain yield, SLN was a key factor connecting leaf N concentration to DM production. The SLN was 1.23 g N/m2 at 905 °Cd in all the crops, however, dissecting the canopy into cohorts, SLN varied. The main section of the canopy that supplied assimilates directly to ear development was the mid-cohort. This cohort was affected by both water and N, increasing SLN from 1.43 to 2.39 g N/m2 with water and from 1.46 to 2.37 g N/m2 with N. The changes at cohort levels were explained by GAI as parameter relating to canopy development and the allocation of N within the leaf, and light penetration through the hierarchical canopy arrangement. The amount of water used to produce the given yield in Experiment 2 depended on crop water use which was converted to WUE. Only the crop under irrigation and N was efficiently converting water to DM at 47 kg DM/mm of water. The WUE for the rainfed crops was 17.9 kg DM/mm and did not differ from the irrigated crop without N which had a WUE of 25.7 kg DM/ha/mm. Leaf and canopy photosynthesis has led to improvements in crop DM and yield through enhanced DM partitioning. In depth understanding into elements of SLN is essential for estimation of the SLN throughout the cropping season. The future of crop improvement strategies is dependent on maximising the leaf and canopy photosynthesis and converting DM accumulation into yield benefits.Publication Open Access The formulation of pasture seed mixture from a diverse pool of six forage species : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2024) Shampasivam, ArulmageswaranOptimising pasture yield and quality is needed to meet the global food demand. Pasture sward ecosystems that create beneficial diversity and productivity effects will contribute to this. This research used a multi-species pasture mixture experiment to identify optimal seed mixture species combinations under irrigated conditions. This reseach underpins the machanism of linking species mixed pasture properties to the beneficial diversity attributed to community responses. A large-scale diversity experiment used 69 mixtures from six pasture species to investigate the impact of different functional gropus. A simple mixture of combinations of 2 to 3 species from a grass and legume functional group were the key components. On average, mixture communities produced 16% higher biomass yield and contained 64% lower weed biomass than the average performance of the monoculture swards evaluated from 2018 to 2021. Pasture sward responses differed depending on the associated component species, and over time. The model identified several binary and ternary mixture combinations for improved biomass production, weed suppression, and maximising quality; crude protein (CP) and metablizable energy (ME). The highest contributions for herbage biomass were from binary and tertiary mixes of perennial ryegrass (PR), cocksfoot (C), white clover (WC) and red clover (RC), and plantain namely; PR*WC, PR*RC, C*RC, P*WC*RC, PR*WC*RC, PR*C*P and PR*RC*SC. Among those mixture communities, PR*WC and PR*RC maintained the greatest productivity over three years, giving an annual average herbage biomass yield of 13.6 and 15.2 t/ha, when no nitrogen fertilizer was applied. The mixture components in the ternary mixture (PR*WC*RC) produced an annual biomass yield of 15 t/ha. The mixture effect on weed suppression was strong and existed in several mixture communities even though increasing species richness continuously reduced unsown species biomass. Diversity contribution to the nutritional composition of herbage material was not beneficial, but the species' relative abundance in the mixture improved the herbage quality. The optimal mixture combination was PR*RC at the ratio of 50:50 sown seeds equivalent to 12.6 : 13.4 kg/ha (26 kg/ha) viable seed rate. This gave a mean herbage biomass yield per regrowth cycle of 1.98 t/ha (16 t/ha/yr), with a mean weed biomass of 0.13 t/ha/yr, 10.8 MJ ME/kg DM and 20.7% protein content. Further, the ternary mixture PR*WC*RC at the proportion of 45:11:44 equivalent of 11.3 : 0.8 : 11.8 kg/ha (24 kg/ha) had a mean yield per regrowth cycle of 1.97 t/ha (16 t/ha) DM, 0.8 t/ha weed yield, 10.8 MJ ME/kg DM and 20.8% protein. This ternary mixture combination at the ratio of 50:15:35 was equivalent to 12.6 : 1 : 9.4 kg/ha (23 kg/ha) and produced a mean yield of 1.95 t/ha (16 t DM/ha), 0.48 t DM/ha weed biomass, 10.1 MJ ME/ha and CP 20.2%. These higher productive mixtures were from legume and non-legume functional groups, which improved the pasture herbage biomass yield and quality compared with their monocultures. The sown species proportion of swards differed over time based on the functional species composition of the mixtures. Among the monoculture swards, grasses maintained a higher sown species proportion than legumes or plantain. On average, mixture communities suppressed the weeds, and the suppressive effect was increased with the increasing number of species in the mixture. PR*RC binary mixture maintained a higher sown botanical composition proportion over the 3 years than PR*WC. Modelled Relative Growth Rate Differences (RGRD), with the sown proportion, revealed that the equal proportion of the component species in the identified ternary mixture (PR:WC:RC) balanced the competitive growth and maintained the sown proportion until the 3rd year after establishment. This deviated from the optimal seed proportion that maximised the sward yield responses. Further, this experiment identified that the reason the sward yields differed was investigated in the third year and showed this was due to the quantity of fraction canopy light interception. Overall, species mixed pasture swards intercepted a higher fraction of canopy light (PAR). Average pre-grazing fraction light interception value of swards (2020/21) across the monocultures and two species mixture commmunities was modelled to the initial sown species component proportion. This quantified the diversity contribution of addtitonal fraction of canopy light interception. This was higher for PR*WC (0.47) than for PR*RC (0.10). The higher fraction of light interception contributed to the diversity attributed to the higher herbage biomass in PR*RC than PR*WC. The highest pre-grazing fraction of light interception and intercepted PAR energy was in summer/spring when temperature and available light levels were highest. However, the positive contribution from RC over WC appeared in autumn when the fraction of light interception from white clover may have been compromised by its shallower roots. In the third year, radiation use efficiency (RUE) of swards differed based on the functional species in the mixture community. Grasses had a lower RUE than clovers. There was a positive relationship between RUE and temperature for monocultures and binary mixtures, especially PR*WC and PR*RC. This research suggests farmers in irrigated conditions should sow a mixed pasture of 2-3 species that comprise a grass and a clover. The PR:RC mixture (50:50 = 12.6 : 13.4 Kg/ha) and PR*WC*RC in both proportion settings (45:11:44 or 50:15:35 = 11.3 : 0.8 : 11.8 kg/ha or 12.6 : 1.0 : 9.4 kg/ha) improved the pasture herbage biomass yield and quality over time compared with their monocultures. These mixtures provided diversity response that persisted and optimised biomass yield with minimal weed content and maintained the botanical composition which inturn optimised herbage quality.Publication Open Access Soil carbon, erosion, and the stormflow mobilisation of sediment and nutrients in a high-country landscape : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2023) Provost, Shyam MichaelThis study was carried out at Mt. Grand Station, a high-country pastoral farm in the South Island of New Zealand. The landscape (400 - 1300 m altitude) supports a gradient and mosaic of native and endemic woody shrub and tussock grassland vegetation amongst more productive exotic pasture, the latter established through aerial seed top-dressing and fertilisation. In recent years several areas of the farm at higher altitudes have been converted to conservation management following Tenure Review, placing additional pressure on the remaining farmland to maximise productivity, a situation similarly faced by many other high-country farms. However, further intensification of pasture grassland would compromise existing less productive native vegetation. This research project investigated soil conservation and loss, and freshwater quality, aiming to advance existing knowledge relating to environmental sustainability of the high-country. Topsoil carbon stocks were quantified beneath various vegetation communities at different altitudes of the station to gain a better understanding of soil carbon and its dynamics. Two watershed catchments were targeted for high-frequency sampling during rainfall events, to investigate the likely significance of water flow on the mobilisation of sediment and nutrients, and to help improve the accuracy of existing run-off estimates. In addition, soil erosion was estimated from differences in residual soil 137Cs activity, which was generated from historic Pacific nuclear testing, between two of the dominant types of vegetation cover. The results revealed the potential for native vegetation to enhance soil carbon sequestration. At low - middle altitudes (450 - 850 m) of the farm, topsoil beneath a woody shrub (kānuka) vegetation cover had significantly higher carbon concentrations and carbon stocks than areas of adjacent pasture. At higher elevations (>1000 m) topsoil beneath dominant snow tussocks had significantly higher carbon, nitrogen and phosphorus concentrations, with higher carbon stocks than adjacent inter-tussock spaces. The total loads of suspended solids, nitrogen and phosphorus exported to catchment waterways were significantly larger during high-flow events in comparison to baseflow conditions, and large proportions of the high-flow loads were mobilised on the rising hydrograph following high rainfall. These findings draw attention to the significance of taking account of the early stages of rainfall events to improve accuracy when quantifying high-country catchment loads. Data for 137Cs were variable but these provisional results indicate that soil beneath kānuka is likely to have undergone lower rates of erosion over the previous 65 years in comparison to areas of adjacent pasture. The combined findings of the three parts of the experimental work in this study are interpreted as being indicative of the present and future potential for South Island high-country farming environments to make a significant contribution towards climate change mitigation through vegetation management, resultant soil building and prevention of soil erosion. It is argued that closer attention to ecological restoration is likely to have mutual benefits for conservation, the farming system and the environment. Maintenance and better-informed management of the mosaic of native and exotic vegetation can play a more important role in longer-term sustainability of this high-country land management system than is currently appreciated.Publication Embargo Novel numerical methods for stochastic ordinary and partial differential equations in modelling complex systems : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2023) Tiwari, ParulMany natural and engineered systems are complex due to inherent uncertainty. Stochastic Differential Equations (SDEs) and Stochastic Partial Differential equations (SPDEs) provide a rigorous mathematical foundation for modelling these systems. Understanding the dynamics of complex systems under stochastic influences is crucial for predicting system behaviour. Numerical techniques often struggle to handle the complexity and stochastic nature of these equations. This research focuses on adapting and enhancing numerical methods to provide efficient and reliable solutions. The numerical accuracy and stability of these methods are assessed through simulations and examples. This study introduces the synthesis of stochastic spectral methods to solve complex systems by representing random variables as a sum of orthogonal polynomials. We applied Polynomial Chaos Expansion (PCE) methods to contaminant transport problem and to differential equations with random forcing term. We compute the Wick exponentials and show that Wick product coincides with the ordinary product for deterministic functions. We use Malliavin calculus to find the derivatives of a stochastic quantity and are visualised through graphs. We discuss numerical challenges associated with the PCE methods and their solution strategies. In all examples, our chosen method does better and allows us to lead the way in developing robust and efficient strategies to deal with randomness, ultimately enhancing the reliability and resilience of complex systems across various scientific and engineering domains.Publication Open Access Fragmentações, Violações, and Resistência: Weaving struggle and dreams in the Carajás corridor of the Brazilian Amazon : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2023) Figueiredo de Almeida Silva Campos, LeilaThe Estrada de Ferro Carajás is an 892 km railroad in Northern Brazil built to transports iron ore extracted by Vale S. A. from Serra dos Carajás in Pará state to ports in São Luís, Maranhão. Over the years, the connection between the railroad to other infrastructure and extractive projects has resulted on a logistics-export corridor – sometimes dubbed an “iron serpent” or “project of death” by local communities. Criss-crossing two Amazonian states, the Carajás corridor cuts through hundreds of territories of traditional peoples and communities, including Indigenous peoples, peasants, and quilombolas. Using document data and in-depth interviews interpreted through reflexive thematic analysis, this thesis aims to understand how the relationship between Vale, the state, and quilombolas contributes to the formation, expansion, and maintenance if the Carajás corridor. This thesis identifies contradictions at the heart of the iron serpent: instead of a connecting entity promoting progress, development, and cohesion, this research positions the railroad as a place of ‘Fragmentação’, ‘Violações’, and ‘Resistência’. Processes of Fragmentação (fragmentation) separate a contiguous quilombola territory in more easily manageable entities to favour the corridor. Violações (violations) encompass the cumulative harm caused by Vale and the Brazilian state in the enactment of resource regulations. Meanwhile, processes of Resistência (resistance) challenge the formation, expansion, and maintenance of the corridor, and are performed by quilombola communities and allies. This thesis brings important contributions to studies on development and resource extraction. Previous studies have tended to position mining companies as the most powerful actors in extractive areas, coercing the state to disregard regulations. My research points to a more nuanced scenario, in which the state itself enables, enacts, and relies on socioenvironmental harm - thus co-producing harm in the corridor alongside Vale. This thesis also introduces the concept of ‘silencing zones’ to reflect the physical, symbolic, and normative strategies enacted by Vale and the state to harm communities in the corridor. Finally, this study contributes to the growing literature on environmental justice by presenting community-led initiatives to resist extractive pursuits within and beyond the state, weaving new threads for state-making and territorial autonomy.Publication Embargo Development of tannins and methoxypyrazines in Pinot noir grapes and management of their extraction into wine : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2023) Wimalasiri, Pradeep M.Pinot noir is the most important red grape variety grown in New Zealand. Managing extraction of tannins and methoxypyrazines (MPs) in winemaking is crucial for producing high quality Pinot noir wine. This study aimed to investigate the development of tannins and MPs in Pinot noir grape skin, seed, and stem tissues during grape ripening and the management of their extraction into wine via common viticultural (leaf removal) and winemaking (whole bunch fermentation) practices. In addition, this study examined how tannin extractability of different grape tissues is influenced by initial tannin concentration and composition that were affected by leaf removal, rootstock, and clone. Analysis of tannin and MP development in skins, seeds, and stems of two Pinot noir clones (AM10/5 and UCD5) showed that on a per berry basis, the highest concentrations of tannins were observed in skins 2-3 weeks after véraison, in seeds at véraison, and in stems 4 weeks before véraison. Stem MPs increased toward véraison and decreased towards harvest, while skin MPs remained consistently low or undetectable levels. Two clones showed similar tannin and MP development trends, but AM10/5 exhibited significantly higher seed and stem tannin levels (per berry) and a lower 3-Isopropyl-2-methoxypyrazine (IPMP) and 3-Isobutyl-2-methoxypyrazine (IBMP) levels than UCD5 at harvest. Stem tannins had a comparable tannin concentration (1.09-1.34 mg/berry) to skin tannins (1.04-1.15 mg/berry) at harvest and a similar mean degree of polymerisation (mDP) to seed tannins but lower than skin tannins. Leaf removal, rootstock, and clone selection were used to manipulate initial berry composition to study the consequent impact on skin, seed, and stem tannin extractability. Leaf removal trial was conducted at 7 days (LR7), 30 days (LR30), and 60 days (LR60) after flowering, comparing to no leaf removal control (LRC). The Swartzman rootstock versus Pinot noir vines on their own roots, and the two clones, AM10/5 and UCD5, were included to assess the impact of rootstock and clone on berry composition. Leaf removal significantly increased anthocyanin concentration, stem, and seed tannin concentration, and mDP of skin tannins. Compared to the own roots, Schwarzman rootstock showed lower seed tannin centration but higher mDP of skin and seed tannins. UCD5 clone showed higher mDP of skin tannins than AM10/5 clone. For the first time, this study reported that stems showed the highest tannin extractability (64%-78%) compared to skins (37-52%) and seeds (26-34%). The consequent impact of different leaf removal timing on Pinot noir wines was also investigated. Results showed that leaf removal treatments are effective in increasing anthocyanin concentration in grapes and reducing MPs in stems. LR7 and LR30 notably enhanced colour density, polymeric pigments, tannin concentration, and reduced IBMP in resultant wines. In addition, LR7 showed significantly higher skin-originated tannin proportion in wines than LRC. These results indicate the extraction management of colour, tannin, and MPs in Pinot noir wines could be effectively achieved through different timing of leaf removal. Whole bunch fermentation, a commonly used Pinot noir winemaking practice, was conducted by comparing two clones (AM10/5 and UCD5) with three treatments, 100% destemmed (DS), 30% whole bunch (WB30), and 60% whole bunch (WB60). Higher proportion of whole bunch addition increased skin and stem originated tannin proportion and MP levels in wines. Clone selection is also important for managing tannin and MP extraction, with AM10/5 grapes producing wines having higher concentrations of tannin, polymeric pigments, and darker colour than UCD5 grapes. AM10/5 wines also had higher concentrations of phenylethyl alcohol, but lower concentrations of IBMP and ethyl esters, indicating more floral but less fruity and green notes in wines. These results indicate the clone and whole bunch, or grape stems could be a useful tool to manipulate tannin and MPs in wines. This research provides winemakers with valuable insights about tannin and MP distribution and relative concentrations in different grape tissues during berry development, as well as implications of leaf removal timing in the vineyard, proportion of whole bunch addition, and clone selection in winemaking to manage and manipulate tannin and MP extraction into wines. These research findings could help winemakers to produce high-quality Pinot noir wines through informed decisions regarding viticultural and winemaking practices.Publication Open Access Outdoor recreation experience of mainland Chinese students in New Zealand : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2023) Qin QinThis thesis investigates the changing role of the culture of origin as a constraint in Mainland Chinese students’ outdoor recreation experience in New Zealand. It aims to better understand their experience by further exploring the influencetial mechanism of one’s cultural background in a cross-cultural scenario. Different countries have different understandings of and ways of practice regarding outdoor recreation. Therefore, when differences arise in cross-cultural scenarios, scholars often turn to culture to seek explanations. In the pursuit of understanding how the culture of origin influences outdoor recreation in cross-cultural scenarios, two explanatory perspectives emerged in previous research. The first perspective regards the role of the culture of origin as the decisive constraint that contributes to the culturally coherent differences in one’s recreational involvement. In studies using this perspective, a set of cultural barriers including traditions and social norms were identified to comprehend what one needs to overcome to participate in cross-cultural scenarios. Meanwhile, the second perspective suggests that the role of culture is not this straightforward, as non-culturally coherent differences also emerge within the same cultural group. Studies from this perspective indicate that different situations, such as local support and social status, can counter the effect of cultural influence as a decisive barrier to outdoor participation. There appears to be a mechanism through which culture changes its role between decisive and situation-interfered influences in one’s practices. Yet, limited attention has been directed toward comprehending this mechanism in the research area. This research explores this mechanism to enhance our understanding of people's outdoor recreation experiences by applying the logic of Archer's analytic dualism concerning the role of culture in cultural encounters. This logic suggests that the role of culture changes based on whether it exerts ideational or practical influence. The ideational influence of culture provides decisive guidance for one’s subsequent actions. Still, once such actions are undertaken, these guidelines turn into practical influences that are affected by other factors, determining the extent of such practices. This logic provides a way to explore the change in the role of the culture of origin embedded in the coexistence of homogeneity and heterogeneity, furthering our understanding of cultural influences. To narrow the scope of this research inquiry to a feasible scale, the outdoor recreation experience of Mainland Chinese students (MCS) in New Zealand was selected. New Zealand and China developed different contexts for understanding and practising outdoor recreation. These differences make outdoor recreation in New Zealand a potential subject for studying the role of the culture of origin. Meanwhile, MCS hold a significant position in the local economy and labour market. A better understanding of how the cultural background affects their outdoor recreation would benefit interested parties aiming to improve the overseas experience of Chinese students or boost revenue in the recreation sectors. Therefore, by focusing on the outdoor recreation experiences of MCS, this research employs in-depth interviews to collect data on cultural influences and their engagement with outdoor recreation. The aim is to establish a connection between the role of culture and their involvement in outdoor recreation. The results indicate that the outdoor experiences of MCS exhibit culturally coherent interpretations of outdoor recreation and situational diversity in practising it. Influenced by their culture of origin, MCS interpret the local way of outdoor recreation as the "Kiwi way," differing from the Chinese way in three aspects: value orientation, way of practice, and the sense of outdoor settings. These cultural differences generate three types of tensions that MCS need to overcome for their participation: 1) dealing with differences in values, where MCS need to maintain their original values while engaging in outdoor activities; 2) addressing variations in the way of practice, requiring them to acquire new knowledge to participate in local outdoor activities; 3) coping with differences in the perception of outdoor environments, necessitating finding adaptable approaches. Moreover, through a comparison of MCS's actual practices, the research results demonstrate that the shared interpretations at the ideational level do not decisively constrain MCS's practices. Their specific activities depend on whether existing resources can alleviate or exacerbate the cultural tensions affecting their engagement in outdoor activities, leading to diversity at the individual practice level. These findings indicate that the changes in the role of culture depend on whether it involves interpreting or practising outdoor recreation. Based on Archer's theoretical logic, it suggests that the influences of culture can be understood as a dualistic constraint role, involving a guiding constraint at the ideational level and a causal constraint at the practical level. At the ideational level, the role of culture involves distinguishing differences and, based on the attributes of these differences, generating diverse practice-oriented constraints. However, at the practical level, the execution of guiding constraints is influenced by environmental factors, leading the role of culture to transform into a coexisting causal constraint with other societal factors. This research investigates how culture influences outdoor recreation, specifically among MCS in New Zealand. Using Archer's analytic dualism, the study reveals a new way to look into cultural influence as a constraint. This enriches theoretical discussions on the interplay between culture and recreational behaviour, paving the way for further exploration in cross-cultural studies. Practically, the findings have implications for enhancing the overseas experience of Chinese students and optimizing the recreation sector.Publication Open Access Targeted supplementation of sheep to control gastrointestinal nematode populations : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2021) Tambunan, Reny DeboraOne potential approach to control GIN parasite and to improve ewe’s immunity during the periparturient period is nutritional supplementation. However, there is limited data regarding the long-term effects of nutritional supplementation on grazing periparturient ewes that have a naturally acquired GIN infection where two or more parasite species are infecting ewes and lambs. This thesis describes a series of experiments designed to analyse the effects of targeted supplementation to twin-bearing ewes on pasture and determine whether the supplementation can provide long-term benefits to their lambs after weaning. Three experiments were carried out at LincolnSheep, Canterbury, New Zealand, over three sequential years (August 2015-April 2018). Before lambing, twin-bearing crossbred ewes (n=140 in 2015, n=128 in 2016, and n=160 in 2017) were randomly allocated to one of two treatments, viz. supplemented and unsupplemented. Ewes on the supplemented paddocks were introduced to an advantage feeder with approximately 50 g/head/d of sheep pellets starting three weeks before lambing and then increased to 0.5 kg/head/d during the first four weeks of lactation. All sheep were allowed to graze on perennial ryegrass/white clover pasture. After weaning, all lambs were drenched and then exposed to a targeted selective treatment (TST) regime while grazing the areas in which ewes had been or not supplemented to determine if any epidemiological benefit of supplementation existed. Weaned lambs (n=240 in 2015, n=210 in 2016, and n=180 in 2017) originating from each treatment were stratified across the treatment area. For each lamb replicate, growth potential was assessed using sentinel lambs that were treated with a long-acting anthelmintic. The remaining lambs in each replicate were subjected to a TST regime where the need for anthelmintic was based on animals achieving acceptable growth rates. Within each farmlet, lambs were rotationally grazed for the remainder of the grazing season, with lambs grazing freshly grown forages, followed by the ewes. In the first study (year 2015 and 2016, Chapter 4), the ewes were undrenched, consequently allowing the development of pre-existing parasite infections. The results in both years showed that supplementation of ewes did not affect ewe LW and BCS or the weight of lamb weaned per ewe (P>0.05 for all). However, supplementation was successful in reducing ewe's FEC to 50% reduction during lactation periods. However, in 2015, the effect was transient, as FEC of supplemented ewes increased and was not different at week 12 of lactation. In 2015, climatic conditions were not favourable for pasture growth, resulting in low pasture availability, with mean pasture mass declining to less than 700 kg DM/ha in all paddocks, and may have resulted in unintentional nutritional stress and increased the concentration of eggs in the faeces. In the 2016 trial, the reduction in ewe FEC was more consistent throughout lactation, indicating a longer-term benefit to the ewe as this extended beyond the pre-patent period of any larvae that would have been ingested after supplementation. The declining number of eggs observed in 2016 at late pregnancy until the 8th week of lactation agrees with the increase of IgA at the same time, which may be due to an improvement in immunity. However, unexpectedly, the T. colubriformis-specific L3 IgA absorbances in supplemented ewes were significantly lower than unsupplemented ewes throughout the experiment in 2016. The reasons for this are unclear but may reflect differences in the larval challenge. Moreover, supplementation also did not have any significant effects on serum proteins, serum urea, and serum phosphorus of the ewes. Before weaning, there was no difference between the mean LW of lambs reared by supplemented or unsupplemented ewes in 2015 (P=0.27), while in 2016, lambs reared by unsupplemented ewes were significantly heavier than those raised by supplemented ewes (P=0.02). After weaning, there were no differences in the performance of lambs between the two treatments in all years (P>0.05 for all), except for a higher number of drenches administered per lamb (P=0.04) of TST lambs in areas where ewes had not been supplemented in 2015. These findings allowed the conclusion that supplementation of ewes during the first four weeks of lactation had no effect on ewe performance but was successful in temporarily reducing faecal eggs by 50%, presumably reflecting better maintenance of immune function through higher nutrient supply, even though this was not detected in parasite specific-immunoglobulin. However, the reduction in parasite contamination was insufficient to provide a measurable and consistent epidemiological benefit to the grazing lambs after weaning. The second trial (year 2017, Chapter 5) aimed to evaluate the effect of supplementation to reduce the establishment of larvae following short-acting drench pre-lambing. The results showed the benefits of ewe supplementation when the existing population is removed, such as the difference in FEC, the greater serum albumin concentrations, and the consistently higher milk protein contents. Similar to the previous studies, supplementation of ewes in 2017 also did not affect ewe LW and BCS or the weight of lamb weaned per ewe (P>0.05 for all). The reduction in FEC following supplementation was not accompanied by the increase in T. colubriformis-specific L3 IgA absorbance; the values decreased over time (P<0.001), possibly indicating that the immune response to ingested larvae was unaffected. The level of serum IgG of supplemented ewes was similar to unsupplemented ewes (P=0.83). However, there was treatment and time interaction (P=0.001) on serum IgG concentrations, reflecting high IgG responses at week 4 of lactation, which then decreased with time in all groups; however, the decline was higher in unsupplemented ewes than their supplemented counterparts at week 8 of lactation. Similarly, supplementation on ewes did not affect milk production and composition (P>0.05 for all). There were extremely weak associations between milk production and lamb growth rate during the lactation period, except for the unsupplemented group in week 4 (P<0.001). Moreover, pastures grazed by supplemented ewes tended to have threefold lower pasture larval than unsupplemented pastures, which can be seen from the tendency of fewer L4 in the tracer lambs grazed areas where ewes had been supplemented. This lower pasture contamination, therefore, resulted in a slight difference in the FEC profile of lambs, effectively delaying the increase in FEC in the lambs throughout the summer. FEC of lambs after weaning increased significantly throughout the grazing season for both groups, although tended to be delayed in TST lambs grazing the areas where ewes had been supplemented, which reached a peak of 65 days after weaning compared with 51 days after weaning in TST lambs grazed unsupplemented areas. The difference in the growth rate of the sentinel lambs and TST lambs clearly shows that there was a substantial larval challenge, with the benefits of supplementation possibly masked due to the TST regime, even though there was no difference in the number of anthelmintic treatments administered. The reduction in the FEC of lactating ewes drenched pre-lambing was not sufficient to result in an epidemiological advantage to their lamb, as shown by results on FEC, worm burden, and growth performance from birth to reach slaughter weight while grazing pastures that were infected naturally by GIN parasites. The third trial (year 2017, in conjunction with the second trial) indicated that supplementation and treatment with moxidectin at the end of supplementation (week four of lactation) appeared to assist the ability of the ewes to limit egg excretion. FEC of supplemented-undrenched and unsupplemented-undrenched groups was significantly increased throughout the lactation period, except at week eight of lactation, where FEC of all groups decreased. Surprisingly, the FEC of supplemented-undrenched ewes rapidly elevated to 1,400 epg at week 12 of lactation, compared to 650 epg in unsupplemented-undrenched ewes. The reason for the speedy elevation of FEC in the first group was probably associated with a decrease in ewes’ immunity, as indicated by lower T. colubriformis-specific L3 IgA and T. colubriformis-specific L3 IgG levels, even though the effect on these values was not significant. Additionally, both drenced and undrenched groups had significantly lower serum albumin concentrations, indicating there was damage to the mucosa of the GI tract of ewes by GIN parasites, which resulted in body protein loss. As expected, long-acting injections of moxidectin at the end of the supplementation period resulted in a consistent trend of higher LW than undrenched groups due to lower parasitic load. Similar to the results from previous trials, supplementation of ewes and administration of long-acting anthelmintic at the end of the supplementation period did not provide clear benefits to their lambs before weaning. However, lambs raised by supplemented and drenched ewes tended to have higher LW, LWG, and weight of lamb weaned per ewe (WLWE) than those raised by unsupplemented groups. It was concluded from the series of experiments from this study that supplementation of ewes during the first four weeks of lactation, whether undrenched, drenched pre-lambing or drenched at the end of the supplementation period, did not affect ewe performance. However, it was temporarily successful in reducing faecal egg counts, presumably reflecting better maintenance of immune function through higher nutrient supply, although this was not detected in parasite-specific immunoglobulins. However, the reduction in parasite contamination was insufficient to provide a measurable and consistent epidemiological benefit to the grazing lambs that may assist with parasite control. If the supplementation of ewes during this time is to be employed as a means of reducing the need for anthelmintics to control parasitism, then the refinement, including an understanding of the specific amino acid requirement and any interaction with BCS, needs to be investigated.Publication Restricted Working capital management practices of small and medium-sized businesses in New Zealand : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2023) Lim, Yew HockSmall and medium-sized businesses (SMEs) contribute significantly to a country’s economic growth. As the business environment changes constantly; SMEs need support and guidance on how to address working capital management (WCM) issues. Such knowledge will enable them to implement WCM effectively, increase their competitive advantage, and ensure their ultimate survival. Knowledge of WCM in SMEs, including a greater understanding of the WCM practices that SMEs actually employ and their motivations for, and barriers to, WCM, is needed to help SMEs adapt to ever-changing conditions. WCM is central to a business’s profitability, growth, and survival. However, only some SMEs manage working capital (WC) well. Since the early 1980s, poor WCM has been identified as the primary cause of SMEs’ failure, with approximately half of all SMEs failing within the first five years. WCM involves the management of four key business components: cash, inventory, accounts receivable, and accounts payable. The goal of WCM is to achieve an optimal WC level, where the business’s current assets are sufficient to meet its obligations or current liabilities. While excessive WC incurs opportunity costs, insufficient WC increases the risk that a business cannot meet its short-term obligations. Despite its critical role in business success, scholarly literature has shown that, due to SMEs’ unique characteristics, many SMEs lack identifiable, systematic, and/or effective WCM procedures. WCM for SMEs is often overlooked in previous studies. Given the importance of WCM, this research addresses omissions in the WCM literature by examining the WCM practices of New Zealand SMEs. More specifically, it identifies SMEs’ WCM practices, their motivators for, and barriers to, adopting (effective) WCM practices, and actions that SMEs could take to modify their WCM practices to address potential WCM issues. It contributes through the collection of qualitative data to provide deeper insights. The findings draw on questionnaire responses from 164 SMEs from 15 industries, and 11 interviews with SMEs, located in the Auckland and Canterbury regions. The research found that many of the participating SMEs lacked an understanding of the importance of WCM and had limited knowledge of WCM practices or procedures that could be taken to manage WC more effectively. While some of the SMEs lacked any identifiable systematic processes, others adopted informal, ad-hoc WCM practices and/or only basic WCM techniques. The identified causes are related to barriers such as resource constraints, having a simple business model with low sales volumes, and a lack of knowledge and expertise in financial management. Consequently, rather than spending time to identify and develop systematic WCM practices, most of the SME management teams of this research focused on revenue-generating activities or activities perceived to generate a higher return. This may provide insight into other aspects of WCM outside the scope of this research, including why SMEs are less efficient in managing WC, and why they are more vulnerable to financial crises. The research identifies WCM actions, from WCM planning to daily operations monitoring, that, when implemented will assist SMEs in addressing potential WCM issues and subsequently, improving the effectiveness of their WCM. Given their significant role in local economies, this research’s findings have implications that extend far beyond individual businesses.Publication Open Access Copper contamination of fruit orchards soils: Biotic Impacts : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2024) Jeon, DasomExtensive use of fungicide copper (Cu) has a more recent history in New Zealand than in many other parts of the world where long-lasting Cu accumulation in soil has become a major environmental issue. However, Cu is extensively applied in New Zealand orchards, including organic orchards, with some awareness that the consequences of its current and future accumulation on soil health are relatively unknown and under-explored. This doctoral study aimed to investigate the impact on soil functional processes and plants of soil copper contamination associated with cherry, apple and kiwifruit orchards, vineyards and hops. The research encompassed experimental work on soil respiration, plant growth, earthworms, soil microbial activity, root growth and plant cell culture through a combination of fieldwork, glasshouse and laboratory studies. The central hypothesis of this study was that accumulation and persistence of Cu in orchard soils are likely to adversely affect critical aspects of soil biology and functionality. Following a detailed survey of accumulation and spatial variability of soil Cu across different fruit orchards up to 73 years old, practical investigations involved soil respirometry, analysis of microbial carbon (C) and nitrogen (N), and rhizobox and pot plant growth assays, as much as possible using in-situ field measurements or soils collected from orchards and transferred to the glasshouse and laboratory. In an earthworm behavioural and Cu-uptake study, a native anecic species was exposed to soils from the same orchard with differing histories of fungicide use. Three hop varieties (Cascade, Nelson Sauvin and Riwaka) were used for plant growth trials on the same soils. Plant stress responses were investigated using callus incubation trials on cell lines isolated from three apple cultivars (Braeburn, Fuji, and Cripps Pink) grown on a Cu-spiked growth medium. All practical work was carried out from 2020 to 2023. The results showed that soil Cu concentrations in orchards frequently and substantially exceeded most published threshold limits. Whilst soil Cu concentrations could largely be explained by modelling the age of the orchards, fruit type and soil organic matter (SOM) also had a large role in Cu retention. When SOM and existing Cu concentrations were amended in four soils from different blocks of the same cherry orchard, the ecotoxicological impact differed, and it was found that SOM could be a more powerful determinant than Cu of the biotic responses. Earthworm survivorship and growth in these soils were significantly determined by both SOM and Cu; earthworms exhibited a preference for soils with concentrations of Cu elevated substantially above background (to 160 mg kg-1), where SOM content was also high. A variable impact of Cu contamination on soil microbial activity was recorded across soils with elevated Cu concentrations (from 195 to 405 mg kg-1). Only a weak correlation was found between soil total Cu concentration and soil respiration when data for all orchards were combined, but the impact of Cu was more evident when each type of fruit orchard was evaluated separately. Microbial biomass carbon (MBC) and nitrogen (MBN) analyses similarly provided only a weak or negligible correlation with soil Cu, but artificially spiked soils provided a more consistent response to elevated Cu. Confounding factors appeared to relate to vegetation cover within and between rows and the amount of cultivation of the soils used to manage weeds (and bronze beetle in apples). The influence of management variables requires a more detailed study. Root growth in hop varieties was negatively affected at Cu concentrations exceeding 263 mg kg-1, whilst best growth was observed at 160 mg kg-1 in conjunction with abundant SOM. In callus culture assays, Cu negatively impacted the growth of Braeburn and Fuji apple varieties at concentrations exceeding 15 mg kg-1, while Cripps Pink had higher Cu tolerance. The value of using biological and ecological indices to assess the impacts of agricultural chemicals and contaminated soils is discussed. The findings have identified detrimental biotic impacts of soil Cu concentrations that already exist in orchards, which are probably reflected in a negative influence on soil health. Transfer rates of Cu to fruits through uptake from soil or from foliar absorption are negligible, but stress responses in plants and soil fauna and impacts on soil biology and ecology have been detected. Currently, the deleterious impact of elevated Cu is largely mitigated by SOM content in combination with the avoidance of low pH in orchard soils. Whilst this implies there is a potential avenue for amelioration of toxicity and maintenance or restoration of soil health, residual fungicide Cu will not significantly dissipate and is likely to continue to accumulate. Sustainable soil health management in New Zealand's orchards is not viable with longer-term continued usage of Cu fungicides.Publication Open Access Using accounting information systems to benefit micro businesses : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2024) Benbow, PamelaNinety percent of all businesses in New Zealand are micro businesses, defined as having zero to five employees. This sector is critical to New Zealand’s economy. Micro businesses create opportunities for new entrepreneurial talents, provide employment and offer consumers choice and variety including specialist goods and services. Central to all businesses is the need for information, managed by the accounting information system (AIS). The AIS supports decision-making, achieving business objectives and managing limited resources. Prior studies and government reports call for further research of micro businesses so that this sector of the economy can be strengthened. This research addresses this call by exploring the benefits of using AIS in micro businesses using multiple methods, including desk-based research, semi-structured interviews with professional accountants, a survey of micro business and finally semi-structured interviews of micro business owners. Findings show that a variety of tools are used, ranging from manual record keeping, to spreadsheets, to computerised AIS, and including a mixture of these tools. The majority of microbusinesses use computerised AIS tools, of which two software providers dominate. Some accounting firms specialise their practice either through industry or choice of AIS. Other accountants accommodate any AIS approach, focusing on the individual micro business needs. AIS use by micro businesses is primarily focused on monitoring cash flow, sales and income activities and compliance reporting (GST and income tax). The greatest utilisation of computerised AIS and add-on tools are observed with these activities. Micro businesses could utilise other features more, especially reporting, as a basis for decision-making. The decision to adopt computerised AIS includes factors affecting the individual business owner (generation, individual knowledge and skill and personal attitude to technology), internal business factors (financial costs, time costs and the business purpose and future) and external business factors (supply chain, regulatory bodies and supporting services). The benefits of using computerised AIS include connectivity, autofill, automated calculations and drilldown. Connectivity through cloud technology provides accessibility to a single version of the data between users regardless of location. Autofill populates data entry screens with information previously captured, reducing the need for typing. Automated calculations automatically completes basic arithmetic in the creation of invoices, supplier bills and reports. Finally, drilldown enables direct access to supporting detail for information provided on screen. These benefits may not be available in older versions of computerised AIS, or versions that only include a subset of the features. This research increases the understanding of factors impacting micro businesses in their decision to implement computerised AIS, and the benefits from doing so. The findings support accountants, government agencies and AIS software developers to devise strategies to support micro businesses. Findings from this research are applicable to micro businesses throughout New Zealand and more globally and will benefit other small businesses outside of the micro definition, both locally and globally.Publication Embargo Artificial Intelligence (AI) and machine learning-driven automation of complex, neurobiological model reduction: A framework based on deep learning, ensemble learning, and sensitivity analysis methodologies : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy in Computer Science at Lincoln University(Lincoln University, 2023) Kumara Pathirannahalage, Samantha Dileshani Kumara PathiranaManaging complexity is a key challenge in systems biology modelling. While detailed models can provide valuable insights into specific biological processes, they can become computationally intensive and challenging to interpret. Conversely, overly simplistic models may lack accuracy and fail to capture essential aspects of the system's behaviour. Hence, this study focuses on reducing the complexity of the models in systems biology while enhancing accuracy, efficiency, and interpretability. This study uses deep learning (DL), a sub field of machine learning (ML) and artificial intelligence (AI), along with sensitivity analysis using partial rank correlation coefficient (PRCC), and extended Fourier amplitude sensitivity test (eFAST) methods to identify significant system behaviour. DL models can analyse and predict system behaviour using large datasets consisting of biological measurements. They can also handle various omics data and integrate them into comprehensive systems biology models. Key objectives of the study include reducing the complexity of computational models using DL methods, identifying significant subprocesses to reduce pathway diagrams, improving the interpretability of the reduced models using sensitivity analysis, implementing models with minimum knowledge in the parameter space, introducing a framework to automate the complexity reduction process using sensitivity analysis and DL, improving model performance with ensemble learning and automated hyperparameter tuning, and testing the reproducibility of the reduced models using simulations. The significance and contribution of the study lie in its automated approach to developing an interpretable meta-model using AI/ML/DL techniques and reducing complexity while maintaining model accuracy. The study tests neurobiology models and uses sensitivity analysis and DL for complexity reduction. The thesis provides reduced pathway diagrams for each of the models used for testing. The study offers a framework to automate the implementation of meta-models and provides insights into input-output relationships and key processes in biological systems. The methodological approach involves using DL/ML/AI methods, ensemble methods, and dimensionality reduction to reduce complexity in VCell models. The framework reads MATLAB files from VCell, identifies parameters and outputs, performs parameter perturbations and simulations, conducts sensitivity analysis, identifies significant reactions, and trains and validates machine learning models based on the results. The thesis builds on previous efforts to develop more interpretable and reliable computational models that can provide meaningful insights into complex biological systems.Publication Embargo Characterisation of storage proteins and their digesta from oat bran, wheat bran and barley, and identification of bioactive peptides derived from oat bran : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2024) Gong, XiAims: The aims of this thesis were to characterise storage proteins extracted from oat bran, wheat bran and barley and the digesta produced from them in an in vitro digestion model, followed by investigating the antioxidant and angiotensin-converting enzyme (ACE) inhibitory activity of the digesta, and finally to identify novel peptides with antioxidant and ACE inhibitory activity in oat bran intestinal digesta. Method: Storage protein concentrates of oat bran, wheat bran and barley were obtained by alkaline extraction and isoelectric precipitation. In vitro digestion model was adapted to generate their digesta protein where their protein/peptide profiles were analysed using sodium dodecyl-sulfate- polyacrylamide gel electrophoresis (SDS-PAGE). The digestibility, degree of hydrolysis and the release of the free amino acids (FAAs) were determined on these digesta. Antioxidant assays including 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS), total phenolic content (TPC), ferric ion reducing antioxidant power (FRAP) assay and oxygen radical absorbance capacity (ORAC) assay were conducted to evaluate the overall antioxidant activity of the crude protein and digesta. The samples were also assessed for ACE inhibitory activity.The storage proteins in oat bran were selected for further analysis by two-dimensional electrophoresis (2-D electrophoresis). The small-intestinal digesta of oat bran protein with the molecular weight (MW) of < 3 kDa was purified by anion-exchange chromatography and the selected fractions were subjected to mass spectrometry (MS) to determine the peptide sequences. Findings: The major storage protein in oat bran protein concentrate were globulin, albumin and avenins, while prolamin, gliadin and albumin predominated in wheat bran protein concentrate, and hordein, albumin and globulin in the barley protein concentrate. These proteins were mostly degraded into polypeptides and smaller protein fractions by the end of intestinal digestion. This process resulted in significantly higher overall antioxidant activity and ACE inhibitory power in digesta. Oat gastric and intestinal digesta showed the highest ABTS scavenging activity of 2 Trolox equivalent mM/g sample. Oat digesta also showed a higher TPC value (200 gallic acid equivalent mg/g sample) compared to wheat bran and barley digesta (150 gallic acid equivalent mg/g sample and 40 gallic acid equivalent mg/g sample). The ACE inhibitory power of all three intestinal digesta was greater than 80%. Because oat digesta showed the highest overall antioxidat and ACE inhibitory activity, oat intestinal digesta was selected for separation by anion exchange chromatography. In all elutes, the highest ABTS scavenging activity reached to 275 Trolox equivalent µM/g sample and the highest ORAC scavenging activity was 170 Trolox equivalent µM/g sample. Four antioxidant anionic fractions and two ACE inhibitory fractions along with the digesta < 3 kDa were subjected to reverse-phase high performance liquid chromatography-tandem mass spectrometry (R-HPLC-MS/MS). Peptides with antioxidant and ACE inhibitory potentials were identified. Conclusion: These investigations have shown that storage proteins derived from oat bran, wheat bran and wholegrain barley are ideal sources to produce bioactive digesta after digestion. The peptides identified in oat bran intestinal digesta displays bioactive nature as an intermediate ACE inhibitor, with the potential of future applications in improving human health.