Department of Wine, Food and Molecular Biosciences

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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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Recent Submissions

  • PublicationOpen Access
    Unveiling a microexon switch: novel regulation of the activities of sugar assimilation and plant-cell-wall-degrading xylanases and cellulases by Xlr2 in Trichoderma virens
    (MDPI, 2024-05) Castañeda-Casasola, Cynthia Coccet; Nieto-Jacobo, María Fernanda; Soares, Amanda; Padilla-Padilla, Emir Alejandro; Anducho-Reyes, Miguel Angel; Brown, Chris; Soth, Sereyboth; Esquivel-Naranjo, Edgardo Ulises; Hampton, John; Mendoza-Mendoza, Artemio
    Functional microexons have not previously been described in filamentous fungi. Here, we describe a novel mechanism of transcriptional regulation in Trichoderma requiring the inclusion of a microexon from the Xlr2 gene. In low-glucose environments, a long mRNA including the microexon encodes a protein with a GAL4-like DNA-binding domain (Xlr2-∝), whereas in high-glucose environments, a short mRNA that is produced encodes a protein lacking this DNA-binding domain (Xlr2-β). Interestingly, the protein isoforms differ in their impact on cellulase and xylanase activity. Deleting the Xlr2 gene reduced both xylanase and cellulase activity and growth on different carbon sources, such as carboxymethylcellulose, xylan, glucose, and arabinose. The overexpression of either Xlr2-∝ or Xlr2-β in T. virens showed that the short isoform (Xlr2-β) caused higher xylanase activity than the wild types or the long isoform (Xlr2-∝). Conversely, cellulase activity did not increase when overexpressing Xlr2-β but was increased with the overexpression of Xlr2-∝. This is the first report of a novel transcriptional regulation mechanism of plant-cell-wall-degrading enzyme activity in T. virens. This involves the differential expression of a microexon from a gene encoding a transcriptional regulator.
  • PublicationOpen Access
    Biofilm formation, sodium hypochlorite susceptibility and genetic diversity of Vibrio parahaemolyticus
    (Elsevier, 2023-01-16) Wang, D; Fletcher, GC; On, Stephen; Palmer, JS; Gagic, D; Flint, SH
    Vibrio parahaemolyticus is a marine oriented pathogen; and biofilm formation enables its survival and persistence on seafood processing plant, complicating the hygienic practice. The objectives of this study are to assess the ability of V. parahaemolyticus isolated from seafood related environments to form biofilms, to determine the effective sodium hypochlorite concentrations required to inactivate planktonic and biofilm cells, and to evaluate the genetic diversity required for strong biofilm formation. Among nine isolates, PFR30J09 and PFR34B02 isolates were identified as strong biofilm forming strains, with biofilm cell counts of 7.20, 7.08 log₁₀ CFU/cm², respectively, on stainless steel coupons after incubation at 25 °C. Free available chlorine of 1176 mg/L and 4704 mg/L was required to eliminate biofilm cells of 1.74–2.28 log₁₀ CFU/cm² and > 7 log₁₀ CFU/cm², respectively, whereas 63 mg/L for planktonic cells, indicating the ineffectiveness of sodium hypochlorite in eliminating V. parahaemolyticus biofilm cells at recommended concentration in the food industry. These strong biofilm-forming isolates produced more polysaccharides and were less susceptible to sodium hypochlorite, implying a possible correlation between polysaccharide production and sodium hypochlorite susceptibility. Genetic diversity in mshA, mshC and mshD contributed to the observed variation in biofilm formation between isolates. This study identified strong biofilm-forming V. parahaemolyticus strains of new multilocus sequence typing (MLST) types, showed a relationship between polysaccharide production and sodium hypochlorite resistance.
  • PublicationOpen Access
    Extraction of tannin, colour and aroma compounds in pinot noir wines as affected by clone selection and whole bunch addition
    (Elsevier, 2024-09) Wimalasiri, PM; Harrison, Roland; Hider, R; Donaldson, I; Kemp, B; Tian, Bin
    Our previous study revealed stem inclusion fermentation reduced anthocyanin, and increased tannin and aroma compounds responsible for green notes. This study further investigated the effect of clone selection and whole bunch fermentation on Pinot noir wine composition, with focus on tannin composition. Three treatments were conducted using two clones (AM10/5 and UCD5) in 2021 and 2022: 100% destemmed (DS), 30% whole bunch (WB30), and 60% whole bunch (WB60). WB60 increased stem and skin derived tannins but reduced seed derived tannin proportion in wines. Clone selection had an impact on tannin composition and an even greater impact on tannin concentration, colour, and aroma compounds. AM10/5 produced wines with higher tannin, polymeric pigments and darker colour. AM10/5 wines also had higher concentration of phenylethyl alcohol, but lower concentrations of 3-isobutyl-2-methoxypyrazine and ethyl esters, indicating more floral but less fruity and green notes.
  • PublicationOpen Access
    A potted vine model to facilitate the understanding of Pinot noir yield-quality seesaw according to root growing conditions
    (2023) Schelezki, Olaf; Moukarzel, Romy; Gregan, S; Trought, M; Jordan, B; Parker, Amber
    Presentation at the inaugural New Zealand Wine Centre Scientific Research Conference on 14 November 2023.
  • PublicationOpen Access
    Snail meat consumption in Buea-Cameroon: Exposures to foodborne pathogens through social practices assessed in 2019 and 2021
    (Springer Nature, 2022-12) Tanyitiku, MN; Nicholas, G; Sullivan, Jon; Njombissie Petcheu, IC; On, Stephen
    Background: Snail meat is an important source of nutrition in Cameroon, but the food safety risks are poorly understood. We characterized public health risks from snail meat consumption as a social system in Cameroon, by examining local snail practices that expose snail meat handlers and consumers to foodborne pathogens. Methods: We used exploratory qualitative approaches, that is, lived experience, face-to-face in-depth interviews, participant observation and a focus group, to explore fifteen key informants’ routines and lived experiences, and perceptions of two health officials on the food safety practices around snail meat consumption in Cameroon. This information was organized and interpreted using Soft Systems Methodology and Social Practice Theory, which permitted a systemic appreciation of local practices. Results: We distinguished five kinds of actors (snail vendors, market sellers, street vendors, street eaters and home consumers), who performed seven successive practices (picking, selling, cracking, washing, cooking, hawking and eating). We then identified three worldviews about snails: family support or to reduce poverty, a source of nutrition and a food choice (taste, preference). Our findings revealed participants’ competences were based on childhood learning and ‘inborn’ experiences, and materials used in snail activities reflected participants’ parentage and ‘state of poverty’. Although most interviewees highlighted ‘unhygienic conditions’ when explaining snail picking locations, participants believed washing and cooking should kill all contaminants. Conclusion: Several opportunities for human exposures to foodborne pathogens including snail picking in domestic wastes and sewage, the selling of unpackaged live snails, improper snail meat washing and hawking in loosely closed buckets, were apparent from our analysis. These findings suggest fruitful opportunities aimed at improving health outcomes among African snail meat handlers and consumers.
  • PublicationOpen Access
    Elevated abundance of Komagataeibacter results in a lower pH in kombucha production; insights from microbiomic and chemical analyses
    (Elsevier, 2024) Ohwofasa, Aghogho; Dhami, Manpreet; Winefield, Christopher; On, Stephen
    Kombucha consumption has grown rapidly worldwide in the last decade, with production at both small- and large scales. The complex fermentation process involves both bacterial and yeast species, but little is known regarding the progression of microbial development during production. We explored the microbial diversity of multiple batches across two kombucha types, i. e commercial scale versus laboratory-made (hereafter “home”) kombucha brew using metabarcoding to characterize both fungal and bacterial communities. We found the microbial community of the commercial kombucha brew to be more complex than that of the home brew. Furthermore, PERMANOVA uncovered significant compositional differences between the bacterial (F = 2.68, R² = 0.23, p = 00.001) and fungal (F = 3.18, R² = 0.26, p = 00.006) communities between batches. For the home brew, both alpha and beta diversity analyses revealed no significant differences between all batches and replicates. When the microbial diversity of the home and commercial kombucha types were directly compared, the former had higher proportions of Ammoniphilus and Komagataeibacter. The commercial kombucha on the other hand were high in Anoxybacillus, Methylobacterium and Sphingomonas. For the fungal communities, the most dominant fungal genera detected in both kombucha types were similar. Linear model revealed significant correlations between some microorganisms and the sugars and organic acids assayed in this study. For example, rising glucose levels correlated with an increase in the relative abundance of Komagataeibacter (F = 7.115, Adj. R² = 0.44, p = 00.0003). We believe these results contribute towards achieving a better control of the kombucha fermentation process and may assist in targeted product diversification.
  • PublicationOpen Access
    Comparative genome identification of accessory genes associated with strong biofilm formation in Vibrio parahaemolyticus
    (Elsevier, 2023-04) Wang, D; Fletcher, GC; Gagic, D; On, Stephen; Palmer, JS; Flint, SH
    Vibrio parahaemolyticus biofilms on the seafood processing plant surfaces are a potential source of seafood contamination and subsequent food poisoning. Strains differ in their ability to form biofilm, but little is known about the genetic characteristics responsible for biofilm development. In this study, pangenome and comparative genome analysis of V. parahaemolyticus strains reveals genetic attributes and gene repertoire that contribute to robust biofilm formation. The study identified 136 accessory genes that were exclusively present in strong biofilm forming strains and these were functionally assigned to the Gene Ontology (GO) pathways of cellulose biosynthesis, rhamnose metabolic and catabolic processes, UDP-glucose processes and O antigen biosynthesis (p < 0.05). Strategies of CRISPR-Cas defence and MSHA pilus-led attachment were implicated via Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation. Higher levels of horizontal gene transfer (HGT) were inferred to confer more putatively novel properties on biofilm-forming V. parahaemolyticus. Furthermore, cellulose biosynthesis, a neglected potential virulence factor, was identified as being acquired from within the order Vibrionales. The cellulose synthase operons in V. parahaemolyticus were examined for their prevalence (22/138, 15.94 %) and were found to consist of the genes bcsG, bcsE, bcsQ, bcsA, bcsB, bcsZ, bcsC. This study provides insights into robust biofilm formation of V. parahaemolyticus at the genomic level and facilitates: identification of key attributes for robust biofilm formation, elucidation of biofilm formation mechanisms and development of potential targets for novel control strategies of persistent V. parahaemolyticus.
  • PublicationOpen Access
    Synthesis of β-cyclodextrin@gold nanoparticles and its application on colorimetric assays for ascorbic acid and salmonella based on peroxidase-like activities
    (MDPI, 2024-03-31) Fan, X; Bao, Y; Chen, Y; Wang, X; On, Stephen; Wang, J
    The peroxidase-like behaviors of gold nanoparticles (AuNPs) have the potential to the development of rapid and sensitive colorimetric assays for specific food ingredients and contaminants. Here, using NaBH₄ as a reducing agent, AuNPs with a supramolecular macrocyclic compound β-cyclodextrin (β-CD) capped were synthesized under alkaline conditions. Monodispersal of β-CD@AuNPs possessed a reduction in diameter size and performed great peroxidase-like activities toward both substrates, H₂O₂ and TMB. In the presence of H₂O₂, the color change of TMB oxidization to oxTMB was well-achieved using β-CD@AuNPs as the catalyst, which was further employed to develop colorimetric assays for ascorbic acid, with a limit of detection as low as 0.2 μM in ddH₂O. With the help of the host-guest interaction between β-CD and adamantane, AuNPs conjugated with nanobodies to exhibit peroxidase-like activities and specific recognition against Salmonella Typhimurium simultaneously. Based on this bifunctional bioprobe, a selective and sensitive one-step colorimetric assay for S. Typhimurium was developed with a linear detection from 8.3 × 10⁴ to 2.6 × 10⁸ CFU/mL and can be provided to spiked lettuce with acceptable recoveries of 97.31% to 103.29%. The results demonstrated that the excellent peroxidase-like behaviors of β-CD@AuNPs can be applied to develop a colorimetric sensing platform in the food industry.
  • PublicationOpen Access
    Efficacy of commercial peroxyacetic acid on Vibrio parahaemolyticus planktonic cells and biofilms on stainless steel and Greenshell™ mussel (Perna canaliculus) surfaces
    (Elsevier, 2023-11-16) Wang, D; Palmer, JS; Fletcher, GC; On, Stephen; Gagic, D; Flint, SH
    The potential of using commercial peroxyacetic acid (PAA) for Vibrio parahaemolyticus sanitization was evaluated. Commercial PAA of 0.005 % (v/v, PAA: 2.24 mg/L, hydrogen peroxide: 11.79 mg/L) resulted in a planktonic cell reduction of >7.00 log₁₀ CFU/mL when initial V. parahaemolyticus cells averaged 7.64 log₁₀ CFU/mL. For cells on stainless steel coupons, treatment of 0.02 % PAA (v/v, PAA: 8.96 mg/L, hydrogen peroxide: 47.16 mg/L) achieved >5.00 log₁₀ CFU/cm² reductions in biofilm cells for eight strains but not for the two strongest biofilm formers. PAA of 0.05 % (v/v, PAA: 22.39 mg/L, hydrogen peroxide: 117.91 mg/L) was required to inactivate >5.00 log₁₀ CFU/cm² biofilm cells from mussel shell surfaces. The detection of PAA residues after biofilm treatment demonstrated that higher biofilm production resulted in higher PAA residues (p < 0.05), suggesting biofilm is acting as a barrier interfering with PAA diffusing into the matrices. Based on the comparative analysis of genomes, robust biofilm formation and metabolic heterogeneity within niches might have contributed to the variations in PAA resistance of V. parahaemolyticus biofilms.
  • PublicationOpen Access
    Effects of repeated tasting sessions on acceptability, emotional responses, and purchasing behaviors of waste-to-value-addedSCOBY (symbiotic culture of bacteria and yeast) ice cream
    (Wiley Periodicals LLC., 2024-04) Mehta, A; Serventi, Luca; Kumar, Lokesh; Torrico, Damir
    This study investigated the effects of repeated exposure on acceptability, emotional responses, and purchase intention of a novel symbiotic culture of bacteria and yeast (SCOBY) ice cream, compared to a control (no extra additives) and a guar gum ice cream sample, using three sessions: a survey (SCOBY information) and two tasting sessions (repeated-exposure effect). Participants initially conducted blind evaluations of all samples, followed by an informed tasting. The blind tasting sessions evoked high arousal emotions for the SCOBY ice cream and positive emotions for the control and guar gum samples. The second session showed a rise in liking for sweetness (5.6–6.5) and texture (5.6–6.7) of the SCOBY samples. Sensory attributes such as flavor (odds ratio = 1.7) and texture (odds ratio = 1.7), coupled with positive emotions such as “happy” (odds ratio = 3.8), “pleasant” (odds ratio = 0.4), and “interested” (odds ratio = 3.8) affected purchase intention. The findings of this study provide valuable insights into participants' liking and emotional responses during repeated exposures to stimuli. Practical Applications: The study's findings show that repeated exposure to novel products enhances consumer acceptance and emotional responses, challenging the current formats of traditional sensory studies. This implies that the introduction of novel products can be successful with repeated tasting exposure strategies. The focus on improving familiarity with sensory attributes, especially flavor and texture, can positively impact purchase intention. This insight can guide product positioning, marketing campaigns, and flavor development efforts, encouraging the successful integration of innovative products into the market.
  • PublicationOpen Access
    Wine aromas
    (MDPI, 2023-12) Tian, Bin; Zhang, J
    Wine has a complex matrix with many volatile compounds present, which evolves over time. These volatile compounds are important to wine quality as they contribute to the aroma and varietal characteristics of wine. Recent development in the analysis of volatile compounds in wine has greatly improved our understanding of the complexity of wine aroma. Analytical methods used for wine aroma fingerprinting have shown potential in determining the origin and quality of wine. Thus, research on volatile compounds responsible for wine aroma and their correlation with wine provenance and wine quality have increasingly attracted great interest from researchers and winegrowers. This Special Issue presents the latest research regarding wine aroma compounds, including, but not limited to, the topics on the characterization of aroma compounds in grapes and wine, factors influencing the production of aroma compounds in wine during fermentation and maturation, and analytical methods for wine aroma analysis.
  • PublicationOpen Access
    Influence of climatic variation on microbial communities during organic Pinot noir wine production
    (Public Library of Science, 2024-02-28) Ohwofasa, Aghogho; Dhami, M; Zhang, Junwen; Tian, Bin; Winefield, Christopher; On, Stephen; Gerós, H
    To assess the possible impact of climatic variation on microbial community composition in organic winemaking, we employed a metabarcoding approach to scrutinize the microbiome in a commercial, organic, Pinot noir wine production system that utilizes autochthonous fermentation. We assessed microbial composition across two vintages (2018 and 2021) using biological replicates co-located at the same winery. Microbial dynamics were monitored over four important fermentation time points and correlated with contemporaneous climate data. Bacterial (RANOSIM = 0.4743, p = 0.0001) and fungal (RANOSIM = 0.4738, p = 0.0001) compositions were different in both vintages. For bacteria, Lactococcus dominated the diversity associated with the 2018 vintage, while Tatumella dominated the 2021 vintage. For fungal populations, while Saccharomyces were abundant in both vintages, key differences included Starmerella, copious in the 2018 vintage; and Metschnikowia, substantive in the 2021 vintage. Ordination plots correlated the climatic variables with microbial population differences, indicating temperature as a particularly important influence; humidity values also differed significantly between these vintages. Our data illustrates how climatic conditions may influence microbial diversity during winemaking, and further highlights the effect climate change could have on wine production.
  • PublicationOpen Access
    Characterisation and extractability of tannins in Pinot noir grape skin, seed, and stem: Impact of leaf removal, clone, and rootstock
    (Elsevier, 2024-06) Wimalasiri, PM; Harrison, Roland; Donaldson, I; Kemp, B; Tian, Bin
    This study examined the impact of leaf removal timing, rootstock, and clone selection on Pinot noir grape composition and subsequent impact on tannin extractability. Results showed that leaf removal increased anthocyanin levels in berries and tannins in stems and seeds, while also raising the mean degree of polymerisation (mDP) of skin tannins. Schwarzman rootstock had lower seed tannins but higher mDP in skin and seed tannins compared to own roots. UCD5 clone exhibited higher mDP in skin tannins than AM10/5 clones in acetone extraction. Tannin extractability was determined by the ratio of model wine-extracted tannins and acetone-extracted tannins. For the first time, this study reported that stems had the highest tannin extractability (64%-78%) compared to skins (37–52%) and seeds (26–34%). Compositional differences in grape tissues from different treatments had no impact on tannin extractability except for grape skins from two treatments. This suggests that tannin extractability is mainly influenced by grape ripeness which largely determines the composition of cell wall materials that can interact with tannins and thus influence tannin extractability. The differences in grape skin tannin extractability observed in this study between treatments were likely due to the significantly different galloylation (G%) levels in the extracted tannins.
  • PublicationOpen Access
    Timing of leaf removal modulates tannin composition and the level of anthocyanins and methoxypyrazines in Pinot noir grapes and wines
    (Elsevier, 2024-02) Wimalasiri, PM; Harrison, Roland; Donaldson, I; Kemp, B; Tian, Bin
    This study aimed to investigate the impact of leaf removal on concentrations of anthocyanin, tannin, and methoxypyrazines (MPs) in Pinot noir grapes and wines. Leaf removal after 7 days (LR7), 30 days (LR30), and 60 days (LR60) of flowering were compared with no leaf removal control (LRC). Grapes and resultant wines were analysed for tannin and aroma composition using liquid chromatography and two-dimensional gas chromatography–mass spectrometry. All leaf removal treatments increased anthocyanin concentration in grapes and reduced MP levels in grape stems compared to LRC, indicating the effectiveness of both early and late leaf removal. Leaf removal after 7 days and 30 days were more effective in enhancing colour density, polymeric pigments, and tannin concentration in wines. Higher grape skin tannin and anthocyanin concentrations, along with lower seed tannin concentration in berries, correlated with higher tannin concentrations in wines. LR7 showed significantly higher skin-originated tannin proportion than LRC, suggesting a useful tool to manage tannin extraction. Aroma composition of resultant wines was influenced by leaf removal, although these differences were not evident in the sensory evaluation.
  • PublicationRestricted
    Modulating acidity and bioactivities of sauerkraut with Proprionibacterium freudenreichii : A dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Food Innovation at Lincoln University
    (Lincoln University, 2024) Luthi, Antonia
    Health and nutrition are inextricably connected, and as consumer demand for health promoting products grows, the food industry is responding with the development of functional foods. Synthetic vitamins are commonly supplemented to maintain good health, particularly Vitamin B12, as it is an essential micronutrient obtained exclusively through the consumption of animal derived foods. This leaves vegans and plant based eaters at risk of deficiency. Studies have shown that Propionibacterium freudenreichii can be successfully co-fermented with Latic acid bacteria (LAB) to produce B12 in grain based substrates. In this study P. freudenreichii was inoculated into a traditional sauerkraut fermentation, resulting in synthesis of B12 at promising levels. Acidity was also modulated when compared with sauerkraut produced by spontaneous LAB fermentation, highlighting the potential for the wider organopleptic appeal of sauerkraut.
  • PublicationEmbargo
    Studies of bioactive compounds in brown and red onions (skin and flesh) : A dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Food Innovation at Lincoln University
    (Lincoln University, 2024) Yang, Bo
    Onions (Allium cepa L.) have been cultivated and consumed for thousands of years around the world. The bioactive compounds in onions such as phenolic compounds, are beneficial for the health of humans and can potentially reduce the risk of some diseases, which will lead to longevity of the population. Onion skin is non-edible and is always discarded by consumers and food producers. However, onion waste, mainly consisting of onion skin, is still a rich source of bioactive compounds. Red and brown onion samples in this dissertation were divided into two parts (skin and flesh) and two different extraction methods using two different solvents were tested. Total phenolic content (TPC) and total flavonoid content (TFC) were conducted to assess the bioactivity of onion extracts. The TPC, TFC values were significantly higher in the skin for both kinds of onions (p < 0.05) and 70% ethanol also had a significantly positive effect on the yields of total phenolic compounds and total flavonoids (p < 0.05) compared with reverse osmosis (RO) water. Red onions (both skin and flesh) had higher values than brown onions. Three antioxidant assays (ABTS, DPPH and FRAP assays) were conducted and onion skin also showed higher antioxidant activity than flesh. High performance liquid chromatography (HPLC) and ultra-high performance liquid chromatography (UPLC) were employed to identify and quantity quercetin in onion skin and flesh. The quercetin content had a similar distribution to TPC and TFC.
  • PublicationEmbargo
    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, Parul
    Many 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.
  • PublicationEmbargo
    Identification and characterisation of Saccharomyces cerevisiae strains isolated from spontaneous fermentation of organic Pinot noir wines : A thesis submitted in partial fulfilment of the requirements for the Degree of Master of Science at Lincoln University
    (Lincoln University, 2024) McKendrey, Jayanta Whitley
    This study characterised Saccharomyces cerevisiae populations from the spontaneous fermentation of organic Pinot noir wines produce in Waipara, Aotearoa New Zealand, using a DNA-based Interdelta typing method to evaluate their strain diversity and population dynamics. One hundred and sixty-one S. cerevisiae isolates from key fermentation stages were differentiated by interdelta typing into 106 different genotypes (profiles), of which 24 were observed more than once. One interdelta genotype was observed among each of the fermentation stages studied. The S. cerevisiae population showed a high level of strain diversity with evident dominant groupings of strains during and between fermentation stages. Saccharomyces cerevisiae strain diversity increased towards the end of fermentation accompanied with late-stage dominance by the species. Spontaneous fermentation of organically produced wine may harbour a genetically diverse population of S. cerevisiae strains but appears to be dominated by few genotypes. The influence of each genotype on the organoleptic properties of the eventual product is unknown at this point. However, the use of interdelta typing to identify strains of special relevance with commercial potential is supported.
  • PublicationEmbargo
    Lamb pH and meat quality: studies on biochemical changes in high pH meat associated with pre-slaughter farmyard stress : A dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Food Innovation at Lincoln University
    (Lincoln University, 2024) Gibbs, Benjamin Hamish
    Producing meat of the highest quality is of the utmost importance to the red meat industry. This study looked at how energy metabolic changes and protein profiles in sheep were affected by stress before post-mortem, this gave critical insights into lamb meat quality. A study of biochemical shifts related to high-pH lamb meat with pre-slaughter stress was conducted. This study was conducted using a sample of 20, six-month-old ram lambs of the Coopworth breed (two individuals were of mixed Coopworth/Hampshire breeds) that were grazed on pasture until culling. Two treatments of control and stress were applied. The control treatment was minimal stress applied before slaughter, sheep were brought straight through the yards to the slaughterhouse. In the stress treatment, stressful conditions were applied via the use of heading dogs moving the sheep around in the yards for 10 minutes, at 30-minute intervals for 3 hours before slaughter. This caused an elevated metabolic rate in these individuals pre-slaughter. Animals were harvested immediately and tissue samples were snap frozen at -80 °C. Energy metabolic changes of the two intermediate twitch muscles Gracilis (G) and Semimembranosus (SM) were studied through the use of a D-Glucose and L-Lactic acid assay. A non- significant difference was seen in the muscles G and SM for their total glycogen levels between the stress and control treatment. In the lactic acid assay, a non-significant difference was seen in the total lactic acid levels between the two muscle fibres between the stress and control treatment. For the protein profile analysis, it was decided to study four muscles, the previous two mentioned, as well as the fast-twitch muscle Longissimus lumborum (LL) and the slow-twitch muscle Supraspinatus (SS). The protein profiles of these muscles were studied through the use of a Bradford protein determination assay and gel electrophoresis imaging. The Bradford assay revealed that there was no relationship between the total soluble protein concentrations and the stress treatment in all four of the muscle fibres. The gel electrophoresis images when analysed showed a significant difference in the relative frequency of two protein bands at around 100 and 16 kDa in the two muscles SM (P-values 0.05 and 0.01) and LL (P-values 0.03 and 0.05). These results show the potential effect of stress on protein profiles, however further protein sequencing is needed before further conclusions can be made. An analysis of post-mortem pH values was also conducted from measurements after 90 minutes and 24 hours post-mortem (ultimate pH). A non-significant difference was seen after 90 minutes but, a significant difference was seen after 24 hours between all four muscle fibres and stress. Stressed carcasses had significantly higher pH values. Notably the slow twitch muscle SS exhibited higher ultimate pH values while the fast twitch LL muscle exhibited lower ultimate pH values. This indicated a fibre-type-specific response to the stress treatment in the muscle samples studied. Overall this study provided valuable insights into biochemical shifts occurring in sheep muscles under stress conditions. Further understanding of these processes is vital for the meat industry especially for the correct grading of meat before export/ sale. Future studies should look at sequencing the specific proteins that affect the stress treatment to see if they are related to meat quality parameters such as colouring, tenderness and the water-holding capacity (WHC) of meat.
  • PublicationEmbargo
    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.