Veterinary and Agricultural Sciences Collected Works - Research Publications
Now showing items 1-12 of 376
The New Era of Canine Science: Reshaping Our Relationships With Dogs
(Frontiers Media SA, 2021)
Canine science is rapidly maturing into an interdisciplinary and highly impactful field with great potential for both basic and translational research. The articles in this Frontiers Research Topic, Our Canine Connection: The History, Benefits and Future of Human-Dog Interactions, arise from two meetings sponsored by the Wallis Annenberg PetSpace Leadership Institute, which convened experts from diverse areas of canine science to assess the state of the field and challenges and opportunities for its future. In this final Perspective paper, we identify a set of overarching themes that will be critical for a productive and sustainable future in canine science. We explore the roles of dog welfare, science communication, and research funding, with an emphasis on developing approaches that benefit people and dogs, alike.
CD8(+) T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope display high naive precursor frequency and TCR promiscuity
(CELL PRESS, 2021-05-11)
To better understand primary and recall T cell responses during coronavirus disease 2019 (COVID-19), it is important to examine unmanipulated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cells. By using peptide-human leukocyte antigen (HLA) tetramers for direct ex vivo analysis, we characterized CD8+ T cells specific for SARS-CoV-2 epitopes in COVID-19 patients and unexposed individuals. Unlike CD8+ T cells directed toward subdominant epitopes (B7/N257, A2/S269, and A24/S1,208) CD8+ T cells specific for the immunodominant B7/N105 epitope were detected at high frequencies in pre-pandemic samples and at increased frequencies during acute COVID-19 and convalescence. SARS-CoV-2-specific CD8+ T cells in pre-pandemic samples from children, adults, and elderly individuals predominantly displayed a naive phenotype, indicating a lack of previous cross-reactive exposures. T cell receptor (TCR) analyses revealed diverse TCRαβ repertoires and promiscuous αβ-TCR pairing within B7/N105+CD8+ T cells. Our study demonstrates high naive precursor frequency and TCRαβ diversity within immunodominant B7/N105-specific CD8+ T cells and provides insight into SARS-CoV-2-specific T cell origins and subsequent responses.
High expression of CD38 and MHC class II on CD8+ T cells during severe influenza disease reflects bystander activation and trogocytosis
Although co-expression of CD38 and HLA-DR on CD8 + T cells reflects activation during influenza, SARS-CoV-2, Dengue, Ebola and HIV-1 viral infections, high and prolonged CD38 + HLA-DR + expression can be associated with severe and fatal disease outcomes. As the expression of CD38 + HLA-DR + is poorly understood, we used mouse models of influenza A/H7N9, A/H3N2 and A/H1N1 infection to investigate the mechanisms underpinning CD38 + MHC-II + phenotype on CD8 + T-cells. Our analysis of influenza-specific immunodominant D b NP 366 +CD8 + T-cell responses showed that CD38 + MHC-II + co-expression was detected on both virus-specific and bystander CD8 + T-cells, with increased numbers of both CD38 + MHC-II + CD8 + T-cell populations observed in the respiratory tract during severe infection. To understand the mechanisms underlying CD38 and MHC-II expression, we also used adoptively-transferred transgenic OT-I CD8 + T-cells recognising the ovalbumin-derived K b SIINFEKL epitope and A/H1N1-SIINKEKL infection. Strikingly, we found that OT-I cells adoptively-transferred into MHC-II −/− mice did not display MHC-II after influenza virus infection, suggesting that MHC-II was acquired via trogocytosis in wild-type mice. Additionally, detection of CD19 on CD38 + MHC II + OT-I cells further supports that MHC-II was acquired by trogocytosis, at least partially, sourced from B-cells. Our results also revealed that co-expression of CD38 + MHC II + on CD8 + T-cells was needed for the optimal recall ability following secondary viral challenge. Overall, our study provides evidence that both virus-specific and bystander CD38 + MHC-II + CD8 + T-cells are recruited to the site of infection during severe disease, and that MHC-II expression occurs via trogocytosis from antigen-presenting cells. Our findings also highlight the importance of the CD38 + MHC II + phenotype for CD8 + T-cell memory establishment and recall. <h4>Summary</h4> Co-expression of CD38 and MHC-II on CD8 + T cells is recognized as a classical hallmark of activation during viral infections. High and prolonged CD38 + HLA-DR + expression, however, can be associated with severe disease outcomes and the mechanisms are unclear. Using our established influenza wild-type and transgenic mouse models, we determined how disease severity affected the activation of influenza-specific CD38 + MHC-II + CD8 + T cell responses in vivo and the antigenic determinants that drive their activation and expansion. Overall, our study provides evidence that both virus-specific and bystander CD38 + MHC-II + CD8 + T-cells are recruited to the site of infection during severe disease, and that MHC-II expression occurs, at least in part, via trogocytosis from antigen-presenting cells. Our findings also highlight the importance of the CD38 + MHC II + phenotype for CD8 + T-cell memory establishment and recall.
Pulse Root Ideotype for Water Stress in Temperate Cropping System
Pulses are a key component of crop production systems in Southern Australia due to their rotational benefits and potential profit margins. However, cultivation in temperate cropping systems such as that of Southern Australia is limited by low soil water availability and subsoil constraints. This limitation of soil water is compounded by the irregular rainfall, resulting in the absence of plant available water at depth. An increase in the productivity of key pulses and expansion into environments and soil types traditionally considered marginal for their growth will require improved use of the limited soil water and adaptation to sub soil constrains. Roots serve as the interface between soil constraints and the whole plant. Changes in root system architecture (RSA) can be utilised as an adaptive strategy in achieving yield potential under limited rainfall, heterogenous distribution of resources and other soil-based constraints. The existing literature has identified a "'Steep, Deep and Cheap" root ideotype as a preferred RSA. However, this idiotype is not efficient in a temperate system where plant available water is limited at depth. In addition, this root ideotype and other root architectural studies have focused on cereal crops, which have different structures and growth patterns to pulses due to their monocotyledonous nature and determinant growth habit. The paucity of pulse-specific root architectural studies warrants further investigations into pulse RSA, which should be combined with an examination of the existing variability of known genetic traits so as to develop strategies to alleviate production constraints through either tolerance or avoidance mechanisms. This review proposes a new model of root system architecture of "Wide, Shallow and Fine" roots based on pulse roots in temperate cropping systems. The proposed ideotype has, in addition to other root traits, a root density concentrated in the upper soil layers to capture in-season rainfall before it is lost due to evaporation. The review highlights the potential to achieve this in key pulse crops including chickpea, lentil, faba bean, field pea and lupin. Where possible, comparisons to determinate crops such as cereals have also been made. The review identifies the key root traits that have shown a degree of adaptation via tolerance or avoidance to water stress and documents the current known variability that exists in and amongst pulse crops setting priorities for future research.
Integrating crop modelling and production economics to investigate multiple nutrient deficiencies and yield gaps
A method is described for integrating crop modelling and production economics to quantify optimum applications of multiple nutrients and yield gaps. The method is demonstrated for crop production in the high‐rainfall zone of southern Australia. Data from a biophysical crop model were used to overcome the persistent problem of inadequate experimental data. The Mitscherlich function was expanded to accommodate four variable inputs – nitrogen, phosphorus, potassium and sulphur – and the expansion path was used to determine the economic optimum application of all four nutrients. Modelling revealed the state‐contingent yield potential and the extent to which unrealised yield could be explained by profit‐maximising behaviour and risk‐aversion by growers. If growers and their advisors were guided by the methods described, they would be better equipped to assess crop nutrient demands and limitations, predict yield potential, additional profit and the risks associated with high input systems in a variable climate. If scientists were more aware of the extra profits and the risks involved (as well as the quantitative relationships between inputs and outputs) when thinking about what to produce and how to do so, they would be more circumspect about the net benefits to be obtained from closing yield gaps.
Carbon sink strength of nodules but not other organs modulates photosynthesis of faba bean (Vicia faba) grown under elevated [CO2] and different water supply
Photosynthetic stimulation by elevated [CO2 ] (e[CO2 ]) may be limited by the capacity of sink organs to use photosynthates. In many legumes, N2 -fixing symbionts in root nodules provide an additional sink, so that legumes may be better able to profit from e[CO2 ]. However, drought not only constrains photosynthesis but also the size and activity of sinks, and little is known about the interaction of e[CO2 ] and drought on carbon sink strength of nodules and other organs. To compare carbon sink strength, faba bean was grown under ambient (400 ppm) or elevated (700 ppm) atmospheric [CO2 ] and subjected to well-watered or drought treatments, and then exposed to 13 C pulse-labelling using custom-built chambers to track the fate of new photosynthates. Drought decreased 13 C uptake and nodule sink strength, and this effect was even greater under e[CO2 ], and was associated with an accumulation of amino acids in nodules. This resulted in decreased N2 fixation, and increased accumulation of new photosynthates (13 C/sugars) in leaves, which in turn can feed back on photosynthesis. Our study suggests that nodule C sink activity is key to avoid sink limitation in legumes under e[CO2 ], and legumes may only be able to achieve greater C gain if nodule activity is maintained.
Dietary Uptake and Depuration Kinetics of Perfluorooctane Sulfonate, Perfluorooctanoic Acid, and Hexafluoropropylene Oxide Dimer Acid (GenX) in a Benthic Fish
Per‐ and poly‐fluoroalkyl substances (PFAS) are ubiquitously distributed throughout aquatic environments and can bioaccumulate in organisms. We examined dietary uptake and depuration of a mixture of 3 PFAS: perfluorooctanoic acid (PFOA; C8HF15O2), perfluorooctane sulfonate (PFOS; C8HF17SO3), and hexafluoropropylene oxide dimer acid (HPFO‐DA; C6HF11O3; trade name GenX). Benthic fish (blue spot gobies, Pseudogobius sp.) were fed contaminated food (nominal dose 500 ng g–1) daily for a 21‐d uptake period, followed by a 42‐d depuration period. The compounds PFOA, linear‐PFOS (linear PFOS), and total PFOS (sum of linear and branched PFOS) were detected in freeze‐dried fish, whereas GenX was not, indicating either a lack of uptake or rapid elimination (<24 h). Depuration rates (d–1) were 0.150 (PFOA), 0.045 (linear‐PFOS), and 0.042 (linear+branched‐PFOS) with corresponding biological half‐lives of 5.9, 15, and 16 d, respectively. The PFOS isomers were eliminated differently, resulting in enrichment of linear‐PFOS (70–90%) throughout the depuration period. The present study is the first reported study of GenX dietary bioaccumulation potential in fish, and the first dietary study to investigate uptake and depuration of multiple PFASs simultaneously, allowing us to determine that whereas PFOA and PFOS accumulated as expected, GenX, administered in the same way, did not appear to bioaccumulate.
Detection of Helminth Ova in Wastewater Using Recombinase Polymerase Amplification Coupled to Lateral Flow Strips
<jats:p>Ascaris lumbricoides is a major soil-transmitted helminth that is highly infective to humans. The ova of A. lumbricoides are able to survive wastewater treatment, thus making it an indicator organism for effective water treatment and sanitation. Hence, Ascaris ova must be removed from wastewater matrices for the safe use of recycled water. Current microscopic techniques for identification and enumeration of Ascaris ova are laborious and cumbersome. Polymerase chain reaction (PCR)-based techniques are sensitive and specific, however, major constraints lie in having to transport samples to a centralised laboratory, the requirement for sophisticated instrumentation and skilled personnel. To address this issue, a rapid, highly specific, sensitive, and affordable method for the detection of helminth ova was developed utilising recombinase polymerase amplification (RPA) coupled with lateral flow (LF) strips. In this study, Ascaris suum ova were used to demonstrate the potential use of the RPA-LF assay. The method was faster (< 30 min) with optimal temperature at 37 °C and greater sensitivity than PCR-based approaches with detection as low as 2 femtograms of DNA. Furthermore, ova from two different helminth genera were able to be detected as a multiplex assay using a single lateral flow strip, which could significantly reduce the time and the cost of helminth identification. The RPA-LF system represents an accurate, rapid, and cost-effective technology that could replace the existing detection methods, which are technically challenged and not ideal for on-site detection in wastewater treatment plants.</jats:p>
Fusion of Spectral and Structural Information from Aerial Images for Improved Biomass Estimation
<jats:p>Efficient, precise and timely measurement of plant traits is important in the assessment of a breeding population. Estimating crop biomass in breeding trials using high-throughput technologies is difficult, as reproductive and senescence stages do not relate to reflectance spectra, and multiple growth stages occur concurrently in diverse genotypes. Additionally, vegetation indices (VIs) saturate at high canopy coverage, and vertical growth profiles are difficult to capture using VIs. A novel approach was implemented involving a fusion of complementary spectral and structural information, to calculate intermediate metrics such as crop height model (CHM), crop coverage (CC) and crop volume (CV), which were finally used to calculate dry (DW) and fresh (FW) weight of above-ground biomass in wheat. The intermediate metrics, CHM (R2 = 0.81, SEE = 4.19 cm) and CC (OA = 99.2%, Κ = 0.98) were found to be accurate against equivalent ground truth measurements. The metrics CV and CV×VIs were used to develop an effective and accurate linear regression model relationship with DW (R2 = 0.96 and SEE = 69.2 g/m2) and FW (R2 = 0.89 and SEE = 333.54 g/m2). The implemented approach outperformed commonly used VIs for estimation of biomass at all growth stages in wheat. The achieved results strongly support the applicability of the proposed approach for high-throughput phenotyping of germplasm in wheat and other crop species.</jats:p>