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The Department of Wine, Food and Molecular Biosciences covers course areas including animal and plant science, biochemistry, food science, horticulture, microbiology, sensory science, viticulture and wine science.
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Item Open Access Survey of methods used for the enumeration of coliform micro-organisms in New Zealand(Lincoln College, 1974-08) Noonan, M. J.Survey of methods used for the enumeration of coliform micro-organisms in New Zealand, this survey was undertaken at the request of the New Zealand Microbiological Society.Item Open Access On electrostatic interactions of adenosine triphosphate–insulin-degrading enzyme revealed by quantum mechanics/molecular mechanics and molecular dynamics(Higher Education Press, 2024-12) Somin, S; Kulasiri, Don; Samarasinghe, SandhyaThe insulin-degrading enzyme (IDE) plays a significant role in the degradation of the amyloid beta (Aβ), a peptide found in the brain regions of the patients with early Alzheimer’s disease. Adenosine triphosphate (ATP) allosterically regulates the Aβ-degrading activity of IDE. The present study investigates the electrostatic interactions between ATP-IDE at the allosteric site of IDE, including thermostabilities/flexibilities of IDE residues, which have not yet been explored systematically. This study applies the quantum mechanics/molecular mechanics (QM/MM) to the proposed computational model for exploring electrostatic interactions between ATP and IDE. Molecular dynamic (MD) simulations are performed at different temperatures for identifying flexible and thermostable residues of IDE. The proposed computational model predicts QM/MM energy-minimised structures providing the IDE residues (Lys530 and Asp385) with high binding affinities. Considering root mean square fluctuation values during the MD simulations at 300.00 K including heat-shock temperatures (321.15 K and 315.15 K) indicates that Lys530 and Asp385 are also the thermostable residues of IDE, whereas Ser576 and Lys858 have high flexibilities with compromised thermostabilities. The present study sheds light on the phenomenon of biological recognition and interactions at the ATP-binding domain, which may have important implications for pharmacological drug design. The proposed computational model may facilitate the development of allosteric IDE activators/inhibitors, which mimic ATP interactions.Item Open Access A machine learning pipeline for predicting Pinot Noir wine quality from viticulture data: Development and implementation(MDPI AG, 2024-10) Kulasiri, Don; Somin, Sarawoot; Kumara Pathirannahalage, SamanthaThe quality of wine depends upon the quality of the grapes, which, in turn, are affected by different viticulture aspects and the climate during the grape-growing season. Obtaining wine professionals’ judgments of the intrinsic qualities of selected wine products is a time-consuming task. It is also expensive. Instead of waiting for the wine to be produced, it is better to have an idea of the quality before harvesting, so that wine growers and wine manufacturers can use high-quality grapes. The main aim of the present study was to investigate the use of machine learning aspects in predicting Pinot Noir wine quality and to develop a pipeline which represents the major steps from vineyards to wine quality indices. This study is specifically related to Pinot Noir wines based on experiments conducted in vineyards and grapes produced from those vineyards. Climate factors and other wine production factors affect the wine quality, but our emphasis was to relate viticulture parameters to grape composition and then relate the chemical composition to quality as measured by the experts. This pipeline outputs the predicted yield, values for basic parameters of grape juice composition, values for basic parameters of the wine composition, and quality. We also found that the yield could be predicted because of input data related to the characteristics of the vineyards. Finally, through the creation of a web-based application, we investigated the balance of berry yield and wine quality. Using these tools further developed, vineyard owners should be able to predict the quality of the wine they intend to produce from their vineyards before the grapes are even harvested.Item Open Access Phosphorus fertiliser is associated with reduced grass grub (Costelytra giveni) fitness in Epichloë endophyte-infected meadow fescue and perennial ryegrass(John Wiley & Sons Inc., 2024) Hewitt, KG; Hofmann, RW; Ball, OJ; Luo, D; Finch, SC; Bryant, Racheal; Popay, AJBACKGROUND: Fertiliser applications are well-established tools in pasture-based agricultural landscapes. This study focuses on the impact of phosphorus (P) fertiliser on grass grub (Costelytra giveni), a major pasture pest. This research investigates the interplay between P, plant growth, and grass grub fitness in Epichloë endophyte-infected perennial ryegrass (Epichloë sp. LpTG-3 strain AR37) and meadow fescue infected with E. uncinata (strain MaxR; AR1017), alongside their endophyte-free counterparts. In a glasshouse trial, plants were grown in P-enriched soil with varying Olsen P levels (9, 18, 28 or 78 mg L¯¹), and grass grubs were introduced. Their survival and weight gain, and plant performance were measured. In a bioassay, grass grubs were placed in specimen vials with P-enriched soils (Olsen P levels 9, 18, 28 and 78 mg L¯¹) and provided with identical plant material to assess their diet consumption and weight gain. RESULTS: In the glasshouse trial, results highlighted a notable decrease in the survival of grass grub on plants infected with MaxR endophyte, but not with AR37, as well as increasing soil Olsen P levels in both plant species. While grass grub decreased plant performance at the low Olsen P level (9 mg L¯¹), this effect diminished with increasing P. Likewise, results from the bioassay showed a decrease in diet consumption with increasing soil Olsen P levels. In both trials increasing Olsen P levels correlated with diminished grass grub performance, revealing a nuanced relationship between soil fertility and pest dynamics. CONCLUSION: The study underscores the pivotal role of selected Epichloë endophyte–grass associations in mitigating grass grub damage across varying phosphorus levels. This study highlights the potential to integrate P applications for sustainable pest control against grass grub. Further field trials are required to validate these findings.Item Open Access Microbiology and water quality(Lincoln College, 1983) Noonan, MJMicroorganisms can have a major effect on water quality. They can be involved in the transformation of a substance which becomes a pollutant when it enters water (e.g. nitrate-N). Microorganisms can be involved in the accumulation of substances which become toxic at higher concentrations (e.g.heavymetals). Those of sanitary significance can carry genes which can be transferred to cause pathogenic microorganisms to become resistant to antibiotics, they can be pathogens themselves, or they can indicate the possible presence of pathogens. Microorganisms and their activities can affect nonsaline surface waters, marine and groundwaters. Efforts to control their influence can include waste treatment, control of water supplies, and selection of environments into which wastes are discharged. The papers in these proceedings cover many aspects of microorganisms and their activities, particularly as they affect water quality in New Zealand.Item Open Access List of cultures of micro-organisms held in New Zealand and methods for their preservation : collections : Forest Research Institute, National Health Institute, New Zealand Dairy Research Institute, University of Otago, University of Waikato, Wallaceville Animal Research Centre(Lincoln College, 1987) Mulcock, APIn August 1947 a specialist conference on Culture Collections of Micro-organisms was held in London. This meeting recommended the formation of a Commonwealth Organisation to be known as "The British Commonwealth Collections of Micro-organisms". The organisation was charged with: 1. Establishing a Permanent Committee 2. Preparing a Directory of Collections 3. Establishing National Committees 4. Preparation of Catalogues by each Collection 5. Distribution of Cultures (freely and without charge) As a result of the formation of the Commonwealth Committee a New Zealand Committee was set up under the aegis of the New Zealand Department of Science and industrial Research. This Committee set about obtaining from culture collections in New Zealand lists of their holdings. At first it was proposed to publish one directory for the whole Commonwealth, however, this proved impractical and so lists were issued country by country as the material became available. A list prepared by the New Zealand was finally dispatched to London in 1965 and was published in 1968 as the "Commonwealth Collection of Micro-organisms Directory of Collections and List of Species Maintained in New Zealand, HMSO London".Item Open Access The quality and movement of groundwater in alluvial aquifers of New Zealand(Lincoln College. Department of Agricultural Biology, 1979) Noonan, MJThese Proceedings are intended as a record of the meeting on the Quality and Movement of Groundwater in Alluvial Aquifers of New Zealand. The meeting was held at Lincoln College and was the second in a series initiated by the North Canterbury Catchment Board and Regional Water Board in February l978.Item Unknown Biochemical characterisation and production kinetics of high molecular-weight (HMW) putative antibacterial proteins of insect pathogenic Brevibacillus laterosporus isolates(BMC, 2024-12) Babar, TK; Glare, Travis; Hampton, John; Hurst, MRH; Narciso, JBackground Bacterial genomes often encode structures similar to phage capsids (encapsulins) and phage tails which can be induced spontaneously or using genotoxic compounds such as mitomycin C. These high molecular-weight (HMW) putative antibacterial proteins (ABPs) are used against the competitive strains under natural environment. Previously, it was unknown whether these HMW putative ABPs originating from the insect pathogenic Gram-positive, spore-forming bacterium Brevibacillus laterosporus (Bl) isolates (1821L, 1951) are spontaneously induced during the growth and pose a detrimental effect on their own survival. Furthermore, no prior work has been undertaken to determine their biochemical characteristics. Results Using a soft agar overlay method with polyethylene glycol precipitation, a narrow spectrum of bioactivity was found from the precipitated lysate of Bl 1951. Electron micrographs of mitomycin C- induced filtrates showed structures similar to phage capsids and contractile tails. Bioactivity assays of cell free supernatants (CFS) extracted during the growth of Bl 1821L and Bl 1951 suggested spontaneous induction of these HMW putative ABPs with an autocidal activity. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis of spontaneously induced putative ABPs showed appearance of ∼ 30 kDa and ∼ 48 kDa bands of varying intensity across all the time intervals during the bacterial growth except in the initial hours. Statistically, spontaneously induced HMW putative ABPs of Bl 1951 exhibited a significant decrease in the number of viable cells of its producer strain after 18 h of growth in liquid. In addition, a significant change in pH and prominent bioactivity of the CFS of this particular time period was noted. Biochemically, the filtered supernatant derived from either Bl 1821L or Bl 1951 maintained bioactivity over a wide range of pH and temperature. Conclusion This study reports the spontaneous induction of HMW putative ABPs (bacteriocins) of Bl 1821L and Bl 1951 isolates during the course of growth with potential autocidal activity which is critically important during production as a potential biopesticide. A narrow spectrum of putative antibacterial activity of Bl 1951 precipitate was found. The stability of HMW putative ABPs of Bl 1821L and Bl 1951 over a wide range of pH and temperature can be useful in expanding the potential of this useful bacterium beyond the insecticidal value.Item Unknown Investigation of potential pollution from a proposed landfill(Lincoln College. Department of Agricultural Biology, 1977) Noonan, MJ; Campbell, AS; Shaw, B; Stanley, RAOf the methods available for the disposal of solid wastes sanitary landfill continues to be the least expensive. There are a number of problems with landfilling, not the least of which is the threat to the purity of underground waters. Since Christchurch city uses a supply of very pure ground water any possible pollution of this water is viewed so seriously that the siting of sanitary landfills in areas where there can be no danger to water supply quality is clearly imperative. Thus an investigation into the effects of dumping domestic and industrial refuse onto an area of sand dunes near Bottle Lake Forest in Christchurch was carried out.Item Unknown Soil contamination by septic tank effluent(Lincoln College, 1973-11) Mulcock, AP; Noonan, MJ; Reay, CAA survey of literature relating to septic tanks and the movement of micro-organisms through soil was made. The septic tank still appears to be the most satisfactory method of treating household wastes. Little experimental evidence is available concerning the movement of microorganisms through soil, but work which has been done indicates that soils vary greatly in their filtering ability. Furthermore soils appear to change in capacity to retain micro-organisms which subsequently die at different rates depending on the nature of the soil. The travel of viruses through ~oil has received negligible attention. Investigations undertaken at two sites in the Tai Tapu Area, near Christchurch, indicated that pollution of the soil by faecal organisms can take place from septic tanks and can extend over quite a wide area. The bacteria may remain viable in the soil for some months, both near the surface and at depth. From samples obtained by drilling holes in the soil it was found that bacteria could apparently move laterally through the soil at 2.0 to 3.0 m depth for considerable distances. Two main conclusions can be drawn from this work. First, soil can become contaminated by septic tank effluent over a wide area. Second, once the soil is contaminated the micro-organisms can persist for long periods.Publication Unknown Factors that influence microbial communities in spontaneously fermented wine, beer, and kombucha: insights from a metabarcoding perspective : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2024) Ohwofasa, AghoghoIt is well established that the world contains a vast diversity of microbes, many of which have been unexplored and even as yet uncultivated. Advances in molecular biology techniques such as metabarcoding have helped in improving our insights into this complex microbial world, in every aspect of human civilization, including food and beverage production. The importance of microbial diversity in the processing of wine and other fermented products in general cannot be overemphasized. In wine for example, grape health and the diversity of microorganisms introduced into the winery depends on the number of microbes who are able to form ecological niches in the vine and soil of the vineyard. With extensive knowledge of microbiome diversity and its interactions or shifts within fermentation processes, this could lead to an improved understanding of this activity. With next generation Sequencing (NGS) techniques, it is now feasible to accurately detect and quantify the relative abundance of microbes found in and around these products. Culture based methods previously used in microbial analysis neglects the non-culturable microbial fraction, an advantage NGS methods possesses over culture based techniques. Performing complex multifactorial analyses is now possible by coupling metabarcoding with bioinformatics tools. This is fast becoming the “go to” strategy in monitoring, traceability of products and diagnostic purposes. If properly harnessed, metabarcoding opens up the possibility of adequately monitoring and describing the microbial population during fermentation and how their profile changes with time. The aim of this research was to employ metabarcoding in exploring the microbiomes associated with spontaneously fermented wine and other foods/products such as kombucha and lambic styled beer in New Zealand. These studies included investigating the influences that the environment and/or climate play in shaping the microbiome of these products. Where applicable, the complex relationship between the microorganisms and the organoleptic and chemical properties of the products was also probed. The first experiment in this work explored the impact of differing environmental systems on the microbial communities utilized by an organic winemaker in producing wines. Results indicated that T. delbrueckii and Fructobacillus could be affected by environmental conditions as they were detected in one system but not the other. Together, significant differences were reported between the fungal (RANOSIM = 0.603, p = 0.0001) and bacterial (RANOSIM = 0.5814, p = 0.0001) diversity found in both systems. Assessment of these microbial differences were done to see if they brought about detectable sensory or chemical variations in the resulting wines. Certain volatile compounds were only found in wines from one of the environmental system but not the other, indicating that significantly different bacterial and/or fungal species could have major roles in synthesising these compounds. Specifically, it can be inferred that Gluconobacter may play a role in the taste (bitterness) and ‘mouth feel’ (astringency/tannin) attributes of Pinot noir wines. To gain insights into how the microbial communities associated with kombucha production might differ based on scale (large commercial scale as compared to a small scale production), another experiment was carried out. For the first time in kombucha literature, results uncovered indicated that the fungal and bacterial diversity associated with the commercial fermentation process had a higher diversity as compared to small scale kombucha production. Interestingly, the core fungal microbiome found in the SCOBY and tea phase of both the commercial and small-scale kombucha types were similar. Using linear modelling unravelled how Komagataeibacter might play a key role and shape the pH of kombucha. To understand if the microbial communities detected at the end of spontaneous beer fermentation varies across vintages, a beer experiment was conducted. Results from this experiment revealed how vintage has a huge influence in shaping the detected microbial populations. Climatic factors such as humidity and maximum temperature were identified as variables that may enhance the relative abundance of Penicillium and Hanseniaspora in beer microbiota. When the microbiome of all three fermented food/products were compared, in comparison to the bacterial communities, similarities can be seen with the fungal populations. Spontaneously fermented wine and kombucha fermentation had considerable amounts of Hanseniaspora, Metschnikowia and Saccharomyces. Beer and kombucha fermentation had substantial Brettanomyces and Saccharomyces proportions. Saccharomyces was the only genus present in significant amounts in all three foods/products. For bacteria, spontaneously fermented Pinot noir wine was dominated by Tatumella (2021 vintage) and Lactococcus (2018 vintage). Komagataeibacter and Gluconobacter were abundant in the home and commercial kombucha brew respectively. Lambic styled beer saw Pediococcus as the most dominant bacteria. Summarily, this research unravelled the complex microbiome of spontaneous Pinot noir wine fermentation, kombucha fermentation and lambic beer brewing. Description of how microbial populations can be affected by environmental and/or climatic influences were done. Where applicable, how these microbial differences could result in sensory and/or chemical variations in the resultant product were assessed. This study has described how metabarcoding can be reliable in assessing the microbiome of fermented food/products.Item Open Access Perspective chapter: Numerical solutions for modelling complex systems with Stochastic Differential and Partial Differential Equations (SDEs/SPDEs)(InTech Open, 2024-07-31) Tiwari, Parul; Kulasiri, Don; Samarasinghe, Sandhya; Kulasiri, DonUnderstanding phenomena ranging from biological processes to financial markets involves uncertainty. Stochastic Differential Equations (SDEs) and Stochastic Partial Differential Equations (SPDEs) serve as robust mathematical frameworks for modelling such systems. Given the stochastic influences within these models, comprehending the dynamics of complex systems becomes pivotal for accurately predicting system behaviour. However, traditional numerical techniques frequently encounter challenges in effectively addressing the intricacies and stochastic properties inherent in these equations. This chapter explores several numerical methods that offer streamlined and dependable solutions capable of handling the complexities inherent in stochastic differential and partial differential equations. Also, numerical challenges associated with these methods are discussed and the solution strategies are also suggested.Item Open Access Elephantopus scaber L. polysaccharides alleviate heat stress-induced systemic inflammation in mice via modulation of characteristic gut microbiota and metabolites(Multidisciplinary Digital Publishing Institute (MDPI), 2024-01) Wang, Chen; Sun, Dongfang; Deng, Qi; Sun, Lijun; Hu, Lianhua; Fang, Zhijia; Zhao, Jian; Gooneratne, RaviElephantopus scaber L. (ESL) is a Chinese herb that is used both as a food and medicine, often being added to soups in summer in south China to relieve heat stress (HS), but its exact mechanism of action is unknown. In this study, heat-stressed mice were gavaged with ESL polysaccharides (ESLP) at 0, 150, 300, and 450 mg/kg/d‾¹ (n = 5) for seven days. The gut microbiota composition, short-chain fatty acids (SCFAs), seven neurotransmitters in faeces, expression of intestinal epithelial tight junction (TJ) proteins (Claudin-1, Occludin), and serum inflammatory cytokines were measured. The low dose of ESLP (ESLL) improved the adverse physiological conditions; significantly reduced the cytokines (TNF-α, IL-1β, IL-6) and lipopolysaccharide (LPS) levels (p < 0.05); upregulated the expression of Claudin-1; restored the gut microbiota composition including Achromobacter and Oscillospira, which were at similar levels to those in the normal control group; significantly increased beneficial SCFAs like butyric acid and 5-HT levels in the faeces of heat-stressed mice; and significantly decreased the valeric acid and glutamic acid level. The level of inflammatory markers significantly correlated with the above-mentioned indicators (p < 0.05). Thus, ESLL reduced the HS-induced systemic inflammation by optimizing gut microbiota (Achromobacter, Oscillospira) abundance, increasing gut beneficial SCFAs like butyric acid and 5-HT levels, and reducing gut valeric and glutamic acid levels.Item Open Access Lincoln University proceedings: Grape & Wine Symposium, 23-24 September 1994(Lincoln University, 1994)Papers presented at the Grape & Wine Symposium, 23-24 September 1994.Item Open Access Proceedings: 5th Grape & Wine Spring School, 27-28 September 1997(Lincoln University, 1997)Papers presented at the 5th Grape & Wine Spring School, 27-28 September 1997.Item Open Access The proceedings of the Grape and Wine Symposium, held at Lincoln University, 20-21 September 1996(Lincoln University, 1996)Papers presented at the Grape and Wine Symposium, Lincoln University, 20-21 September 1996.Item Open Access The proceedings of the Grape and Wine Symposium held at Lincoln University, 19-20 September 1998(Lincoln University, 1998)Papers presented at the Grape and Wine Symposium held at Lincoln University, 19-20 September 1998.Item Open Access Lincoln University proceedings: Grape & Wine Symposium, 17-19 September 1993(Lincoln University, 1993)Papers delivered at the Grape & Wine Symposium, Lincoln University, 22-23 September 1993.Item Open Access Lincoln University proceedings : Grape & Wine Symposium, 22-23 September 1995(Lincoln University, 1995)Papers delivered at the Grape & Wine Symposium, 22-23 September 1995.Item Open Access Calcium caseinate enhancement of bread and its role in manipulating the glycaemic response and antioxidant potential of the product(Wiley on behalf of Institute of Food Science and Technology, 2024) Idahagbon, Nosa B; Kumar, Lokesh; Nicholas, Robert J; Oluyemi, Mary B; Brennan, Charles SThe impact of supplementing bread with calcium caseinate was studied at substitution levels of 5%, 10% and 15%. The research assessed the baking properties, nutritional value, glycaemic response and antioxidant activity of the experimental bread samples. Addition led to a significant increase in protein content, reaching up to 22% of the total energy supply at 15% substitution. Essential amino acids, such as valine, leucine and isoleucine, more than doubled in concentration at the 15% substitution level. Furthermore, the incorporation of calcium caseinate improved the textural properties of the bread, significantly increasing the bread volume and reducing setback viscosity (P< 0.05). The predicted glycaemic response, as measured by the area under the glucose release curve, showed a notable reduction in sugar levels at 15% substitution. These results suggest that bread enriched with calcium caseinate can serve as a valuable protein source for the population, offering both enhanced nutritional benefits and favourable baking characteristics.