@prefix dcat: . @prefix dct: . @prefix foaf: . @prefix vcard: . @prefix xsd: . a dcat:Dataset ; dct:description """The myrtle rust and kauri dieback spaces desperately need a suite of fully integrated management tools and approaches to saving our ngahere (forest).\r \r To this end, Ngā Rākau Taketake is investing in research and related activities in the field of Tools and Technologies for Detection and Management. \r \r This team has used an extensive outreach process to socialise new technologies, assess important values and concerns, and ensure research, operations and case studies are integrated.\r \r __Theme Co-leads:__\r \r - David Milner, Kahu Environmental \r \r - Marion Wood, Plant and Food Research""" ; dct:identifier "73cdc842-c015-4f9d-99cd-5edf58c54834" ; dct:issued "2023-11-06T21:21:27.778880"^^xsd:dateTime ; dct:modified "2025-01-27T02:19:56.686759"^^xsd:dateTime ; dct:publisher ; dct:title "Control, Protect, Cure" ; dcat:contactPoint [ a vcard:Organization ; vcard:hasEmail ] ; dcat:distribution , , , , , , , , , , , , , , , , , , , , , , , . a dcat:Distribution ; dct:description """###The soil microbiota associated with New Zealand’s kauri (*Agathis australis*) forests under threat from dieback disease###\r \r **June 2021**\r \r **Byers A. 2021. [The soil microbiota associated with New Zealand’s kauri (*Agathis australis*) forests under threat from dieback disease.](https://researcharchive.lincoln.ac.nz/bitstreams/9fcb8bd0-7fe3-486a-9a37-82f1dcf704fd/download) Unpublished Doctoral thesis, Lincoln University. 194 p. **\r \r **ABSTRACT**\r \r The primary aim of this research was to characterise the taxonomic diversity of the kauri soil microbiota and their response to dieback, whilst screening members of the soil microbiota against *P. agathidicida* to test their potential to inhibit the pathogen. A secondary aim was to quantify differences in soil microbiota between kauri and adjacent pine (*Pinus radiata*).\r \r **KEYWORDS**\r \r *Phytophthora agathidicida*;\r *Agathis australis*;\r kauri dieback;\r soil microbiota;\r disease suppressive soils;\r microbial ecology;\r forest pathology;\r forest disturbance;\r functional gene analysis;\r seedling infection study;\r phospholipid fatty acid (PLFA) analysis;\r in vitro screening;\r *Burkholderia*;\r *Penicillium*;\r microbial antagonism""" ; dct:issued "2024-02-16T02:51:01.647020"^^xsd:dateTime ; dct:modified "2024-02-16T02:51:01.647020"^^xsd:dateTime ; dct:title "THESIS: Soil microbiota associated with kauri forests" ; dcat:accessURL . a dcat:Distribution ; dct:description """###AI structural modelling and peptides - A Proof-of-Concept step to prepare for novel lateral flow tools that detect myrtle rust or kauri dieback with specificity by design###\r \r **May 2024**\r \r **Sun X, Rikkerink E. 2024. AI structural modelling and peptides - A Proof-of-Concept step to prepare for novel lateral flow tools that detect myrtle rust or kauri dieback with specificity by design. A Plant & Food Research report prepared for: Biological Heritage, Ngā Rākau Taketake Theme 5 Control, Protect, Cure. Milestone No.102185. Contract No. 39454 Var 2. Job code: P/313069/13. PFR SPTS No. 25595. 10 p. **\r \r **NOTE** \r \r This report is embargoed until 31/05/2025. For further information please contact Xiaolin Sun at Plant and Food Research: [Xiaolin.Sun@plantandfoodresearch.co.nz](mailto:Xiaolin.Sun@plantandfoodresearch.co.nz)\r \r **ABSTRACT**\r \r __Background__ \r \r Lateral flow devices to detect pathogens are becoming increasingly common. They are easy to deploy, stable, rapid, and relatively cheap and they have economies of scale as well. One of the biggest problems with lateral flow devices is that they are typically based on monoclonal antibodies that act as “binding agents” to the “target” organism, but also often bind other closely related organisms. As antibodies are not really designed, but created by random processes and then selected based on their ability to bind a target, finding an antibody that both binds well AND is specific is often a difficult, time-consuming and costly task; it involves screening of a large panel of potential candidates before an applicable one is found. The crux of our idea is to avoid the need for generating antibodies and move to trial “designed peptides” as the “binding agents” on lateral flows instead of antibodies. One remaining advantage of antibodies, however, is that they have multiple binding sites and when more than one site binds to the target, this creates a cooperative binding scenario that leads to the highest possible binding strengths. Single peptides may not be able to match these binding strengths. Our idea is to design a pair of peptides that bind to distinct parts of the target, and see if this can lead to similar cooperative binding advantages for peptides.\r Antibodies have been widely used in lateral flow tests to detect particular target analyte proteins or protein fragments. A stable and strongly binding antibody with high specificity is needed to obtain a high-quality test strip. However, this is the bottleneck of the production in terms of the excessive cost as well as time of making a suitable antibody. One of the properties of antibodies that makes them such a good binding reagent in immune systems is that they are made up of several variable sites. The natural process of antibody generation creates a large number of variations at these sites that are then combined to create a large pool of differential binding affinities. From this pool, antibodies that bind well to the foreign protein targets detected are ultimately selected and then amplified to protect the host. When more than one variable region binds the target, the strength and selectivity of the binding are both increased through co-operative binding effects at two or more of these variable sites.\r \r __Project Origin and Scope__\r \r We have been working on constructing peptides that bind to known targets. In one case we have used the recent boon in predicted protein structures that flow from structural prediction Artificial Intelligence (AI) programmes, such as AlphaFold2 (AF2). We propose to use these tools as a proof-of-principle to test the idea of whether we can significantly improve binding strength to the target by using two binding peptides together. We have a test bed machine that we use to assess peptide binding kinetics (the BiacoreX100) and also have existing antibodies that bind to the same target that we can compare with the two-peptide approach.\r We put forward here an innovative idea to replace binding antibodies with peptides produced from scratch based on AI-generated AF2 structural protein models of relevant protein target(s) such as surface proteins in the kauri dieback disease agent *Phytophthora agathidicida*. AF2 models have now been generated for many proteins in public databases and we expect more to be generated over time. Our AF2 modelling research with a particular pair of proteins that interact in planta as well as in the AI-predicted models has suggested that we may be able to design peptides from these models that will bind their protein binding target. In our model, a series of alpha helices from one protein bound our target plant protein RIN4. We sought to first demonstrate that peptides that produce two of these helices could be used to bind to this protein target, and then secondly to test if we could combine (or “multiplex”) the two peptides together. This two-peptide approach would be tested to determine if it could mimic improved co-operative binding, analogous to the way many useful antibodies show this effect. This proof-of-concept project used the information, tools, protein extracts and data we already had for the interacting protein pair, but was extended to include the idea of a two-peptide system and the use of AI models to assess their binding potential. This concept could potentially be extended to include single proteins for which AF2 models exist, using internal, interacting secondary structures such as alpha helices and beta sheets in the AF2 structure predictions.\r \r __Project Aims__ \r \r If our approach proves successful, we will have a way to computationally create multiplexed-binding reagents for any protein with predicted structural data to replace the “trial and error prone”, wet laboratory approach of antibody generation. Such a “design-based approach” would potentially revolutionise the creation of detection systems for particular organisms or proteins such as lateral flow devices that currently rely on having a high-quality antibody binding reagent made from costly procedures including animal facilities. Our first proposed target for this novel technology would be *Phytophthora agathidicida*, as soon as sufficient high-quality genome and gene curation data are available to identify likely surface-exposed proteins and to generate the required AF2 models.\r \r __Results Summary__\r \r Our initial results demonstrated that the two peptides we generated could bind the target protein if that protein were bound to a chip used in our BiacoreX100 test system. Initial tests to repeat the assay with the peptides bound to such chips were not successful, and we now have a probable explanation for this result. We surmise the linkers we used to attach these peptides were not long enough and thus far enough away from the surface of the chip to allow the protein target to fold into its recognising protein shape and bind. This inability of the peptides to bind their target thus prevented us from assaying co-operative binding, which we were intending to demonstrate by increased binding affinity to mixtures of the two peptides bound to chips (when compared with the peptides by themselves).\r \r This research was funded by the Ministry of Business, Innovation and Employment (Ngā Rākau Taketake – Myrtle Rust and Kauri Dieback Research, C09X1817).\r \r """ ; dct:issued "2024-05-24T01:34:43.886287"^^xsd:dateTime ; dct:modified "2024-05-24T01:34:43.886287"^^xsd:dateTime ; dct:title "SI6 REPORT: Next Generation Lateral Flow Tests " . a dcat:Distribution ; dct:description """###Control, Protect, Cure 2021###\r \r **June 2021**\r \r **Akariro Films. 2021. Control, Protect, Cure - Video for Kaurilands Summit 2021. YouTube, BioHeritage Challenge.**\r \r **ABSTRACT**\r \r This video directed by Ngāriki Ngatae (Akaririo Films) was screened at the online Kaurilands Summit 2021.""" ; dct:issued "2024-06-06T22:34:37.826964"^^xsd:dateTime ; dct:modified "2024-06-06T22:34:37.826964"^^xsd:dateTime ; dct:title "VIDEO: Control, Protect, Cure 2021" ; dcat:accessURL . a dcat:Distribution ; dct:description """###The Fatty Acid Methyl Ester (FAME) profile of *Phytophthora agathidicida* and its potential use as diagnostic tool###\r \r **September 2021**\r \r **Lacey RF, Sullivan-Hill BA, Deslippe JR, Keyzers RA, Gerth ML. 2021. [The Fatty Acid Methyl Ester (FAME) profile of *Phytophthora agathidicida* and its potential use as diagnostic tool.](https://academic.oup.com/femsle/article-pdf/368/17/fnab113/40331050/fnab113.pdf) FEMS Microbiology Letters 368(17). **\r \r **ABSTRACT** \r \r In New Zealand, *Phytophthora agathidicida* is threatening the survival of kauri, an endemic, culturally and ecologically important tree species. The current\r method for detection is time-consuming and requires high levels of expertise to\r assess, thus limiting the analytical sample throughput. Here, we characterized the fatty acid methyl ester (FAME) profile of *P. agathidicida* and compared it with the FAME profile of *P. cinnamomi* to assess the efficacy of FAME analysis as a\r diagnostic tool for detecting the pathogen in soil samples.\r \r **KEYWORDS**\r \r *Phytophthora*; *Phytophthora agathidicida*; diagnostics; fatty acid methyl ester analysis""" ; dct:issued "2024-01-22T01:57:09.091810"^^xsd:dateTime ; dct:modified "2024-01-22T01:57:09.091810"^^xsd:dateTime ; dct:title "PAPER: Fatty Acid Methyl Ester (FAME) profile" ; dcat:accessURL . a dcat:Distribution ; dct:description """###NRT Tools for Detection RA1A: - Microfluidic cytometer biosensor platform for novel detection of *Phytophthora agathidicida*###\r \r **March 2024**\r \r **Zhang P, Williams D, Travas-Sejdic J. 2024. NRT Tools for Detection RA1A: - Microfluidic cytometer biosensor platform for novel detection of *Phytophthora agathidicida*. 10 p. **\r \r **NOTE**\r \r This report is not available online. Please contact Dr. Marion Wood to request further details: [Marion.Wood@plantandfood.co.nz](mailto:Marion.Wood@plantandfood.co.nz)\r \r **ABSTRACT**\r \r In this work, we developed an innovative and effective solution for detecting zoospores, integrating electrochemical sensing with microfluidic chips. To optimize the device design and deepen our comprehension of the sensing process, we conducted finite element simulations of electrical signals, passive flow and attractant diffusion. We designed and fabricated our microfluidic sensor based on the knowledge we learned from the simulation. In the sensing test, the sensor demonstrated remarkable sensitivity, yielding high signal-to-noise ratio outputs upon the passing of zoospores. We demonstrated that the device could be used in-field. This sensing system holds significant potential for further development into a fully portable device, serving as a valuable tool for on-site pathogen detection applications.""" ; dct:issued "2024-04-25T23:14:54.725209"^^xsd:dateTime ; dct:modified "2024-04-25T23:14:54.725209"^^xsd:dateTime ; dct:title "RA1A REPORT: Microfluidic cytometer biosensor platform" . a dcat:Distribution ; dct:description """###Cultural monitoring tools: A mana whenua narrative###\r \r **March 2024**\r \r **Reihana K. 2024. Cultural monitoring tools: A mana whenua narrative. 20 p. **\r \r **ABSTRACT**\r \r This report reflects the narrative captured whilst developing and trialing a cultural monitoring survey tool for the Ngā Rākau Taketake Theme, Control Protect, Cure; Cultural monitoring tools project. The development of the tool process and the feedback from the field trials with 6 hapū within the 3 case study regions is summarised here. This report documents the development process which was conducted in 2021 to 2023.""" ; dct:issued "2024-04-24T00:26:02.149883"^^xsd:dateTime ; dct:modified "2024-04-24T00:26:02.149883"^^xsd:dateTime ; dct:title "RA3B REPORT: Cultural Monitoring Tools" ; dcat:accessURL ; dcat:byteSize 2523924.0 ; dcat:mediaType "application/pdf" . a dcat:Distribution ; dct:description """### Why understanding the biology of *Phytophthora agathidicida* matters###\r \r **May 2023**\r \r **Vink JNA. 2023. Why understanding the biology of *Phytophthora agathidicida *matters. Kaurilands Summit 2023, Whangārei, New Zealand, 11/05/2023.**\r \r """ ; dct:issued "2024-08-29T20:06:31.505393"^^xsd:dateTime ; dct:modified "2024-08-29T20:06:31.505393"^^xsd:dateTime ; dct:title "RA3A PRESENTATION: Understanding Phytophthora agathidicida biology" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Control, Protect, Cure 2022###\r \r **June 2022**\r \r **Akariro Films. 2022. Control, Protect, Cure - Video for Kaurilands Summit 2022. YouTube, BioHeritage Challenge. **\r \r **ABSTRACT**\r \r The ‘Control, Protect, Cure’ team have been using an extensive outreach process to develop and socialise new technologies, assess important values and concerns, and ensure research, operations and case studies are integrated effectively. \r \r Click 'play' to view what they've been up to in the first three years of the programme.\r \r This video directed by Ngāriki Ngatae (Akaririo Films) was screened at the online Kaurilands Summit 2022.\r \r This research programme is funded by Ngā Rākau Taketake, which is administered by New Zealand's Biological Heritage National Science Challenge | Ngā Koiora Tuku Iho.\r """ ; dct:issued "2024-07-22T23:06:38.360867"^^xsd:dateTime ; dct:modified "2024-07-22T23:06:38.360867"^^xsd:dateTime ; dct:title "VIDEO: Control, Protect, Cure 2022 " ; dcat:accessURL . a dcat:Distribution ; dct:description """**June 2024**\r \r A presentation by Dr Andrea Grant (Social Scientist, Scion) on mahi from the Control, Protect Cure Theme, developing a monitoring and evaluation framework that supports cultural exchange and learning between mātauranga and science knowledge systems for biosecurity tool research.""" ; dct:issued "2024-06-26T00:58:44.513699"^^xsd:dateTime ; dct:modified "2024-06-26T00:58:44.513699"^^xsd:dateTime ; dct:title "RA5 PRESENTATION: Navigating conceptual shifts" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Kauri Rescue Citizen Science Evaluation of Kauri Dieback Treatment Tools.###\r \r **March 2024**\r \r **Horner I, Barton M. 2024. Kauri Rescue Citizen Science Evaluation of Kauri Dieback Treatment Tools. p 40.**\r \r **ABSTRACT**\r \r Kauri dieback caused by *Phytophthora agathidicida* is resulting in decline and death of kauri trees throughout kaurilands. Many diseased or threatened trees are on private land, and landowners are left feeling helpless as their kauri trees decline around them. \r \r Kauri Rescue started as a citizen science project in 2016 funded by the Biological Heritage National Science Challenge, and then became a charitable trust in 2020. \r \r Supported by further Ngā Rākau Taketake funding, this research project built on previous efforts, involving private landowners in treating and monitoring diseased trees. It aimed to evaluate the effectiveness of phosphite treatments and the accuracy of data collected by participants.\r \r Participants chose one of four treatment options or left trees untreated, with phosphite concentrations of 4% or 6% injected at varying intervals around the trunk. The project targeted 500 trees with reliable baseline data from the initial 3163 trees and 109 participants. Participants collected data on their trees, with professionals auditing a sample for accuracy. This research used ordinal regression to analyse how treatments affected tree health and compared data accuracy between participants and auditors.""" ; dct:issued "2024-06-14T03:31:18.684483"^^xsd:dateTime ; dct:modified "2024-06-14T03:31:18.684483"^^xsd:dateTime ; dct:title "SI1 REPORT: Evaluation Citizen Science Treatment Tools" ; dcat:accessURL ; dcat:byteSize 2764844.0 ; dcat:mediaType "application/pdf" . a dcat:Distribution ; dct:description """###Assessing the *in planta* efficacy of oxathiapiprolin as a potential treatment for kauri dieback disease###\r \r **December 2024**\r \r **Robinson HF, Palmer JTT, Gerth ML. 2024 PREPRINT. [Assessing the in planta efficacy of oxathiapiprolin as a potential treatment for kauri dieback disease.](https://doi.org/10.1101/2024.12.01.626252) bioRxiv 2024.12.01.626252**\r \r **ABSTRACT**\r \r *Phytophthora agathidicida*, a plant pathogenic oomycete, causes fatal dieback disease in New Zealand kauri trees (*Agathis australis*). Currently, few treatments exist to prevent or cure this infection. Previous research has demonstrated the potent in vitro inhibition of multiple lifecycle stages of *P. agathidicida* by the oomycide oxathiapiprolin. In this study, we have evaluated the efficacy of oxathiapiprolin in planta as either a protective or curative treatment. Kauri seedlings (1–2 years old) were treated with 10 or 50 mg of oxathiapiprolin, in the form of Zorvec Enicade, per seedling as a soil drench either before (7 days) or after (15 days) inoculation with *P. agathidicida* NZFS 3770 to test for protective and curative activities, respectively. Results showed that oxathiapiprolin treatments successfully protected the kauri seedlings from disease, with the higher dose (50 mg) demonstrating greater efficacy. However, the treatments did not cure kauri seedlings already infected with *P. agathidicida*, likely because the infection was already well-established by the time of treatment. This study demonstrates that, while oxathiapiprolin shows protective effects against *P. agathidicida* infection in kauri seedlings, its lack of curative properties significantly limits its potential as a practical tool for managing kauri dieback disease.\r \r **KEYWORDS**\r \r oxathiapiprolin;\r *Phytophthora agathidicida*;\r *Agathis australis*;\r soil drench;\r oomycete\r \r """ ; dct:issued "2025-01-15T02:50:55.721648"^^xsd:dateTime ; dct:modified "2025-01-15T02:50:55.721648"^^xsd:dateTime ; dct:title "RA3A PAPER: Assessing efficacy of oxathiapiprolin " ; dcat:accessURL . a dcat:Distribution ; dct:description """###Robust detection of Phytophthora agathidicida: from laboratory to in-field beta testing.###\r \r **March 2024**\r \r **Broom M. 2024. Robust detection of *Phytophthora agathidicida*: from laboratory to in-field beta testing. 5 p. **\r \r **ABSTRACT**\r \r The goals of this project were to develop \r \r 1): the prototype hardware device for Phytophthora agathidicida in-field diagnostics \r \r 2): microfluidic chips with dried reagents for detecting phytophthora DNA \r \r 3): extractions of soil containing phytophthora DNA and \r \r 4): deliver a training workshop to demonstrate the prototype diagnostic tests. \r """ ; dct:issued "2024-04-23T10:11:33.720690"^^xsd:dateTime ; dct:modified "2024-04-23T10:11:33.720690"^^xsd:dateTime ; dct:title "RA1A REPORT: Robust detection of P. agathidicida" ; dcat:accessURL ; dcat:byteSize 687566.0 ; dcat:mediaType "application/pdf" . a dcat:Distribution ; dct:description """###Detection and prevention: Improving techniques to manage *Phytophthora agathidicida*, the causal agent of kauri dieback###\r \r **December 2021**\r \r **Thurston A. 2021. [Detection and prevention: Improving techniques to manage *Phytophthora agathidicida*, the causal agent of kauri dieback](https://researcharchive.lincoln.ac.nz/bitstreams/1a5784a3-b4ff-47ad-bcd3-b324dc66ef41/download). Unpublished Masters of Science thesis, Lincoln University. 202 p. **\r \r **ABSTRACT**\r \r Real-time polymerase chain reaction (qPCR) and loop-mediated isothermal amplification (LAMP) have been published as molecular detection techniques for *P. agathidicida*; however, they are not yet optimized for testing environmental samples, such as soils.\r \r In this research two experiments were conducted.\r \r 1. DNA extraction methods from the qPCR protocol were modified, with a focus on improving both cell lysis and extract purity. We then compared the efficacy of DNA recovery between a manual DNA extraction method and two commercial DNA extraction kits.\r Despite efforts to reduce the co-precipitation of humic acids with DNA, extract purity remained too compromised for downstream analysis without the use of a commercial clean-up kit. *P. agathidicida* was detected in all manually extracted samples, whereas detection with commercial extraction kits was inconsistent.\r   \r \r 2. The efficacy of four anti-oomycete fungicides along with five essential oils (EOs) were tested on *P. agathidicida* mycelial growth.\r The sensitivity range and average values (in parentheses) of fungicide concentrations that reduced mycelial growth by 50% (EC50) for ethaboxam, fluopicolide, mandipropamid, and oxathiapiprolin were 0.072 to 0.104 µg/ml (0.087), 0.303 to 0.414 µg/ml (0.369), 0.018 to 0.022 µg/ml (0.020), and 1.30 x 10-4 to 1.70 x 10-4 µg/ml (1.55 x 10-4), respectively. Exotic plant EOs (*Thymus vulgaris* and *Pelargonium graveolens*) more effectively inhibited mycelial growth than indigenous plant EOs (kānuka and mānuka), although essential oils as a whole were significantly less effective at reducing mycelial growth when compared to fungicides.""" ; dct:issued "2023-11-06T23:43:51.139777"^^xsd:dateTime ; dct:modified "2023-11-06T23:43:51.139777"^^xsd:dateTime ; dct:title "SI2 THESIS: Improving techniques to manage *Phytophthora agathidicida*" ; dcat:accessURL . a dcat:Distribution ; dct:description """###A high-throughput automated qPCR for *Phytophthora agathidicida* to determine risk of spread by nursery plants###\r \r **February 2024**\r \r **Dobbie K, O'Neill R, Simpson S, McLay E, McDougal R. 2024. A high-throughput automated qPCR for *Phytophthora agathidicida* to determine risk of spread by nursery plants. A report for New Zealand’s Biological Heritage National Science Challenge: Ngā Rākau Taketake. 19 p. **\r \r **NOTE:** \r \r This report is embargoed until 01/03/2025. For further information please contact Kiryn Dobbie at Scion Research: [Kirryn.Dobbie@scionresearch.com](mailto:Kirryn.Dobbie@scionresearch.com)\r \r **ABSTRACT**\r \r *Phytophthora agathidicida* (PA), the causal agent of kauri dieback disease, threatens the long-term survival of kauri (*Agathis australis*) in Aotearoa. Currently, PA presence can only be confirmed via a soil test, which includes a soil baiting step. The soil baiting protocol is a lengthy, labour-intensive, and costly process. Several factors can affect the accuracy of this test and potentially result in false negative and/or false positive detection. These factors include the presence of other oomycetes, in particular *P. cinnamomi*, which has been shown to mask the detection of PA. There are several molecular techniques being explored, including a PCR-based technique that can detect PA directly from soil and soil water and qPCR assays for detection of PA and a Loop-Mediated Isothermal Amplification (LAMP) assay that can detect PA from soil baits. These molecular techniques have not yet been assessed for the detection of PA in the presence of another pathogen, such as *P. cinnamomi* as part of their validation process. Furthermore, automation of PCR-based assays could substantially speed up diagnostics from soil baiting for PA. Slipstream Automation provides both robotic, higher-throughput and improved consistency in DNA extractions and qPCR as well as being an automated service. They provide support for organisations involved in Marker Assisted Selection (MAS) and other large-scale DNA extraction/genetic screening projects. Slipstream Automation costs are significantly lower per sample, and have higher throughput than molecular methods that are currently used for the detection of PA. The aim of this project was to test the possibility of using the high-throughput systems as a viable, cost effective and efficient method for testing of samples for PA. We used two qPCR assays to detect PA in infected soil baits as a model system. In addition, we assessed the effect *P. cinnamomi* has on the detection of PA using the same qPCR assays and other molecular methods if applicable.\r \r __The problem__\r \r The current soil baiting protocol for detecting PA is a lengthy, labour-intensive, and costly process. Several factors can affect the accuracy of this test and potentially result in false negative and/or false positive detection. These factors include the presence of other oomycetes, in particular P. cinnamomi, which has been shown to mask the detection of PA.\r \r __Client initiatives__\r To investigate the potential of developing a protocol for a high-throughput qPCR assay or assays to detect PA in soil baits and potentially leachates and soils using high-throughput qPCR.\r \r __This project__\r \r The aim of this project was to test the potential of high-throughput qPCR as a viable cost effective and efficient method for testing of environmental samples for PA. We used two qPCR assays to detect PA in infected soil baits as a model system. In addition, we assessed the effect *P. cinnamomi* had on the detection of PA using the same qPCR assays and other molecular methods if applicable.\r \r __Key results__\r \r - Baits were tested using Slipstream Automations, high-throughput qPCR from three different soil baiting experiments which were named experiment 1, 2 and 3.\r \r - For the detection of PA from bait plant material there was a difference in sensitivity between the two qPCR assays. This was due to the gene copy number in the target organism genome.\r \r - Using the Internal Transcribed Spacer (ITS) assay and the ras-related Ypt protein (Ypt1) with DNA of baits from the positive controls (soils baits known to be infected with PA), we found target DNA amplified from 100% and 96% of the baits respectively.\r \r - Using the ITS assay and the Ypt1 assay with DNA of baits from the negative controls (baits known not to be infected with PA) we amplified target DNA from 37% and 2% of the baits respectively\r \r - Target DNA was amplified in all treatments from all studies using both the ITS and Ypt1 including the *P. cinnamomi* treatment.\r \r - More baits amplified target DNA in experiment 1 than from experiment 2 and 3 which was consistent with what was found from the traditional soil baiting morphological results.\r \r - Optimisation of the two qPCRs should eliminate the false negatives and false positives that are currently occurring.\r \r - This high-throughput automated qPCR method for detecting PA could be a fast and cost-effective option for screening soil baits.\r \r __Implications of results for the client__\r \r This pilot study has shown promising results although false positive and false negatives were detected. Further optimisation of these qPCRs for PA using Slipstreams high-through automatic methods could speed up diagnostics significantly reduce costs for the detection of PA in soils.\r \r __Further work__\r \r - Our results should be viewed as a fast succeed/fail pilot study. We conclude that the pilot study succeeded, and results have not ruled out the use of these techniques\r \r - Further trouble shooting to optimise the qPCRs to ensure no false negative or false positive results occur should be carried out, this would include:\r \r - Run a High-Resolution Melting (HRM) assay on negative control samples and *P. cinnamomi* treatment samples that have amplified target DNA to determine if cross contamination of the PA has occurred in these baits.\r \r - Carry out further serial dilutions for ITS and Ypt1 assay standard curves to reach sensitivity limits of detection and allow an assessment of potential Cq cut-off values for high Cq amplification that may be considered not positive.\r \r - Test the cedar DNA in isolation of PA with the ITS and Ypt1 assays to ensure there are no false positive results and ensure that the cedar DNA is not interfering with the Ypt1 assay resulting in false negative results.\r \r - Test *P. cinnamomi* DNA in isolation of PA with the ITS and Ypt1 assays to ensure that there are no false positive detections.\r """ ; dct:issued "2024-05-20T03:08:59.466867"^^xsd:dateTime ; dct:modified "2024-05-20T03:08:59.466867"^^xsd:dateTime ; dct:title "SI7 REPORT: High-throughput qPCR for Phytophthora agathidicida" . a dcat:Distribution ; dct:description """###Validate decontamination interventions to manage myrtle rust pathways###\r \r **November 2022**\r \r **Padamsee M, Shin-Clayton S. 2022. Validate decontamination interventions to manage myrtle rust pathways. LC4127. Checked by Lee Hill and Alana Den Breeyen.**\r \r **ABSTRACT**\r \r This report outlines research to determine the efficacy of potential treatments to deactivate and kill *Austropuccinia psidii* urediniospores; including Sterigen treatment (at concentrations of 1%, 2%, 5%), bleach, ethanol and soap solutions.""" ; dct:issued "2024-05-21T03:35:45.226132"^^xsd:dateTime ; dct:modified "2024-05-21T03:35:45.226132"^^xsd:dateTime ; dct:title "RA2 REPORT: Myrtle rust decontamination treatments" ; dcat:accessURL ; dcat:byteSize 1094409.0 ; dcat:mediaType "application/pdf" . a dcat:Distribution ; dct:description """###Development and deployment of an *Austropuccinia psidii* biotype differential diagnostic test###\r \r **March 2024**\r \r **Kalamorz F, Soewarto J, Frampton R, Smith G. 2024. RA1B-MR Diagnostics: Development and deployment of an *Austropuccinia psidii* biotype differential diagnostic test. A Plant & Food Research report prepared for: Biological Heritage. Milestone No. 90988. Contract No. 39454. Job code: P/313069/01. PFR SPTS No. 25282. 21 p.**\r \r **ABSTRACT**\r \r Five Loop Mediated Isothermal Amplification (LAMP) assays, designed by USA-based colleagues to specifically diagnose four of the genetic clusters (clades) of *Austropuccinia psidii* (Pandemic (two assays), Eucalyptus, Guava, South African) were tested at The New Zealand Institute for Plant and Food Research Limited (PFR), Lincoln using a plasmid with an insert containing the differential sequence targets. The LAMP assay was also tested against 12 genomic DNA preparations from fungal spores collected from infected plants in Aotearoa-New Zealand.\r \r This report provides the findings of these assays. """ ; dct:issued "2024-04-24T01:09:23.317010"^^xsd:dateTime ; dct:modified "2024-04-24T01:09:23.317010"^^xsd:dateTime ; dct:title "RA1B REPORT: A. psidii biotype differential diagnostic test" ; dcat:accessURL ; dcat:byteSize 1331496.0 ; dcat:mediaType "application/pdf" . a dcat:Distribution ; dct:description """###Project Summary NRT Tools - Zoospore BioSensor Electronics Report.###\r \r **March 2024**\r \r **Helps R, Stephens L. 2024. Project Summary NRT Tools - Zoospore BioSensor Electronics Report. 54 p. Confidential Report**\r \r **NOTE**\r \r This report is not available online. Please contact Dr. Marion Wood to request further details: [Marion.Wood@plantandfood.co.nz](mailto:Marion.Wood@plantandfood.co.nz) \r \r **ABSTRACT**\r \r This technical report summarises the development activities performed by InFact Ltd for the Ngā Rākau Taketake (NRT) Programme. This centred around the development of specialised electronics for the detection of phytophthora zoospores within a microfluidic device.\r \r inFact facilitated a design thinking workshop focusing on how on to progress the research from a lab tool to a field tool. The team identified primary device requirements and challenges and developed concept designs for a field-based device, which influenced the microfluidic device design.\r \r The underlying concept for the zoospore detection system is that the electrical impedance between electrodes located across a micro-channel will change slightly as a zoospore passes through the channel. A lock-in amplifier (LIA) was used to detect and measure weak narrow-band signals contained within large amounts of electromagnetic interference and electrical noise.\r Initial testing was based on a LIA development kit, which was evaluated and optimised. Design improvements were identified, including increasing amplifier gain and improving mains interference rejection which were embodied in a bespoke, battery powered portable electronics platform for improved zoospore detection device.\r \r Supporting mounting platforms, hardware and cabling solutions were developed that allowed experimental setup to be tested and evaluated by Plant and Food Research and the University of Auckland. Testing showed that the system could successfully detect zoospores.""" ; dct:issued "2024-04-25T23:03:54.330014"^^xsd:dateTime ; dct:modified "2024-04-25T23:03:54.330014"^^xsd:dateTime ; dct:title "RA1A: REPORT: Zoospore BioSensor Electronics" . a dcat:Distribution ; dct:description """###Austropuccinia psidii*: the threat of other strains###\r \r **March 2021**\r \r **Soewarto J. 2021. *Austropuccinia psidii*: the threat of other strains. Beyond Myrtle Rust Webinar Series. 15/03/2021**\r \r **ABSTRACT**\r \r The pandemic strain of *Austropuccinia psidii* (myrtle rust) present in New Zealand is the most widely distributed strain of the pathogen globally. It is also different to the strains present in South America and in South Africa, which have different host ranges and severity. If these other myrtle rust strains were introduced into New Zealand, this could lead to additional myrtle species becoming infected, making myrtle rust an even more serious threat to our natural diversity. As part of biosecurity preparedness research for New Zealand, local researchers are working with scientists in South Africa and Uruguay to test the susceptibility of New Zealand germplasm against different strains of *A. psidii*. \r \r This presentation is run by Scion-based researcher Julia Soewarto, where she focuses on the results from the artificial inoculation of the South African strain of *A. psidii* on four iconic New Zealand species: *Leptospermum scoparium *(mānuka), *Kunzea robusta *(kanuka), *K. linearis* (mānuka rawiri) and *Metrosideros excelsa* (pōhutukawa). This study provided new insights into the host range of the South African strain of *A. psidii* and suggested it represents a serious threat for New Zealand native Myrtaceae and for other Myrtaceae species worldwide.\r """ ; dct:issued "2024-05-20T02:55:49.251975"^^xsd:dateTime ; dct:modified "2024-05-20T02:55:49.251975"^^xsd:dateTime ; dct:title "RA1B WEBINAR: A. psidii - the threat of other strains" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Updating the toolbox in the fight against *Phytophthora agathidicida*###\r \r **May 2023**\r \r **Wood M. 2023. Updating the toolbox in the fight against *Phytophthora agathidicida*. Kaurilands Summit 2023, Whangārei, New Zealand, 11/05/2023.**\r \r \r """ ; dct:issued "2024-08-29T20:03:09.696946"^^xsd:dateTime ; dct:modified "2024-08-29T20:03:09.696946"^^xsd:dateTime ; dct:title "PRESENTATION: Updating the toolbox" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Plant-pathogen management in a native forest ecosystem###\r \r **June 2023**\r \r **Mainwaring JC, Vink JNA, Gerth ML. 2023. [Plant-pathogen management in a native forest ecosystem](https://www.sciencedirect.com/science/article/pii/S0960982223001872/pdfft?md5=86e31c8b5fe41c6b536b7ad075471b9a&pid=1-s2.0-S0960982223001872-main.pdf). Current Biology 33(11): R500-R505.**\r \r **ABSTRACT**\r \r Forest ecosystems all over the world are facing a growing threat from plant-disease outbreaks. As pollution, climate change, and global pathogen movement intensify, so too do the impacts of forest pathogens. In this essay, we examine a case study of the New Zealand kauri tree (*Agathis australis*) and its oomycete pathogen, *Phytophthora agathidicida*. We focus on the interactions between the host, pathogen, and environment — the building blocks of the ‘disease triangle’, a framework used by plant pathologists to understand and manage diseases. We delve into why this framework is more challenging to apply to trees than crops, taking into account the differences in reproductive time, level of domestication, and surrounding biodiversity between the host (a long-lived native tree species) and typical crop plants. We also address the difficulties in managing *Phytophthora* diseases compared to fungal or bacterial pathogens. Furthermore, we explore the complexities of the environmental aspect of the disease triangle. In forest ecosystems, the environment is particularly complex, encompassing diverse macro- and microbiotic influences, forest fragmentation, land use, and climate change. By exploring these complexities, we emphasize the importance of targeting multiple components of the disease triangle simultaneously to make effective management gains. Finally, we highlight the invaluable contribution of indigenous knowledge systems in bringing a holistic approach to managing forest pathogens in Aotearoa New Zealand and beyond.\r \r **KEYWORDS**\r \r Plant-pathogen management;\r Native forest ecosystem;\r Disease triangle;\r *Phytophthora agathidicida*;\r Environmental complexity;\r Indigenous knowledge systems;\r Forest fragmentation;\r Climate change;\r New Zealand kauri tree;\r Reproductive time""" ; dct:issued "2024-05-21T03:53:38.303571"^^xsd:dateTime ; dct:modified "2024-05-21T03:53:38.303571"^^xsd:dateTime ; dct:title "RA3A PAPER: Native forest plant pathogen management" ; dcat:accessURL . a dcat:Distribution ; dct:description """**March 2024**\r \r This living tool was developed to respond to the urgent need of mana whenua to have a Te Ao Māori-based tool to capture their worldview and data, to formulate and articulate their response to kauri dieback and myrtle rust.""" ; dct:issued "2024-05-24T00:27:02.107470"^^xsd:dateTime ; dct:modified "2024-05-24T00:27:02.107470"^^xsd:dateTime ; dct:title "BRIEF: Cultural monitoring tools" ; dcat:accessURL ; dcat:byteSize 983172.0 ; dcat:mediaType "application/pdf" . a dcat:Distribution ; dct:description """###Establishing Molecular Biology Tools for *Phytophthora agathidicida*###\r \r **May 2023**\r \r **Hayhurst M. 2023. [Establishing Molecular Biology Tools for *Phytophthora agathidicida*](https://openaccess.wgtn.ac.nz/ndownloader/files/40568180). Unpublished Masters thesis, Victoria University of Wellington. 144 p.**\r \r **ABSTRACT**\r \r The goal of this research was to establish molecular biology methods for the study of *P. agathidicida* by \r \r - identifying a suitable target for genome editing with CRISPR-Cas and design guide RNAs for the target; and \r \r - establishing a method to produce and transform *P. agathidicida* protoplasts.""" ; dct:issued "2024-02-15T23:38:55.470376"^^xsd:dateTime ; dct:modified "2024-02-15T23:38:55.470376"^^xsd:dateTime ; dct:title "THESIS: Molecular Biology Tools for *Phytophthora agathidicida*" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Sensing a Threat###\r \r **March 2024**\r \r Our researchers are working to inform methods for controlling the disease and its symptoms by better understanding the responsible *Phytophthora agathidicida* (PA) pathogen. A collaborative team from Plant and Food Research, Auckland University and inFact Ltd. has been working on an exciting tool to detect and study a particular stage of the PA life cycle: the zoospore.\r \r \r """ ; dct:issued "2024-06-26T23:20:43.528977"^^xsd:dateTime ; dct:modified "2024-06-26T23:20:43.528977"^^xsd:dateTime ; dct:title "BRIEF: Sensing a Threat" ; dcat:accessURL ; dcat:byteSize 6597967.0 ; dcat:mediaType "application/pdf" . a dcat:Distribution ; dct:description """###Efficacy of commercially available *Phytophthora* (sp) lateral flow ImmunoStrips in the sensitive detection of *Phytophthora agathidicida*###\r \r **June 2024**\r \r **Wood M, Pushparajah S, Milner D. 2024. Efficacy of commercially available *Phytophthora* (sp) lateral flow ImmunoStrips in the sensitive detection of *Phytophthora agathidicida*. A report for New Zealand’s Biological Heritage National Science Challenge: Ngā Rākau Taketake. 16 p. **\r \r **NOTE**\r \r This report is embargoed until 31/05/2025. For further information please contact Marion Wood: [Marion.Wood@plantandfood.co.nz](mailto:Marion.Wood@plantandfood.co.nz)\r \r **ABSTRACT**\r \r __Background:__ \r \r The interest in, and uptake of readily available, commercially attractive lateral flow devices (ImmunoStrips) has recently undergone a significant phase-change due to their extensive use associated with the Covid-19 pandemic. The use of similar ImmunoStrips designed to specifically detect plant pathogens is also currently feasible due the availability of similar, commercially convenient devices. However, such plant pathogen directed devices are prone to issues with sensitivity and the possibility of delivering false positive and negative results. This research has set out to evaluate the commercially available *Phytophthora* spp. lateral flow device (LFD) (Pocket Diagnostic Abingdon Health PLC) rapid tests and explore their potential when coupled to an additional downstream qPCR-based amplification step to identify *Phytophthora agathidicida* (PA) quickly and simply in plant and/or soil samples. Such lateral flow devices are routinely used to detect a multitude of pathogens, but their reliability can be severely restricted due to their cross reactivity with other related *Phytophthora* species or even with non-related pathogens such as *Pythium* (sp). Using these serological diagnostic strips as means of enriching for *Phytophthora* in a biological sample, DNA can be purified and eluted from a positive test strip and subsequently analysed specifically for PA using either qPCR (as recently reported by McDougal et al., 2021) or by using digital droplet PCR (ddPCR). This second technique is reported to require less stringent sample preparation and so may lend itself to the laboratory-based diagnostic analyses of soil-based samples. \r \r __Project aims:__\r \r To address this this research proposal has four main themes: (i) using a positive test strip as the basis for downstream DNA isolation and sequential qPCR analysis to detect *Phythophthora agathidicida*; (ii) using a positive test strip as the basis for downstream DNA isolation and sequential ddPCR analysis to detect PA (iii) evaluate the ease of use of the LFDs in the field and their potential role for pathogen surveillance both as originally intended as a point of use detection test kit and as an alternative to the need for soil sampling for diagnostic purposes from a mana whenua perspective and (iv) using LFD strips as means of enriching for *Phytophthora* (sp) in a biological sample, viable pathogens may be cultivated from a positive test strip and subsequently analysed specifically for PA (and other potential co-immobilised pathogens) using either visual characteristics and/or baiting assay and diagnosed using a supplemental molecular assay such as LAMP (as recently reported by Winkworth et al., 2020), qPCR (McDougal et al., 2021) or potentially ddPCR.\r \r __Project results:__\r \r The use of molecular strategies, such as qPCR and ddPCR to identify specific plant pathogens remains attractive but is limited by their lack of ability to be translated into a robust field-based tool. Overcoming the need for costly transportation of soil samples to laboratories for downstream diagnostic testing remains a desirable goal. This research indicates that the use of Whatman® 1 cm filter paper discs are a cheap, readily available matrix that may have the potential to be used in the field to sequester PA (or other plant pathogens suspended in a soil slurry) for sending to laboratories for downstream testing. This is an attractive alternative and is being evaluated further. ddPCR has been demonstrated to be a robust alternative to the standard qPCR-probe strategy and is relatively easy to use but is reliant on costly hardware. The specificity demonstrated using the ddPCR strategy, without the need for a costly probe, further suggests that ddPCR is a strong contender as an alternative molecular technique for the diagnostic identification of PA, but unlike qPCR it is highly unlikely to be available as a portable tool. Further work to assess the specificity of the assays and their available primer/probe combinations is on-going.\r \r Overcoming the dependency of sending soil samples back to laboratories, in terms of time and cost is highly desirable. Our initial findings suggest that the use of the sample pad of the Agdia Phytophthora ImmunoStrip® provides a useful matrix for sequestering PA, potentially providing significant savings to field users who no longer have to harvest and transport weighty soil samples to the laboratory for downstream molecular validation. However, this cost could be further significantly reduced with the alternative use of Whatman® filter paper discs that are much easier to handle and cheaper than the ImmunoStrips or soil samples themselves. This early-stage research requires additional development to ascertain the false positive / false negative rates and whether the sequestered PA can be also used to plate on selective medium for visual confirmation of the PA pathogen but looks to be promising and warrants further development.\r Unfortunately, the direct application of the Agdia Phytophthora ImmunoStrip® to detect PA in soil baiting scenarios failed, irrespective of whether the soil sample was previously assessed as being PA positive following plating on selective media and/or molecular validation using qPCR. This strongly suggests that these ImmunoStrips, in their current format, are unsuitable as a robust in-field diagnostic/surveillance tool, and it is not recommended that they are used in this manner for the detection of PA.""" ; dct:issued "2024-06-04T20:44:22.633830"^^xsd:dateTime ; dct:modified "2024-06-04T20:44:22.633830"^^xsd:dateTime ; dct:title "SI3 & SI4 REPORT: Lateral flow ImmunoStrips Efficacy" . a foaf:Organization ; foaf:name "Ngā Rākau Taketake Inventory" .