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This collection contains items published by Lincoln University researchers where we do not have the full text or cannot make it open access. Instead we provide the bibliographic data (title, author, date etc), the abstract, and where relevant a link to the publisher's site.

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    Trends in DNA barcoding and metabarcoding
    (NRC Research Press, 2019-03) Adamowicz, Sarah J; Boatwright, James S; Chain, Frédéric; Fisher, Brian L; Hogg, Ian D; Leese, Florian; Lijtmaer, Darío A; Mwale, Monica; Naaum, Amanda M; Pochon, Xavier; Steinke, Dirk; Wilson, John-James; Wood, Susanna; Xu, Jianping; Xu, Sen; Zhou, Xin; van der Bank, Michelle
    This open-access special issue features 12 full articles representing emerging trends from the international DNA barcoding community. Several articles highlight how DNA-based techniques are elucidating the species diversity, biogeography, and conservation status of Africa’s biodiversity. Another prominent theme is the movement towards big biodiversity data using high-throughput, individual-based DNA barcoding methods, which preserve voucher specimens and abundance data, as well as bulk sample-based metabarcoding. Methodological developments are enhancing the detection of specific species and whole communities using environmental DNA (eDNA) barcoding and metabarcoding. Data are also expanding in terms of genetic coverage; in this issue, a new database is established for a secondary fungal DNA barcode marker, and multi-kingdom, multi-marker biodiversity surveys are gaining traction. DNA barcode sequence data, often combined with complementary markers or taxonomic information, are increasingly contributing to large-scale phylogenetic projects, with implications for understanding evolutionary history, community structure, and conservation priorities.
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    Metagenomic insights to the functional potential of sediment microbial communities in freshwater lakes
    (Pensoft Publishers, 2022-03-25) Biessy, Laura; Pearman, John K; Waters, Sean; Vandergoes, Marcus J; Wood, Susanna
    Molecular-based techniques offer considerable potential to provide new insights into the impact of anthropogenic stressors on lake ecosystems. Microbial communities are involved in many geochemical cycling processes in lakes and a greater understanding of their functions could assist in guiding more targeted remedial actions. Recent advances in metagenomics now make it possible to determine the functional potential of entire microbial communities. The present study investigated microbial communities and their functional potential in surface sediments collected from three lakes with differing trophic states and characteristics. Surface sediments were analysed for their nutrient and elemental contents and metagenomics and metabarcoding analysis undertaken. The nutrients content of the surface sediments did not show as distinct a gradient as water chemistry monitoring data, likely reflecting effects of other lake characteristics, in particular, depth. Metabarcoding and metagenomics revealed differing bacterial community composition and functional potential amongst lakes. Amongst the differentially abundant metabolic pathways, the most prominent were clusters in the energy and xenobiotics pathways. Differences in the energy metabolism paths of photosynthesis and oxidative phosphorylation were observed. These were most likely related to changes in the community composition and especially the presence of cyanobacteria in two of the three lakes. Xenobiotic pathways, such as those involving polycyclic aromatic hydrocarbons, were highest in the lakes with the greatest agricultural land-use in their catchment. These results highlight how microbial metagenomics can be used to gain insights into the causes of differences in trophic status amongst lakes.
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    Tetrodotoxin in marine bivalves and edible gastropods: A mini-review
    (Elsevier, 2019-12) Biessy, Laura; Boundy, Michael J; Smith, Kirsty F; Harwood, D Tim; Hawes, Ian; Wood, Susanna
    Tetrodotoxin (TTX) is a potent neurotoxin responsible for countless human intoxications and deaths around the world. The distribution of TTX and its analogues is diverse and the toxin has been detected in organisms from both marine and terrestrial environments. Increasing detections seafood species, such as bivalves and gastropods, has drawn attention to the toxin, reinvigorating scientific interest and regulatory concerns. There have been reports of TTX in 21 species of bivalves and edible gastropods from ten countries since the 1980's. While TTX is structurally dissimilar to saxitoxin (STX), another neurotoxin detected in seafood, it has similar sodium channel blocking action and potency and both neurotoxins have been shown to have additive toxicities. The global regulatory level for the STX group toxins applied to shellfish is 800 μg/kg. The presence of TTX in shellfish is only regulated in one country; The Netherlands, with a regulatory level of 44 μg/kg. Due to the recent interest surrounding TTX in bivalves, the European Food Safety Authority established a panel to assess the risk and regulation of TTX in bivalves, and their final opinion was that a concentration below 44 μg of TTX per kg of shellfish would not result in adverse human effects. In this article, we review current knowledge on worldwide TTX levels in edible gastropods and bivalves over the last four decades, the different methods of detection used, and the current regulatory status. We suggest research needs that will assist with knowledge gaps and ultimately allow development of robust monitoring and management protocols.
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    Seasonal and spatial variations in bacterial communities from tetrodotoxin-bearing and non-tetrodotoxin-bearing clams
    (Frontiers Media S.A., 2020-08-05) Biessy, Laura; Pearman, John K; Smith, Kirsty F; Hawes, Ian; Wood, Susanna
    Tetrodotoxin (TTX) is one of the most potent naturally occurring compounds and is responsible for many human intoxications worldwide. Paphies australis are endemic clams to New Zealand which contain varying concentrations of TTX. Research suggests that P. australis accumulate the toxin exogenously, The aim of this study was to identify potential bacterial TTX-producers by exploring differences in bacterial communities in two organs of P. australis: the siphon and digestive gland. Samples from the digestive glands of a non-toxic bivalve Austrovenus stutchburyi that lives amongst toxic P. australis populations were also analyzed. Bacterial communities were characterized using 16S ribosomal RNA gene metabarcoding in P. australis sourced monthly from the Hokianga Harbor, a site known to have TTXbearing clams, for 1 year, from ten sites with varying TTX concentrations around New Zealand, and in A. stutchburyi from the Hokianga Harbor. Tetrodotoxin was detected in P. australis from sites all around New Zealand and in all P. australis collected monthly from the Hokianga Harbor. The toxin averaged 150 µg kg−1 over the year of sampling in the Hokianga Harbor but no TTX was detected in the A. stutchburyi samples from the same site. Bacterial species diversity differed amongst sites (p < 0.001, F = 5.9) and the diversity in siphon samples was significantly higher than in digestive glands (p < 0.001, F = 65.8). Spirochaetaceae (4–60%) and Mycoplasmataceae (16–78%) were the most abundant families in the siphons and the digestive glands, respectively. The bacterial communities were compared between sites with the lowest TTX concentrations and the Hokianga Harbor (site with the highest TTX concentrations), and the core bacterial communities from TTX-bearing individuals were analyzed. The results from both spatial and temporal studies corroborate with previous hypotheses that Vibrio and Bacillus could be responsible for the source of TTX in bivalves. The results from this study also indicate that marine cyanobacteria, in particular picocyanobacteria (e.g., Cyanobium, Synechococcus, Pleurocapsa, and Prochlorococcus), should be investigated further as potential TTX producers.
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    Emerging HAB research issues in freshwater environments
    (Springer, 2018) Burford, Michele A; Hamilton, David P; Wood, Susanna
    Freshwater harmful algal blooms (HABs) have been a major challenge for many decades, affecting water supplies, recreational use of water and aquatic ecosystems. The blooms of most concern, and that receive the greatest research attention, are toxic cyanobacteria. Much of the research focus has been on understanding the response of cyanobacterial species and communities to environmental conditions. As cyanobacteria are prokaryotes and have relatively simple genomes, they have been the focus of molecular studies that complement traditional ecological and physiological approaches. These complementary approaches have provided new insights into understanding how cyanobacteria species respond to environmental conditions. Molecular and physiological studies are increasingly focussed on strain variability and the implications for managing and modelling blooms and toxin production. Additionally, there have been substantial advances in techniques used to measure and monitor blooms including remote sensing, pigment sensors and molecular methods. Despite the research which has improved understanding of the physiology of cyanobacteria, and an enhanced ability to measure HABs at the scales needed to link environmental drivers and blooms, there has been a less rapid development of deterministic models. Improved coordination and collaboration amongst disciplines is essential to enhance our ability to predict the timing and extent of harmful cyanobacterial blooms.
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    Current applications and technological advances in quantitative real-time PCR (qPCR): A versatile tool for the study of phytoplankton ecology
    (Elsevier, 2022) Coyne, KJ; Wang, Y; Wood, Susanna; Countway, PD; Greenlee, SM; Clementson, L; Eriksen, R; Willis, A
    This chapter presents an overview of quantitative real-time PCR (qPCR), with a focus on harmful algae blooms (HABs). It includes an overview of the technology and describes the early development of qPCR assays to detect cryptic species. A review of multispecies and ecotype- or strain-level detection approaches by qPCR is provided. This is followed by examples of qPCR to investigate factors impacting phytoplankton distributions and activities. Approaches to evaluate changes in gene expression are then presented, along with a case study investigating species-specific responses to nitrogen input. Recent advancements in qPCR are discussed, with a case study demonstrating the use of portable qPCR and a comparison to lab-based instruments, followed by a description of droplet digital PCR (ddPCR), a novel advancement in technology that resolves some key issues in the use of qPCR for environmental research and monitoring. The chapter ends with a discussion of efforts to adapt qPCR for community-based science programs, with the potential to enhance our understanding of phytoplankton ecology and improve predictive capabilities for HAB events.
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    How deeply and profoundly important blue spaces are to humans
    (Danish Architectural Press, 2023-05-19) Ryu, Soo J.; Lund, Anna Aslaug; Carstensen, Jeppe Sengupta
    Q & A with Timothy Beatley (TB) professor at the Department of Urban and Environmental Planning, School of Architecture at University of Virginia.
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    A continuum between the upland and the ocean
    (Danish Architectural Press, 2023-05-19) Ryu, Soo J.; Lund, Anna Aslaug; Carstensen, Jeppe Sengupta
    Interview with Susannah Drake (SD), founder of DLand Studio and adjunct professor at the Cooper Union for the Advancement of Science and Art.
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    Imagining diverse futures
    (Danish Architectural Press, 2023-06) Letkemann, Joel Peter Weber; Baumeister, Ruth; Dayer, Carolina; Kozminska, Urszula; Laplace, Ricelli; Ryu, Soo J.; Building Diversity
    Who is the architect? explores how the figure of the architect has been constructed and challenged in recent years. Traditionally perceived as male, Western and individualistic, architects are now being urged to redefine themselves in a more diverse, inclusive manner. The publication discusses the need to challenge norms and establish caring as an essential quality in the architectural discourse. With the threat of environmental collapse and other societal challenges, the need for collective teamwork and empathy has become central in establishing a common understanding that includes all beings. Building Diversity aims to tackle these issues and explore topics on diversity and equality in the architectural field's past, present and future. The publication features thoughts and ideas from a broad range of countries and diverse perspectives on the architectural field, contributing to a wider dialogue about inclusion, intersectionality and progress. Building Diversity is not intended to provide concrete solutions but aims to stimulate discussion and open up venues for hosting dialogues pointing to possible paths and the expansion of perspectives. It is an important contribution to the ongoing conversation about diversity and equality in the architectural field.
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    Diversity in geoscience: Participation, behaviour, and the division of scientific labour at a Canadian geoscience conference
    (Canadian Science Publishing, 2018-10) King, L; MacKenzie, L; Tadaki, M; Cannon, S; McFarlane, K; Reid, D; Koppes, M; Kellett, Dawn
    Effective policies promoting diversity in geoscience require understanding of how the values and practices of the community support the inclusion of different social groups. As sites of knowledge exchange and professional development, academic conferences are important culturing institutions that can alleviate or reproduce barriers to diversity in geoscience. This study examines diversity at a 2017 geoscience conference, the joint Canadian Geophysical Union and Canadian Society of Agricultural and Forest Meteorology annual meeting, through observation of participation, presentation content, and behaviour in conference sessions. Across 256 observed presentations, women constituted 28% of speakers, whereas women of colour made up only 5%. Participation rates differed between disciplinary sections, with the most populous sessions (Hydrology and Earth Surface) having the lowest percentage of women. Examination of presentation content reveals that the methods and scholarly contributions of both women and people of colour differed from the majority, suggesting an intellectual division of labour in geoscience. Examination of audience behaviours between presenters reveals how a “chilly climate” can be experienced by women and other marginalized demographics in conferences. We argue that there is more to be done than simply increasing numbers of women or other minorities in geoscientific spaces, and we suggest pathways to making geoscience a more inclusive and democratic pursuit.
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    Generative AI and case teaching in horticultural education: Advantages, challenges and ethics
    (2025) Rombach, Meike
    I facilitate innovative case-based teaching in horticulture by strategically integrating generative AI to enhance student engagement with real-world scenarios. Through structured comparative analysis between AI-generated and scholarly outputs, students develop critical evaluation skills whilst gaining hands-on experience with data analysis and case memo writing. Our evidence-based approach demonstrates the importance of equitable AI access and thoughtful implementation, offering transferable insights for case teaching across disciplines.
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    Exposure of Proso millet starch to superheated steam: Effect on physicochemical, techno-functional, rheological behavior, digestibility, and related mechanism
    (Elsevier, 2025-03-15) Karmakar, M; Kheto, A; Sehrawat, R; Kumar, Y; Gul, K; Routray, W; Kumar, Lokesh
    In the present study, proso millet starch (PMS) was treated with SHS (120–160 °C for 1–5 min) to investigate the molecular interactions and techno-functional, rheological, and digestible properties. Exposure to SHS induced the degradation of helical structure, and longer chains, reducing amylose, blue value, optical density, and relative crystallinity. Meanwhile, SHS treatment might have introduced hydro‑carbonyl groups, eventually increasing water absorption capacity, swelling power, and transparency. As per SEM images, SHS-treated PMS had rough and irregular polygon surfaces with small pinholes. Compared to control, SHS treatment slightly improved the elastic nature of PMS samples. Furthermore, SHS treatment at 140 and 160 °C for 3 and 5 min increased the slowly digestible and resistant starch content. Multivariate analysis suggests that SHS treatment could be performed at 140 °C for 3 min to modify the PMS.
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    Events and wellbeing research: Key arguments, gaps and future directions
    (Cognizant Communication Corporation, 2023-01-23) Walters, Trudie
    This note reviews the wellbeing research published in Event Management since 2000. It starts by discussing what is meant by wellbeing, then presents an analysis of themes and trends centred around questions of whose wellbeing, what wellbeing, and how to approach wellbeing. Interest in the topic has increased in the last five years. A range of theoretical approaches and methodologies have been adopted, demonstrating interdisciplinarity. In recent times, conceptual frameworks have been developed within event studies as the subject matures. However, studies have centred on the subjective wellbeing benefits of events in an individual, white, Western, non-disabled context, with sports events dominating. There is a need for research that investigates: non-Western understandings and perspectives, including those of Indigenous peoples; the wellbeing benefits of events for a wider range of stakeholders; a broader range of both event and wellbeing types; and longitudinal studies on the longevity of wellbeing benefits.
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    Examining the value realization of ecological agricultural products in China: A tripartite evolutionary game analysis
    (Elsevier BV, 2025-02) Dong, J; Chen, J; Zhang, Y; Cong, Lei; Dean, David; Wu, Q
    Agricultural products are essential for nutrition and food security, particularly in China where agricultural production capacity is growing steadily. Despite the benefits of Ecological Agricultural (EA) products, including environmental protection and enhanced consumer utility, their widespread adoption and maximization of value are impeded by various factors. This study explores the intricate tripartite relationship – government, agribusiness, and consumer, in the value realization of EA products in China by establishing an evolutionary game model. The purpose is to illuminate the evolution of system equilibrium strategies across various scenarios and examine how significant external factors influence these strategies, thereby summarizing the evolutionary process of EA products' value realization and providing guidance for stakeholders' decision-making processes. The results indicate that with increased government regulatory efforts, technological advancements, and scale expansion in agribusiness, as well as the refinement of market mechanisms, the production cost of EA products decreases, leading to a steady rise in EA product prices and economic benefits for consumers purchasing them. Ultimately, the value of EA products was primarily realized through market forces. Simulation analysis using Matlab further validated the model's effectiveness and precision, highlighting the influence of government regulatory measures, consumer green sensitivity and preferences, and product base value on system equilibrium strategies. These conclusions provide insights for policymakers to facilitate the realization of EA product value and promote green and low-carbon agricultural development.
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    ‘A shared vision and a common enemy’: Reframing narratives of crisis and climate politics through Aotearoa's COVID-19 response and recovery
    (Wiley, 2024) Cretney, Raven; White, I
    The COVID-19 pandemic catalysed a time of significant upheaval and change at multiple levels of politics and society. Early on, connections were made with the climate crisis. This featured strongly in global calls for a green recovery and the opportunities for pandemic stimulus to spur co-benefits with climate action. Highlighting the global and cascading nature of crises in the Anthropocene, the pandemic provided an opportunity to shed light on the political and societal determinants of multiple crises and the often temporary hopes for transformation that arise in their wake. While there is much literature on how crises provide these ‘windows of opportunity’ for attention and resources, there is much less attention on how the experience of, and discourses associated with, an emergent crisis reframe the politics of more chronic ones. This paper uses an analysis of media articles released during the pandemic in Aotearoa New Zealand to analyse the ways that COVID-19 reframed narratives relating to climate change politics in four key ways: the possibilities for collective action, the need for greater ambition, threats to progress and premonitions of future crises. We argue that these new narratives offer insights into how the place-specific experience and response to one crisis can reframe another, and which narratives may become elevated or obscured. In doing so, we demonstrate how the pandemic acted as more than a window of opportunity, becoming a temporary catalyst for new framings of the climate crisis and crisis-driven political change more generally.
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    Identifying and classifying broader scale of disaster impacts to better inform disaster management policies and practice
    (Springer Nature, 2024) Tennakoon, KP; Serrao-Neumann, S; Cretney, Raven
    Disasters are often assessed by factors such as their magnitude, severity and impact on affected communities. Typically, disaster management policies are largely informed by learnings from large-scale disasters. Many studies, however, have shown that cumulative smaller scale disaster impacts have similar outcomes comparable to larger scale disasters. This indirectly contributes to a lack of consistency in and paucity of data related to both smaller-scale disasters and their associated cumulative impacts. This paper argues that greater attention needs to be paid to collecting disaster impact data on a range of disaster-scale events along with their cumulative impacts to better inform disaster management policies and practice. The paper aims to test the hypothesis that a better understanding of a wide range of disaster scale types and their impacts on communities, including small-scale disasters, enables the development of more just, consistent and equitable disaster management policies and practice. Analysing economic costs, evacuation and rainfall data from past flood events that affected Aotearoa-New Zealand over the last three decades, the paper found discrepancies and lack of coherence in disaster data collection and reporting, along with a predominant reliance on rainfall intensity data for disaster risk reduction and planning. The findings also confirmed the importance of identifying economic damages for a range of disaster scales, including those from small-scale disasters. This highlights the need for developing a spectrum to better classify and identify disaster impacts based on various spatial and temporal contexts. The paper concludes by affirming that such database would provide much needed evidence for developing a methodology that enables the identification of the level of disaster impacts; thereby guiding the implementation of more just, consistent and equitable disaster management policies and practice.
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    Stochasticity in chiral symmetry breaking
    (Springer Nature, 2025-02-11) Kulasiri, Don
    We explore stochastic behavior in chemical transformations far from equilibrium in this chapter. We build on the mathematical machinery developed so far to study the role of noise in these transformations. By using a case study of chiral symmetry breaking, we show distinct changes in the system behavior in the presence of noise.
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    Numerical investigations of WSDEs in chemical transformations
    (Springer Nature, 2025-02-11) Kulasiri, Don
    We develop numerically approximate solutions of WSDEs in this chapter. We follow the theoretical framework briefly presented in Chap. 5 and extend it to the applications in chemical reactions in noisy systems. We study several WSDEs which model different reactions often with multiplicative noise. The Mathematica® codes for the solutions are given in the appendices.
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    An investigation of deterministic chemical reactions and their stability
    (Springer Nature, 2025-02-11) Kulasiri, Don
    In this chapter, we discuss deterministic chemical reactions in the closed and open systems. We attempt to understand the stability of stationary states in both situations using the excess entropy production, which we discuss in Chap. 1. Then we investigate the behavior of the reactions using numerical solutions. We use three examples to illustrate that the deterministic formulations of chemical reactions lead to complex behavior patterns even without potential noise in systems. In open systems, reactions can easily be oscillatory depending on the reaction rate coefficients and initial conditions. However, the existence of nonequilibrium stationary states (NESSs) in dissipative structures is well documented, the analysis presented here is heuristic to show the complexities prior to delving into stochastic situations in next two chapters.