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Biology subjects

Flies, A. S.

Publications and source records attributed to Flies, A. S..

17 recordsLinked to original sources
bioRxiv2026

A Smart Bait Dispenser with Real-time Monitoring for Species-Specific Bait Delivery

1. Remote image capture using trail cameras has become an essential part of many wildlife monitoring and management programs. Oral bait vaccination has been a valuable tool in wildlife disease management, but baits are generally dropped on the ground or delivered by devices that are typically developed to utilise physical and behavioural characteristics of the target species. Both approaches can result in a high proportion of baits being consumed by non-target species. Merging years of trail camera research knowledge with new technologies allows for development of more specific bait delivery options. 2. We developed an open-source smart bait dispenser that uses field-based image classification to selectively deliver baits to the target species. The system's long-range wide area network-based remote telemetry provides updates to an online dashboard in near real time to show camera triggers, target species detections, and baits dispensed. We trialled four dispensers with placebo baits for 62 nights across three field sites in Tasmania, Australia to deliver baits to Tasmanian devil (Sarcophilus harrisii). 3. The dispensers recorded 2106 motion triggers, of which 876 were triggered by animals. The onboard devil classification model achieved 98.6% accuracy, 75.0% precision, 77.4% recall, and a 76.2% F1-score. The dispenser released 41 placebo baits in total, of which 31 were target-specific distributions in response to presence of Tasmanian devils at the dispenser, hence achieving an overall bait delivery success rate of 75.6%. Importantly, no animal was able to forcibly retrieve baits from the dispenser. Observed average battery life across trials was 19.2 nights. 4. These results clearly demonstrate the effectiveness of our innovative bait dispenser for targeted bait delivery, offering a versatile ecological tool that can be tailored for various species by simply updating the image classification model. This adaptable system can support critical initiatives like wildlife oral bait vaccination and supplementary feeding after wildlife translocations.

ecology↗
bioRxiv2026

Ethyl-iophenoxic acid as a serum biomarker for marsupial species in oral bait trials

Ethyl-iophenoxic acid (Et-IPA) is widely recognized as a useful biomarker to confirm oral bait consumption in eutherian species. In historical studies on marsupials, Et-IPA was rapidly eliminated from brushtail possums (Trichosurus vulpecula) and swamp wallabies (Wallabia bicolor) suggesting limited use for marsupial species. However, a 1 mg oral dose of Et-IPA was detectable in the marsupial Tasmanian devils (Sarcophilus harrisii) for [≥] 56 days suggesting the biomarker can be used in a devil bait vaccine program. To assess Et-IPA marking in off-target marsupials that may consume baits, we administered 1 mg oral doses of Et-IPA to brushtail possums, forester kangaroos (Macropus giganteus tasmaniensis), spotted-tailed quolls (Dasyurus maculatus) and eastern quolls (Dasyurus viverrinus). Liquid chromatography with tandem mass spectrometry was used to detect and quantify serum Et-IPA. Et-IPA was detected in the serum on day 2 but was not detected by day 14 in any of the species tested, including the two quoll species which are in the same carnivorous Dasyuridae family as the devils. The rapid elimination of Et-IPA in the marsupials included in this study suggests it is not useful as a biomarker for these species. Furthermore, rapid elimination in the kangaroos and possums suggests that Et-IPA is unlikely to accumulate in the food chain following distribution of Et-IPA-marked oral bait vaccines for Tasmanian devils. Short summary for non-expertsA recent study in Tasmanian devils (Sarcophilus harrisii) challenged the concept that ethyl iophenoxic acid (Et-IPA) is not a useful serum biomarker for marsupials. Using the same sensitive liquid chromatography-tandem mass spectrometry method we detected serum Et-IPA in four marsupial species on day two post-ingestion but by day 14, serum Et-IPA was undetectable. These findings indicate that Et-IPA is an unsuitable biomarker for these species and suggest that Et-IPA from devil bait vaccines is unlikely to bioaccumulate in the Tasmanian environment.

zoology↗
bioRxiv2025

Development of a point-of-care field diagnostic test for DFT1 and DFT2

The Tasmanian devil (Sarcophilus harrisii) population has undergone a major decline in the wild due to the epidemics of two transmissible cancers known as devil facial tumours 1 (DFT1) and devil facial tumour 2 (DFT2). Understanding the distribution and prevalence of DFT1 and DFT2 is challenging as they can only be detected in field conditions when tumours are large enough to be visually observed. This impedes our ability to understand how the devil population is evolving in response to the tumours. PCR-based diagnostics are available, but the technique is not field-applicable. To overcome these hurdles, we developed an ultrasensitive and field-deployable rapid diagnostic tool. We used a technique called Specific High-Sensitivity Enzymatic Reporter Unlocking (SHERLOCK), which combines an isothermal nucleic acid amplification step with CRISPR-based recognition and activation of reporter probes to indicate target sequence detection. This system requires only portable laboratory equipment, making it more amenable to field conditions. The results showed that our test can detect DFT1 and DFT2 DNA within the attomolar range. We then confirmed that the test can detect DFT1 in the field using non-invasive swab samples. The SHERLOCK test can be used for more active monitoring and management approaches that are not currently possible.

molecular biology↗
bioRxiv2025

Identification of Expressed Endogenous Retroviral Element Associated Long Terminal Repeats in Devil Facial Tumour Cells

The Tasmanian devil (Sarcophilus harrisii) population has undergone a major decline in the wild due to the epidemics of two transmissible cancers known as devil facial tumours (DFT1 and DFT2). A multipronged conservation strategy is in place, but a vaccine that prevents devils from developing devil facial tumour disease would be a major step towards recovering the wild devil population. Critical to an effective DFT vaccine are target antigens. Putative non-coding regions of genomes have been identified as potential tumour-specific antigens for human cancer. These non-coding regions include long terminal repeats of endogenous retroviral elements. We identified 11,193 ERV LTR transcripts that were expressed in DFT1 or DFT2 transcriptomes but not in healthy tissue samples. Using a proteogenomic approach, we identified 33 ERV LTR peptides unique to DFT1 and/or DFT2 immunopeptidomes; four of these were validated in subsequent screens with synthetic peptides. Our study shows the potential for ERV LTRs as novel vaccine targets against DFT1 and DFT2. This method can be applied to other species for the development of cancer vaccine targets that may be shared across tumour types. summaryERV LTRs are present in the Tasmanian devil genome and devil facial tumour cell transcriptomes and immunopeptidome.

cancer biology↗
bioRxiv2025

A study on edge devices for image classification of the Tasmanian devil (Sarcophilus harrisii) for vaccine delivery

O_LIA target-specific bait dispenser is required for oral bait vaccination of the endangered Tasmanian devil (Sarcophilus harrisii) against the deadly devil facial tumour disease. Development of a broadly extendible dispenser would be a beneficial ecological tool. A camera-based edge device with an onboard deep learning model can be used to identify the target species using image classification. It is important to choose a suitable edge device for the dispensers effective application in power constrained environments. C_LIO_LIWe evaluated four edge devices for the smart bait dispenser-ArduinoPro Nicla Vision, ArduinoPro Portenta H7 with Vision Shield (LoRa), Raspberry Pi 3 Model B+ and Raspberry Pi Zero 2 W. Two simple convolutional neural networks, and four fine-tuned pretrained models (MobileNetV2, MobileNetV3Small, ResNet50V2, and ResNet152V2) were trained on trail camera images of devil and non-devil species. These models were evaluated across four metrics and post-training quantised for deployment. The edge devices were assessed on inference latency of each model in seconds (s) and power consumption in watt (W). C_LIO_LIWe found that a simple CNN based image classification model yielded the best overall result of [~]96% across all metrics. Raspberry Pi 3 Model B+ and Zero 2 W could run all the six models whereas Portenta failed to run the two ResNet models and Nicla Vision failed to run all four pretrained models. All edge devices were found to be quick enough for dispenser application (average inference latency of 0.718 s). Portenta consumed the lowest power during inference (0.19 W), idle (0.185 W), and light sleep (0.045 W) states whereas Nicla Vision consumed the lowest power during deep sleep (0.002 W). C_LIO_LIOverall, we found that simple traditional CNNs was best suited for species classification in a camera-based smart bait dispenser for vaccination of Tasmanian devils. We conclude that ArduinoPro Portenta H7 with Vision Shield is the most competent device for this edge AI application. We suggest integration of this system with a microcontroller unit like ATtiny85 to minimise inactive power consumption of the dispenser. This method can be readily adapted for other species in vaccination and supplemental feeding projects. C_LI

ecology↗
bioRxiv2024

Isolation of an infectious mammalian chu-like virus from tumor cells of the endangered Tasmanian devil (Sarcophilus harrisii)

Jingchuvirales (negative-sense RNA viruses) were initially discovered in invertebrates, with both exogenous and endogenous jingchuviruses subsequently identified in fish, reptiles and mammals. To date, jingchuviruses have only been described metagenomically. By screening primary tumor tissues and tumor cell lines from the endangered Tasmanian devil (Sarcophilus harrisii), we isolated Tasmanian devil chu-like virus (TDCV) from cultures of Tasmanian devil facial tumor disease (DFTD) cells. Cell infection experiments demonstrated active virus replication in Tasmanian devil tumor cells, but not mosquito cells. The absence of viral replication in fibroblasts in cell culture and the lack of RNA detection in several organs suggested that replication was associated with tumor cells. Phylogenetic analysis revealed that TDCV likely represents a novel virus family. This is the first isolation of a jingchuvirus, demonstrating their capacity to infect mammalian cells, and providing in vitro avenues to understand the biology of TDCV and its association with tumor cell infection.

microbiology↗
bioRxiv2024

Differentially expressed growth factors and cytokines drive phenotypic changes in transmissible cancers

The Tasmanian devil is threatened by two deadly transmissible Schwann cell cancers. A vaccine to protect Tasmanian devils from both devil facial tumour 1 (DFT1) and devil facial tumour 2 (DFT2), and improved understanding of the cancer cell biology, could support improved conservation actions. Previous transcriptomic analysis has implicated phenotypic cellular plasticity as a potential immune escape and survival mechanism of DFT1 cells. This phenotypic plasticity facilitates transition from a myelinating Schwann cell to a repair Schwann cell phenotype that exhibits mesenchymal characteristics. Here, we have identified cytokines and growth factors differentially expressed across DFT cell phenotypes and investigated their role in driving phenotypic plasticity and oncogenic properties of DFT cells. Our results show that NRG1, IL16, TGF{beta}1, TGF{beta}2 and PDGFAA/AB proteins have significant and distinct effects on the proliferation rate, migratory capacity and/or morphology of DFT cells. Specifically, PDGFR signalling, induced by PDGFAA/AB, was a strong enhancer of cell proliferation and migration, while TGF{beta}1 and TGF{beta}2 induced epithelial-mesenchymal transition (EMT)-like changes, inhibited proliferation and increased migratory capacity. These findings suggest complex interactions between cytokine signalling, phenotypic plasticity, growth and survival of DFTs. Signalling pathways implicated in the propagation of DFT are potential targets for therapeutic intervention and vaccine development for Tasmanian devil conservation.

cancer biology↗
bioRxiv2023

Conversion of mouse-derived hybridomas to Tasmanian devil recombinant IgG antibodies

The hybridoma method for production of monoclonal antibodies has been a cornerstone of biomedical research for several decades. Here we convert the monoclonal antibody sequence from mouse-derived hybridomas into a "devilised" recombinant antibody with devil IgG heavy chain and IgK light chain. The chimeric recombinant antibody can be used in functional assays, immunotherapy, and to improve understanding of antibodies and Fc receptors in Tasmanian devils. The process can be readily modified for other species.

immunology↗
bioRxiv2022

Automated analysis of PD1 and PDL1 in lymph nodes and the microenvironment of transmissible tumors in Tasmanian devils

The wild Tasmanian devil (Sarchophilus harrisii) population has suffered a devastating decline due to two clonal transmissible cancers. Devil facial tumor 1 (DFT1) was first observed in 1996, followed by a second genetically distinct transmissible tumor, devil facial tumor 2 (DFT2), in 2014. DFT1/2 frequently metastasize, with lymph nodes being common metastatic sites. Downregulation of MHC-I by DFT1 cells is a primary means of evading allograft immunity aimed at polymorphic MHC-I proteins. DFT2 cells constitutively express MHC-I, and MHC-I is upregulated on DFT1/2 cells by interferon gamma, suggesting other immune evasion mechanisms may contribute to overcoming allograft and anti-tumor immunity. Human clinical trials have demonstrated PD1/PDL1 blockade effectively treats patients showing increased expression of PD1 in tumor draining lymph nodes, and PDL1 on peritumoral immune cells and tumor cells. The effects of DFT1/2 on systemic immunity remain largely uncharacterized. This study applied the open-access software QuPath to develop a semiautomated pipeline for whole slide analysis of stained tissue sections to quantify PD1/PDL1 expression in devil lymph nodes. The QuPath protocol provided strong correlations to manual counting. PD-1 expression was approximately 10-fold higher than PD-L1 expression in lymph nodes and was primarily expressed in germinal centers, whereas PD-L1 expression was more widely distributed throughout the lymph nodes. The density of PD1 positive cells was increased in lymph nodes containing DFT2 metastases, compared to DFT1. This suggests PD1/PDL1 exploitation may contribute to the poorly immunogenic nature of transmissible tumors in some devils and could be targeted in therapeutic or prophylactic treatments.

immunology↗
bioRxiv2022

A human adenovirus encoding IFN-γ can transduce Tasmanian devil facial tumour cells and upregulate MHC-I

The devil facial tumour disease (DFTD) has led to a massive decline in the wild Tasmanian devil (Sarcophilus harrisii) population. The disease is caused by two independent devil facial tumours (DFT1 and DFT2). These transmissible cancers have a mortality rate of nearly 100%. An adenoviral vector-based vaccine has been proposed as a conservation strategy for the Tasmanian devil. This study aimed to determine if a human adenovirus serotype 5 could express functional transgenes in devil cells. As DFT1 cells do not constitutively express major histocompatibility complex class I (MHC-I), we developed a replication-deficient adenoviral vector that encodes devil interferon gamma (IFN-{gamma}) fused to a fluorescent protein reporter. Our results show that adenoviral-expressed IFN-{gamma} was able to stimulate upregulation of beta-2 microglobulin, a component of MHC-I, on DFT1, DFT2, and devil fibroblast cell lines. This work suggests that human adenoviruses can serve as vaccine platform for devils and potentially other marsupials.

immunology↗
bioRxiv2022

Evaluation of oral baits and distribution methods for Tasmanian devils (Sarcophilus harrisii)

ContextDiseases are increasingly contributing to wildlife population declines. Tasmanian devil (Sarcophilus harrisii) populations have locally declined by 82% largely due to the morbidity and mortality associated with two independent transmissible devil facial tumours (DFT1 and DFT2). Toxic baits are often used as a management tool for controlling vertebrate pest populations in Australia, but in other areas of the world oral baits are also used to deliver vaccines or pharmaceuticals to wildlife. Oral vaccine bait products have been distributed for more than 50 years at a landscape scale to protect wildlife from rabies virus and contributed to the elimination of fox rabies from more than ten European nations. An oral bait vaccine to protect against devil facial tumours has been proposed as a management tool to improve the population health, resiliency and fitness of wild Tasmanian devils. AimOur goal was to evaluate the potential use of edible baits as vehicles for vaccine delivery to Tasmanian devils. MethodWe tested placebo versions of baits that are already used in Australia. Key resultsCaptive devils consumed all types of placebo baits but exhibited a preference for ruminant- and fish-based baits. Captive devils also consumed inert capsules inserted into placebo baits. Bait fate trials in the field revealed that baits were generally removed within 24 hours. Tasmanian pademelons (Thylogale billardierii), brushtail possums (Trichosurus vulpecula), and Eastern quolls (Dasyurus viverrinus) were the most common nontarget bait competitors at six private properties in southern Tasmania; wild devils removed approximately 5% of ground baits at these sites. We also evaluated an automated bait dispenser, which reduced nontarget uptake and resulted in over 50% of the baits being removed by devils. ConclusionsThis study demonstrates that captive and wild devils will accept and consume placebo versions of commercial baits. Bait dispensers or modified baits or baiting strategies are needed to increase bait uptake by devils. ImplicationsBait dispensers can be used at a regional scale to deliver baits to Tasmanian devils. These could act as vehicles for preventive or therapeutic vaccines to mitigate the impacts of disease on devil populations. Short summaryThis study aimed to test oral baits as potential vaccine delivery vehicles for Tasmanian devils. Captive and wild devils consumed placebo versions of commercial baits used on mainland Australia. Abundant non-target species, such as brushtail possums, Tasmanian pademelons, and eastern quolls consumed most baits in the wild. Implementation of automated bait dispensers increased bait uptake by devils to over 50% at the same regional field sites.

zoology↗
bioRxiv2021

Ethyl-Iophenoxic acid as a serum marker for oral baiting of carnivorous marsupials

ContextEthyl-Iophenoxic acid (Et-IPA) has been widely used as a bait biomarker to determine oral bait consumption by vertebrate wildlife species. Oral bait vaccines have been delivered to numerous wildlife species to protect them from disease. The Tasmanian devil (Sarcophilis harrisii), the largest extant carnivorous marsupial species, is threatened by the transmissible cancers known as devil facial tumour disease (DFTD). Development of a protective DFTD vaccine is underway, and an oral bait has been proposed to deliver the vaccine in the wild. The bait delivery system requires a biomarker that can be detected for several months post-consumption in Tasmanian devils. AimTo determine the suitability of Et-IPA as a bait biomarker in the Tasmanian devil. MethodTwo Tasmanian devils were fed 50 mg Et-IPA (4.5 to 7.1 mg Et-IPA/kg bodyweight). Liquid chromatography with tandem mass spectrometry (LC-MS/-MS) was used to directly measure Et-IPA in baseline serum samples and samples collected on days 1, 14, 26 and 56 post-baiting. Key resultBoth devils retained serum Et-IPA concentrations at two orders of magnitude above negative control sera when this study concluded. ConclusionsEt-IPA is a useful bait biomarker for Tasmanian devils and can be included in future DFTD bait vaccine field trials to determine bait vaccine uptake.

zoology↗
bioRxiv2021

Regulation of MHC-I and MHC-II by CIITA in transmissible cancers

MHC-I and MHC-II molecules are critical components of antigen presentation and T cell immunity to pathogens and cancer. The two monoclonal transmissible devil facial tumours (DFT1, DFT2) exploit MHC-I pathways to overcome immunological anti-tumour and allogeneic barriers. This exploitation underpins the ongoing transmission of DFT cells across the wild Tasmanian devil population. We have previously shown that constitutive expression of NLRC5 can induce stable upregulation of MHC-I on DFT1 and DFT2 cells, but unlike IFNG-treated cells, NLRC5 does not upregulate PDL1. MHC-II expression is crucial for CD4+ T cell activation and is primarily confined to haematopoietic antigen presenting cells. Transcriptomic analysis of DFT1 and DFT2 cell lines showed that several genes of the MHC-I and MHC-II pathways were upregulated in response to constitutive overexpression of the class II transactivator (CIITA) gene. This was further supported by upregulation of MHC-I protein on DFT1 and DFT2 cells, but interestingly MHC-II protein was upregulated only on DFT1 cells. The functional significance of the MHC upregulation on DFT cells was shown using serum from devils with natural or immunotherapy-induced DFT1 regressions; binding of serum IgG was stronger in CIITA-transfected cells than wild type cells, but was less than binding to NLRC5 transfected cells. This new insight into regulation of MHC-I and MHC-II in cells that naturally overcome allogeneic barriers can inform vaccine, immunotherapy, and tissue transplant strategies for human and veterinary medicine.

immunology↗
bioRxiv2020

NLRC5 regulates expression of MHC-I and provides a target for anti-tumor immunity in transmissible cancers

Downregulation of major histocompatibility complex I (MHC-I) on tumor cells is a primary means of immune evasion by many types of cancer. Additionally, MHC-I proteins are a primary target of immune-mediated transplant rejection. Transmissible tumors that overcome allograft rejection mechanisms and evade anti-tumor immunity have killed thousands of wild Tasmanian devils (Sarcophilus harrisii). Interferon gamma (IFNG) upregulates surface MHC-I expression on devil facial tumor (DFT) cells but is not sufficient to induce tumor regressions. Transcriptome analysis of IFNG-treated DFT cells revealed strong upregulation of NLRC5, a master regulator of MHC-I in humans and mice. To explore the role of NLRC5 in transmissible cancers, we developed DFT cell lines that constitutively overexpress NLRC5. Transcriptomic results suggest that the role of NLRC5 as a master regulator of MHC-I is conserved in devils. Furthermore, NLRC5 was shown to drive the expression of many components of the antigen presentation pathway. To determine if MHC-I is a target of allogeneic immune responses, we tested serum from devils with anti-DFT responses including natural DFT regressions against DFT cells. Antibody binding occurred with cells treated with IFNG and overexpressed NLRC5. However, CRISPR/Cas9-mediated knockout of MHC-I subunit beta-2-microglobulin (B2M) eliminated antibody binding to DFT cells. Consequently, MHC-I could be identified as a target for anti-tumor and allogeneic immunity and provides mechanistic insight into MHC-I expression and antigen presentation in marsupials. NLRC5 could be a promising target for immunotherapy and vaccines to protect devils from transmissible cancers and inform development of transplant and cancer therapies for humans.

immunology↗
bioRxiv2020

Tasmanian devil CD28 and CTLA4 capture CD80 and CD86 from adjacent cells

Immune checkpoint immunotherapy is a pillar of human oncology with potential for non-human species. The first checkpoint immunotherapy approved for human cancers targeted the CTLA4 protein. CTLA4 can inhibit T cell activation by capturing and internalizing CD80 and CD86 from antigen presenting cells, a process called trans-endocytosis. Similarly, CD28 can capture CD80 and CD86 via trogocytosis and retain the captured ligands on the surface of the CD28-expressing cells. The Tasmanian devil (Sarcophilus harrisii) population has declined by 77% due to transmissible cancers that evade immune defenses despite genetic mismatches between the host and tumours. We used a live cell-based assay to demonstrate that devil CTLA4 and CD28 can capture CD80 and CD86. Mutation of evolutionarily conserved motifs in CTLA4 altered functional interactions with CD80 and CD86 in accordance with patterns observed in other species. These results suggest the potential for checkpoint immunotherapies can be translated to evolutionarily divergent species.

immunology↗
bioRxiv2019

Immune checkpoint proteins are conserved across 160 million years of evolution and are expressed on transmissible cancers

Immune checkpoint immunotherapy has revolutionized medicine, but translational success for new treatments remains low. Around 40% of humans and Tasmanian devils (Sarcophilus harrisii) develop cancer in their lifetime, compared to less than 10% for most species. Additionally, devils are affected by two of the three known transmissible cancers in mammals. Unfortunately, little is known about of immune checkpoints in devils and other non-model species, largely due to a lack of species-specific reagents. We developed a simple cut-and-paste reagent development method applicable to any vertebrate species and show that immune checkpoint interactions are conserved across 160 million years of evolution. The inhibitory checkpoint molecule CD200 is highly expressed on devil facial tumor cells. We are the first to demonstrate that co-expression of CD200R1 can block CD200 expression. The evolutionarily conserved pathways suggest that naturally occurring cancers in devils and other species can serve as models for understanding cancer and immunological tolerance. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/831404v3_ufig1.gif" ALT="Figure 1"> View larger version (108K): org.highwire.dtl.DTLVardef@14ff10eorg.highwire.dtl.DTLVardef@15acfd4org.highwire.dtl.DTLVardef@102a37dorg.highwire.dtl.DTLVardef@3b726c_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗