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Advancing the environmental DNA and RNA toolkit for aquatic ecosystem monitoring and management
No full textThe application of environmental DNA (eDNA) and RNA (eRNA) technologies to aquatic ecosystem monitoring and management has increased rapidly in the last decade. These methods are providing many new and exciting opportunities for enhanced biodiversity assessment, ecological health evaluation, and species detection. This special issue of PeerJ Life and Environment brings together 20 innovative studies that collectively advance the eDNA toolkit. Four key themes are covered: (i) Methodological advancements, (ii) Ecological health assessments and biomonitoring, (iii) Species detection, and (iv) Application and management. The studies cover a suite of topics including; optimizing sample collection, developing species-specific assays, evaluating bioindicator species, assessing microbial activity, and biodiversity monitoring in diverse freshwater and marine habitats. Emerging applications, such as the use of genome skimming to identify new fish markers, showcase the many new advancements in this field. The studies in this issue also highlight challenges, including the need for standardized protocols and ethical considerations that must be addressed before these tools can be implemented or adopted for decision making at national or global scales. Together, these contributions demonstrate the transformative potential of environmental nucleic acids’ technologies for advancing aquatic conservation and management. By bridging methodological rigor with applied research, the studies in this special issue provide an important resource for researchers, policymakers, and practitioners committed to sustainable aquatic ecosystem stewardship
Trialling the SmartWorm® application in New Zealand sheep farms
No full textGastrointestinal nematodes (GIN) remain a major health and productivity challenge for grazing livestock globally, including New Zealand where widespread anthelmintic resistance has been reported. This was a pilot study evaluating the effectiveness of SmartWorm®, an app-based decision-support tool for Targeted Selective Treatment (TST) of internal parasites to reduce drench use without compromising lamb growth under New Zealand conditions. A total of 1738 ewe lambs across three commercial farms were allocated to either a TST or Blanket Treatment (BT) group (treated every 28 days) and monitored over a 90-day period. All animals were drenched at the start of the trial, after which BT animals received treatment at each subsequent weighing. SmartWorm was used to determine drenching need for TST animals based on individual animal performance relative to expectation. Faecal egg counts (FEC), weight gain, and treatment frequency were assessed. 2 Across all farms, TST reduced anthelmintic use by 37–57 % compared with BT, with no significant differences in liveweight gain (P = 0.510). There was a weak but significant treatment effect on FEC (P = 0.01), and a linear relationship (R =0.8951, P < 0.001 with one outlier removed) between BT group FEC and TST rate, indicating the system’s responsiveness to parasite challenge. This study demonstrates that implementing TST using this app can enable reduced anthelmintic use without compromising performance—an important step towards sustainable parasite management on New Zealand sheep farm
Make openness trusted: A case of integrating ORCID with Journals@Lincoln
No full textResearch integrity issues aren’t new. With the rising pressures for researchers to publish or perish, and fast development of technologies such as AI, how we access trusted scholarly information has become increasingly challenging. This lightning talk aims to bring awareness to the issues of research integrity. It will use the integration between ORCID and Journals@Lincoln as an example to show how we can help to uphold trust through providing validated information. ORCID stands for Open Researcher and Contributor ID, and is a free, unique, persistent identifier for researchers. ORCID also allows publishers, funders or institutions to send research information to researchers’ ORCID profiles. Journals@Lincoln provides a publishing platform for Lincoln University editors to host open access journals. The integration allows us to embed ORCID in the editorial and publication workflows to increase readers’ confidence in Journals@Lincoln and prevents research misconduct. https://journals.lincoln.ac.nz
The spatial effect of airport proximity on house prices: A quantile regression analysis for the New Zealand market
No full textThis study contributes to understanding the link between the housing market and airport location
proximity, whilst examining the entirety of the house price distribution. The research investigates
this association across four key urban areas within New Zealand proximal to an international
airport – Auckland, Wellington, Christchurch, and Queenstown. Applying hedonic and quantile
regression, the analysis reveals that proximity to airports on house prices has a heterogeneous
pricing effect. Results show that distance comprises a positive pricing effect within Auckland and
Christchurch, whereas in Wellington and Queenstown the pricing effect is negative. The quantile
regression findings further revealed differences between lower and higher priced properties value,
given distance and proximity to airports within each city region. The Christchurch region reveals
contrasting findings, showing there to be a higher positive pricing effect for higher-priced housing,
which gradually decreases when moving down the quantiles. It is argued that this higher positive
pricing for higher priced properties is due to particularities in the housing market close to
Christchurch Airport
The unfinished implications of ‘finished’ land reform: Local experiences of the Comprehensive Agrarian Reform Program in Leyte, Philippines
No full textThe Philippines’ Comprehensive Agrarian Reform Program (CARP) involved major land redistribution from 1988 to 2014. The program sought to alleviate poverty, promote rural development and social justice through land redistribution. Through qualitative inquiry, this research highlights farmer's voice and experiences throughout the implementation of CARP. Our research draws on 75 in-depth interviews and field observations on the island of Leyte in 2018 – 30 years on from CARP and 4 years after the program was officially finished. The focus of this analysis is the individual experiences of beneficiaries of CARP, who received land parcels in the 1990s under CARP. This paper argues that the seemingly ‘finished’ program has protracted and unresolved implications for local communities. We further make three specific arguments in this paper. First, that beneficiaries experience a ‘land titling and payment loop’. In this condition, beneficiaries are caught in a cyclical dilemma of needing to complete land payments to obtain imprescriptible land titles. Yet, they also need land titles to access the credit market in order to increase farm production and income that enables them to pay for the land. Second, beneficiaries continue to experience tension and conflict that result in ‘court cases, land sales, and threats of violence’, which renders many farmers landless. Lastly, we argue that CARP altered the community relationship as beneficiaries endure lasting ‘stigma and prejudice’. These conditions highlight that land tenure security extends beyond redistribution and titling and is significantly shaped by social cohesion and belonging
Characterization of proteins and phenolic compounds extracted from plant seeds press cakes and potential utilization in wine fining
No full textPress cakes, a byproduct of seed processing, are often underutilized despite their rich bioactive composition. This study investigates the potential of proteins and phenolic compounds extracted from press cakes of various plant seeds for application in wine fining. Protein fractions (albumins, globulins, prolamins, and glutenins) were characterized using SDS-PAGE, while phenolic compounds were quantified for total phenolics, tannins, and flavonoids, with antioxidant activity assessed via ABTS and DPPH assays. Sauvignon Blanc and Pinot Noir grape seeds exhibited the highest phenolic and antioxidant activities among the samples. Wine fining trials demonstrated the efficacy of extracted proteins, particularly from hazelnut and flax seeds, in reducing tannin levels in red wines, suggesting their suitability as sustainable alternatives to conventional fining agents. This study underscores the importance of upcycling plant seed press cakes, which are typically treated as waste, into value-added products, aligning with circular economy principles. By exploring sustainable uses for these byproducts, the research aims to address both environmental concerns and the demand for eco-friendly winemaking practices, paving the way for innovative and sustainable wine production methods
Exploring potential biomarkers of inflammatory disease in sheep presenting with pleurisy/pneumonia and parasitic infections : A thesis submitted in fulfilment of the requirements for the Degree of Master of Applied Science
No full textInflammatory diseases of sheep, specifically the pneumonia-pleurisy complex and parasitic infections, impact productivity, health and welfare. Infected sheep can have reduced growth rates and an increased predisposition to other infections. The immune system is a key mechanism for defending against invading pathogens, and within this system, inflammation plays a crucial role in defence. However, when inflammation becomes excessive or uncontrolled, it can compromise the ability to mount an effective immune response and cause tissue damage.
Ovine pneumonia is a respiratory disease characterised by inflammation of the lung tissue. It can progress to pleurisy, which is the inflammation of the pleura, the membranes that surround the lungs. Inflammation of the pleura can generate fibrous ‘adhesions’ between the lungs and walls of the thoracic cavity.
Parasitic infections of sheep, including nematode parasite infections, can cause inflammation of the gastrointestinal tract. This can result in the loss of condition and productivity. The effect on health is similar to that observed for pneumonia-pleurisy.
The diagnosis of pneumonia-pleurisy can be difficult, because many cases are subclinical until they develop to the stage where damage to the lungs has occurred. In New Zealand, pleurisy-affected carcasses are often only detected at slaughter, which results in the carcasses being downgraded. This results in financial loss for farmers and for the industry. Similarly, parasitic infections from nematode parasites like Teladorsagia spp. are often undetectable until clinical signs like weight-loss or decreased growth are observed. These too can cause financial loss for farmers.
This study explored potential biomarkers of inflammation that might have value in identifying sub- clinical inflammatory diseases like pneumonic-pleurisy and parasitism. The lambs investigated were selected from three separate studies, the ‘Lincoln University cohort’ (n = 33) and a ‘Parasite cohort’ (n = 6 control, n = 6 infected), which were compared to a third ‘Kaikōura cohort’ (n = 34).
All the lambs had blood samples collected to determine the concentration of four pro-inflammatory cytokines (IL-1β, TNF-α, IFN-y and IL-17A), and an inflammatory marker CRP (C-reactive protein), using commercially available enzyme-linked immunosorbent assays (ELISAs). It was hoped these kits would illustrate the inflammatory response/immune status of the sheep to distinguish animals with pneumonia-pleurisy or parasitism from non-affected animals, and to determine whether these potential biomarkers were associated with other performance measurements, including carcass weights for all three cohorts and the faecal egg count of lambs in the parasite cohort.
ELISAs are widely used to detect and quantify specific proteins, with the kits tested potentially illustrating the inflammatory status of the individual lambs. Nevertheless, ELISAs do have several limitations, including the availability of appropriate kits and whether they are effective and robust for the intended use. The results obtained with the selected ELISA kits varied across the three groups. At slaughter, 11 out of 123 lambs from the Lincoln University cohort were recorded as having pleurisy. The Lincoln University cohort lambs had detectable levels of TNF-α, IL-1β and CRP; the Parasite cohort had detectable levels of TNF-α; and the Kaikōura cohort had detectable levels of TNF-α and IL-17A. The Parasite cohort had changes in tissue derived from their abomasum, but these changes were not reflected in fluctuations in serum biomarker levels.
Collectively, the findings of this study highlighted some challenges associated with using commercially available sheep ELISA kitsets, and their ability to produce meaningful results when used on lambs. The tests are costly, both for the reagents required and because of the time associated with performing them. This suggests that in their current form they may be unfavourable as diagnostic tools. Further research into the use of the currently available ELISA kitsets is required before they have improved value as diagnostic tests in sheep
Modeling molecular level mechanisms of oxidative stress generation induced by agrochemicals in CKDu initiation
No full textOxidative stress is identified as a primary factor contributing to the failure of renal function. The excessive generation of oxidative stress is observed in CKDu patients in many experiments. Agrochemicals are identified as a major inducer of oxidative stress. Oxidative stress is induced mainly by direct generation of ROS through enzyme activation and by depleting antioxidant enzymes. To study how toxic exposure to agrochemicals alters the oxidative stress level in CKDu, a mathematical model of the body’s Redox system was developed and simulated how toxic exposure to agrochemicals, particularly arsenic toxicity, increases oxidative stress in cells. This model was employed to study how the molecular mechanisms of ROS generation are affected in CKDu. The study explores how arsenic concentration levels alter the oxidative stress levels and molecular interactions involved. The model indicates that the mitochondrial electron transport chain complex III is the primary contributor to ROS production, which needs to be validated through wet lab experiments. Sensitivity analyses on the model revealed that parameters associated with superoxide production are susceptible to perturbations. Further analysis shows that enzyme-driven reactions, especially those involving superoxide generation, catalase, and glutathione peroxidase, are crucial in governing oxidative stress generation in CKDu. According to the sensitivity analysis results, both NOX (NADPH oxidase) and SOD2 (superoxide dismutase 2) appear to be promising drug target
Comparing physics‐based, conceptual and machine‐learning models to predict groundwater levels by BMA
No full textGroundwater level observations are used as decision variables for aquifer management, often in conjunction with models to provide predictions for operational forecasting. In this study, we compare different model classes for this task: a spatially explicit 3D groundwater flow model (MODFLOW), an eigenmodel, a transfer‐function model, and three machine learning models, namely, multi‐layer perceptron models, long short‐term memory models, and random forest models. The models differ widely in their complexity, input requirements, calibration effort, and run‐times. They are tested on four groundwater level time series from the Wairau Aquifer in New Zealand to investigate the potential of the data‐driven approaches to outperform the MODFLOW model in predicting individual target wells. Further, we wish to reveal whether the MODFLOW model has advantages in predicting all four wells simultaneously because it can use the available information in a physics‐based, integrated manner, or whether structural limitations spoil this effect. Our results demonstrate that data‐driven models with low input requirements and short run‐times are competitive candidates for local groundwater level predictions even for system states that lie outside the calibration data range. There is no “single best” model that performs best in all cases, which motivates ensemble forecasting with different model classes using Bayesian model averaging. The obtained Bayesian model weights clearly favor MODFLOW when targeting all wells simultaneously, even though the competing approaches had the chance to fine‐tune for each tested well individually. This is a remarkable result that strengthens the argument for physics‐based approaches even for seemingly “simple” groundwater level prediction task
