Biology subjects

Perry, T.

Publications and source records attributed to Perry, T..

10 recordsLinked to original sources

bioRxiv2026

Monotreme transcriptomes shed light on evolution of lactation and placentation

Placentation and lactation are hallmark mammalian reproductive traits and key processes facilitating the transfer of nutrients from the mother to the offspring. The basal mammalian lineage of egg-laying monotremes features a short gestation period supported by a simple placenta and an elongated lactation, similar to marsupials. Eutherian mammals by contrast evolved longer gestation facilitated by extensive placentation and shorter lactation. To understand the gene expression underpinning maternal-foetal nutrient transfer across mammals, we generated transcriptome datasets for the monotreme reproductive tract and mammary gland and compared this to expression in representative species from the other mammalian clades: marsupials (Tammar wallaby) and eutherians (mouse). This revealed extensive overlapping gene expression between the therian placenta and monotreme reproductive tract, including the first observation of retroviral gene expression in the echidna reproductive tract. Interestingly, we discovered that transport and development functions supporting foetal growth are expressed in echidna mammary gland and eutherian placenta, likely a signature of the shift from prolonged lactation to longer placentation. Together, this demonstrates that diverse modes of maternal-foetal nutrient transfer are underpinned by similar gene networks across mammals.

evolutionary biology↗

bioRxiv2026

Undergraduate student practicals generate high-quality data for microbiome research

The increasing prominence and accessibility of microbiomics has provided an opportunity for authentic research experiences in the undergraduate practical classroom. In recent years, this approach has contributed to published research projects. However, there is little information evaluating the quality of student-generated data compared to that of trained researchers. To investigate this, we designed an undergraduate practical component in which 37 final-year genetics students generated microbial profiles of 22 echidna scats using matched samples that were also profiled by an experienced researcher. DNA yield, 16S PCR success, sequencing library size and microbial diversity were compared between the groups in order to assess both the ability and accuracy of students in characterising faecal microbiota. Our research revealed that students were able to produce research-grade microbiome data comparable to a postgraduate researcher. Importantly, we found that students did not introduce contamination at a higher rate than the trained researcher. These findings reinforce that the undergraduate classroom is a valuable approach for microbiome research in addition to its benefits for student engagement and experience. The design and successful implementation of these practicals provide a template for a variety of research-led microbiome teaching.

scientific communication and education↗

bioRxiv2024

FOXP Genes Regulate Purkinje Cell Diversity in Cerebellar Development and Evolution

Mammalian cerebellar development is thought to be influenced by distinct Purkinje cell (PC) subtypes. However, the degree of PC heterogeneity and the molecular drivers of this diversity have remained unclear, hindering efforts to manipulate PC diversification and assess its role in cerebellar development. Here, we demonstrate the critical role of Foxp genes in cerebellar development by regulating PC diversification. We identified 11 PC subtypes in the embryonic mouse cerebellum through single-cell RNA sequencing. Using a novel unsupervised method, we mapped these subtypes in three-dimensional space, revealing discrete PC subtypes predictive of adult cerebellar organization, including longitudinal stripes and lobules. These subtypes exhibit unique combinations of Foxp1, Foxp2, and Foxp4 expression. Deletion of Foxp2 and Foxp1 disrupts PC diversification, leading to altered cerebellar patterning, including the loss of a specific Foxp1-expressing subtype and the cerebellar hemisphere. The Foxp1-expressing PC subtype is much more abundant in the fetal human cerebellum than in mice, but rare in the chick cerebellum, correlating with cerebellar hemisphere size in these species. This highlights the significance of Foxp1-expressing PCs in cerebellar hemisphere development and evolution. Therefore, our study identifies Foxp genes as key regulators of PC diversity, providing new insights into the developmental and evolutionary underpinnings of the cerebellum.

developmental biology↗

bioRxiv2024

Pouch microbiome changes during lactation in the short-beaked echidna (Tachyglossus aculeatus)

Monotreme and marsupial early development is characterised by a short gestation, the birth of the young at an early stage of development, and a long lactation in the pouch or pseudo-pouch. The lack of a functional adaptive immune system in these altricial young raises questions about how they survive in a microbe-rich world. Previous studies on marsupial pouches have revealed changes to pouch microbe composition during lactation but no information is available in monotremes. We investigated changes in the echidna pseudo-pouch microbiome during different stages of the reproductive cycle and whether this differs between wild and zoo-managed animals. Swab samples were obtained from wild and captive echidna pseudo-pouches outside of breeding season, during courtship and breeding, and during lactation. 16S rRNA gene metabarcoding revealed that the pseudo-pouch microbiome undergoes dramatic changes during lactation, with a reduction in bacterial taxa that may be pathogenic. These changes were not observed in samples taken outside of breeding season or during courtship and mating. This showed that the echidna pseudo-pouch environment changes during lactation to accommodate young that lack a functional adaptive immune system. This study pioneers pouch microbiome research in monotremes, provides new biological information on echidna reproduction, and may also provide information about the effects of captive management to inform breeding programs in the future.

genomics↗

bioRxiv2023

Bushfire alters the gut microbiome in endangered Kangaroo Island echidnas (Tachyglossus aculeatus multiaculeatus)

Kangaroo Island experienced extensive bushfires in December 2019 and January 2020, affecting almost half of the island. This impacted several threatened species including the Kangaroo Island echidnas (Tachyglossus aculeatus multiaculeatus). Echidnas can often survive fires, however, changes in soil chemistry and food availability raises questions about the impact on echidna gut health and foraging behaviours. Due to local participation in the citizen science project, EchidnaCSI, echidna scats were collected before and after the fires to directly assess how fire affects their gut microbiomes. Metabarcoding of scat microbiota (n = 13) revealed substantial changes in bacterial composition of echidna faeces post-bushfire when compared to samples collected prior to bushfires. Before the fires, echidna gut microbiomes were more variable and contained mostly soil-associated bacteria, whereas post-fire samples shifted to uniform bacterial communities consisting of lactic acid and gut commensal bacteria. Interestingly, changes were observed in scats collected in both burnt and unburnt regions of the island, suggesting echidnas are foraging between these areas. This is the first study to document changes in gut microbiome of any mammal following bushfires. More work is needed to investigate if the gut bacterial communities continue to change as areas recover from fires.

genomics↗

bioRxiv2023

Experimentally induced active and quiet sleep engage non-overlapping transcriptomes in Drosophila

Sleep in mammals can be broadly classified into two different physiological categories: rapid eye movement (REM) sleep and slow wave sleep (SWS), and accordingly REM and SWS are thought to achieve a different set of functions. The fruit fly Drosophila melanogaster is increasingly being used as a model to understand sleep functions, although it remains unclear if the fly brain also engages in different kinds of sleep as well. Here, we compare two commonly used approaches for studying sleep experimentally in Drosophila: optogenetic activation of sleep-promoting neurons and provision of a sleep-promoting drug, Gaboxadol. We find that these different sleep-induction methods have similar effects on increasing sleep duration, but divergent effects on brain activity. Transcriptomic analysis reveals that drug-induced deep sleep ( quiet sleep) mostly downregulates metabolism genes, whereas optogenetic active sleep upregulates a wide range of genes relevant to normal waking functions. This suggests that optogenetics and pharmacological induction of sleep in Drosophila promote different features of sleep, which engage different sets of genes to achieve their respective functions.

neuroscience↗

bioRxiv2022

Multi-omic spatial profiling reveals the unique virus-driven immune landscape of COVID-19 placentitis

COVID-19 placentitis, a rare complication of maternal SARS-CoV-2 infection, only shows detectable virus in the placenta of a subset of cases. We provide a deep multi-omic spatial characterisation of placentitis from obstetrically complicated maternal COVID-19 infection. We found that SARS-CoV-2 infected placentas have a distinct transcriptional and immunopathological signature. This signature overlaps with virus-negative cases supporting a common viral aetiology. An inverse correlation between viral load and disease duration suggests viral clearance over time. Quantitative spatial analyses revealed a unique microenvironment surrounding virus-infected trophoblasts characterised by PDL1-expressing macrophages, T-cell exclusion, and interferon blunting. In contrast to uninfected mothers, ACE2 was localised to the maternal side of the placental trophoblast layer of almost all mothers with placental SARS-CoV-2 infection, which may explain variable susceptibility to placental infection. Our results demonstrate a pivotal role for direct placental SARS-CoV-2 infection in driving the unique immunopathology of COVID-19 placentitis. Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

immunology↗

bioRxiv2021

Low doses of the organic insecticide spinosad trigger lysosomal defects, ROS driven lipid dysregulation and neurodegeneration in flies

The plight of insect populations around the world and the threats it poses to agriculture and ecosystems has thrown insecticide use into the spotlight. Spinosad is an organic insecticide, considered less harmful to beneficial insects than synthetic insecticides, but its mode of action remains unclear. Using Drosophila, we show that low doses of spinosad reduce cholinergic response in neurons by antagonizing D6 nAChRs. D6 nAChRs are transported to lysosomes that become enlarged and accumulate upon spinosad treatment. Oxidative stress is initiated in the central nervous system, and spreads to midgut and disturbs lipid storage in metabolic tissues in a D6-dependent manner. Spinosad toxicity was ameliorated with the antioxidant N-Acetylcysteine amide (NACA). Chronic exposures lead to mitochondrial defects, severe neurodegeneration and blindness in adult animals. The many deleterious effects of low doses of this insecticide reported here point to an urgent need for rigorous investigation of its impacts on beneficial insects.

neuroscience↗

bioRxiv2019

The spread of resistance to imidacloprid is restricted by thermotolerance in natural populations of Drosophila melanogaster

Imidacloprid, the worlds most utilised insecticide1, has raised considerable controversy due to its harmful effects on non-pest species2-6 and there is increasing evidence showing that insecticides have become the primary selective force in many insect species7-14. The genetic response to insecticides is heterogeneous across population and environment15-17, leading to more complex patterns of genetic variation than previously thought. This motivated the investigation of imidacloprid resistance at different temperatures in natural populations of Drosophila melanogaster originating from four climate extremes replicated across two continents. Population and quantitative genomic analysis, supported by functional tests, demonstrated a polygenic basis to resistance and a major trade-off with thermotolerance. Reduced genetic differentiation at resistance-associated loci indicate enhanced gene flow at these loci. Resistance alleles showed stronger evidence of positive selection in temperate populations compared to tropical populations. Polygenic architecture and ecological factors should be considered when developing sustainable management strategies for both pest and beneficial insects.

evolutionary biology↗

bioRxiv2017

Partitioning The Roles Of Insect And Microbial Enzymes In The Metabolism Of The Insecticide Imidacloprid In Drosophila melanogaster

Resistance to insecticides through enhanced metabolism is a worldwide problem. The Cyp6g1 gene of the vinegar fly, Drosophila melanogaster, is a paradigm for the study of metabolic resistance. Constitutive overexpression of this gene confers resistance to several chemical classes of insecticides, including the neonicotinoids exemplified by the insecticide imidacloprid (IMI). The metabolism of IMI in this species has been previously shown to yield oxidative and nitro-reduced metabolites. While levels of the oxidative metabolites are correlated with CYP6G1 expression, nitro-reduced metabolites are not, raising the question of how these metabolites are produced. Some IMI metabolites are known to be toxic, making their fate within the insect a second question of interest. These questions have been addressed by coupling the genetic tools of gene overexpression and CRISPR gene knock-out with the sensitive mass spectrometric technique, the Twin-Ion Method (TIM). Analysing axenic larvae indicated that microbes living within D. melanogaster are largely responsible for the production of the nitro-reduced metabolites. Knock-out of Cyp6g1 revealed functional redundancy, with some metabolites produced by CYP6G1 still detected. IMI metabolism was shown to produce toxic products that are not further metabolized but readily excreted, even when produced in the Central Nervous System (CNS), highlighting the significance of transport and excretion in metabolic resistance.

genetics↗