Biology subjects

Sawyer, A.

Publications and source records attributed to Sawyer, A..

9 recordsLinked to original sources

bioRxiv2026

Prenatal stress interacts with embryonic loss of Fgfr2 to increase locomotor hyperactivity in mice

Attention-deficit/hyperactivity disorder (ADHD) is a developmental psychiatric disorder associated with a complex interplay of genetic and environmental risk factors. We have shown embryonic dorsal forebrain loss in mice of fibroblast growth factor receptor 2 (Fgfr2), which has a critical role in normal brain development, results in ADHD-relevant phenotypes: increased locomotion and sociability, and impaired working memory postnatally. How such genetic vulnerabilities interact with environmental exposures to translationally model human ADHD risk remains unclear. Here, we pair the embryonic hGFAP-cre Fgfr2 conditional knockout (Fgfr2 cKO) mouse model with prenatal repetitive restraint stress, modeling an environmental factor associated with ADHD risk, to assess adult offspring behaviors and dopamine transporter (DAT) levels. Offspring of prenatally stressed, Fgfr2 cKO mice show increased locomotion (80% compared to non-stressed, Fgfr2 cKO animals). Prenatal stress led to a trend increase in impulsivity and trend decrease in working memory but did not affect sociability. There were no interactions with Fgfr2 cKO observed in these behaviors. Neurobiologically, prenatal stress led to a trend decrease in medial frontal cortex DAT, but these changes did not correlate with behavior. Taken together, our findings implicate prenatal stress as a potential contributor to gene-environment interactions for ADHD risk, supporting its use in translational animal models of childhood psychiatric disorders.

neuroscience↗

bioRxiv2025

Impact of N6-methyladenosine (m6A) machinery on HIV-1 replication in primary CD4+ T cells

N6-methyladenosine (m6A) is the most prevalent internal modification of cellular and viral RNA and is critical to the regulation of its localization, stability, and translation. Previous studies on the role of m6A during HIV-1 replication have produced conflicting results. Since m6A function can vary dramatically by cell type and state, here we aimed to clarify the role of the m6A machinery during HIV-1 replication in primary CD4+ T cells. Using CRISPR-Cas9 we targeted 46 cellular genes implicated in m6A or 5-methylcytosine (m5C) regulation and measured subsequent HIV-1 replication in primary CD4+ T cells. Only knockout of the m6A writer complex auxiliary proteins VIRMA and WTAP, and the m6A reader YTHDF2 were validated as significantly decreasing HIV-1 replication. In contrast, knockout of METTL3 or METTL14, which form the catalytic core of the writer complex, resulted in only marginal changes in HIV-1 infection, despite significant decreases in total cellular m6A levels. Chemical inhibition of METTL3 led to a dose-dependent decrease in HIV-1 infection, coupled with an increase in protein levels of METTL3 and other writer complex members. Expression of writer proteins was also co-dependent, revealing complex regulatory feedback mechanisms. Overall, these results clarify the role of epitranscriptomic machinery during HIV-1 replication in primary CD4+ T cells and suggest regulation by auxiliary members of the m6A writer complex is more influential than the function of the catalytic core itself on HIV-1 infection in primary CD4+ T cells. IMPORTANCEm6A is the most common chemical modification on cellular and viral RNA and regulates its stability, localization, and translation. m6A modification and its regulation varies dramatically between cell types and cell states. In this study, we investigated the role of m6A factors during HIV-1 infection of physiologically relevant primary CD4+ T cells. Using CRISPR-Cas9 to knockout 46 cellular genes implicated in RNA modification, we found only the m6A writer complex auxiliary members WTAP and VIRMA, and the reader YTHDF2, significantly affected HIV-1 replication in these cells. In contrast, knockout of METTL3 or METTL14, which form the catalytic core of the writer complex, resulted in marginal changes in HIV-1 infection, despite larger reductions in total cellular m6A levels. Our findings suggest regulation by auxiliary members of the m6A writer complex is more influential than the function of the catalytic core itself on HIV-1 infection in primary CD4+ T cells.

microbiology↗

bioRxiv2024

dsRNAmax: a Multi-Target Chimeric dsRNA Designer for Safe And Effective Crop Protection

Crop protection is undergoing significant evolution, transitioning toward sustainable approaches that minimise impacts on the environment and human health. Exogenous application of double-stranded RNA (dsRNA) that silences pest or pathogen genes via RNAi (RNA interference) has promise as a safe and effective next generation crop protection platform without the need for genetic modification. However, exogenous dsRNA application at scale presents challenges. Specifically, a single dsRNA sequence needs to balance targeting the standing variation in a target pest or pathogen group against the potential for adverse impacts in a vast array of non-target and beneficial organisms at the application site and broader environment. To address these competing demands, we present dsRNAmax (https://github.com/sfletc/dsRNAmax), a software package that employs k-mer based assembly of chimeric dsRNA sequences to target multiple related RNA sequences, to broaden the target spectrum. The package ensures designed dsRNAs have no defined contiguous sequence homology with any off-target sequences, which can range from single transcriptomes through to metagenome sequence data and beyond. The efficacy of this package is demonstrated by a dsRNAmax-designed dsRNA that inhibits multiple root-knot nematode species but not a non-target nematode species, despite its susceptibility to environmental RNAi and high homology of the target gene. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/628581v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@c776c5org.highwire.dtl.DTLVardef@1468e45org.highwire.dtl.DTLVardef@1268b08org.highwire.dtl.DTLVardef@171ee19_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Intragenomic variants of a putative effector drive early-stage infection in a broad host-range rust fungus

Rust fungi are pathogens that impact plants of environmental, agricultural, cultural, and economic importance. Their mechanisms of pathogenicity are not well-understood but are likely governed by effectors, secreted proteins that manipulate host cellular processes to facilitate infection and suppress immune responses. We sought to understand how three effector candidates (EFC1, EFC2, and EFC3) expressed in the first stages of Austropuccinia psidii (myrtle rust) infection influence pathogenicity. We experimentally tested gene function through application of double-stranded RNA (dsRNA) and characterised the genomic landscape of putative effectors expressed during infection to assess whether putative effectors are needed for infection, and whether they are under selection pressure. One of the three screened candidates, EFC1, met our criteria of an effector in that it was predicted to be secreted, and was needed to cause but not maintain infection. We identified that this effector belongs to a gene family of intragenomic variants in tandem repeats flanked by transposable elements. Single nucleotide polymorphisms among these variants have signatures of non-neutral selection. This effector has predicted structural homology to a glycosaminoglycan-binding domain and may have a role in pectin or chitin-binding. We hypothesise that intragenomic variability in this family of effector genes facilitates host-range versatility in the A. psidii-Myrtaceae pathosystem.

microbiology↗

bioRxiv2023

Substantial urbanization-driven declines of larval and adult moths in a subtropical environment

Recent work has shown the decline of insect abundance, diversity, and biomass, with potential implications for ecosystem services. These declines are especially pronounced in regions with high human activity, and urbanization is emerging as a significant contributing factor. However, the scale of these declines and the traits that determine variation in species-specific responses remain less well understood, especially in subtropical and tropical regions, where insect diversity is high and urban footprints are rapidly expanding. Here, we surveyed moths across an entire year in protected forested sites across an urbanization gradient to test how caterpillar and adult life stages of subtropical moths (Lepidoptera) are impacted by urbanization. Specifically, we assess how urban development affects the total abundance of caterpillars and adult moths, and quantify how richness and phylogenetic diversity of macro-moths are impacted by urban development. Additionally, we determine the effects of urban warming on species-specific adult macro-moth abundance while accounting for urban development and explore how life-history traits condition species responses to urban stressors. At the community level, we find that urban development decreases caterpillar biomass and adult moth abundance. We also find sharp declines of adults in response to urban development across the moth phylogeny, leading to a decrease in species richness and phylogenetic diversity in more urban sites. Finally, our study found that smaller macro-moths are less impacted by urban development than larger macro- moths in subtropical environments, perhaps highlighting the tradeoffs of metabolic costs of urban heat island effects favoring smaller moths over the relative benefits of dispersal for larger moths. In summary, our research underscores the far-reaching consequences of urbanization on moths and provides compelling evidence that urban forests alone may not be sufficient to safeguard biodiversity in cities.

ecology↗

bioRxiv2021

Intact double stranded RNA is mobile and triggers RNAi against viral and fungal plant pathogens

Topical application of double-stranded RNA (dsRNA) as RNA interference(RNAi) based biopesticides represents a sustainable alternative to traditional transgenic, breeding-based or chemical crop protection strategies. A key feature of RNAi is its ability to act non-cell autonomously, a process that plays a critical role in plant protection. However, the uptake of dsRNA upon topical application, and its ability to move and act non-cell autonomously remains debated and largely unexplored. Here we show that when applied to a leaf, unprocessed full-length dsRNA enters the vasculature and rapidly moves to multiple distal below ground, vegetative and reproductive tissue types in several model plant and crop hosts. Intact unprocessed dsRNA was detected in the apoplast of leaves, roots and flowers after leaf application and maintained in subsequent new growth. Furthermore, we show mobile dsRNA is functional against root infecting fungal and foliar viral pathogens. Our demonstration of the uptake and maintained movement of intact and functional dsRNA stands to add significant benefit to the emerging field of RNAi-based plant protection.

plant biology↗

bioRxiv2020

Extended amygdala-parabrachial circuits alter threat assessment to regulate feeding

An animals evolutionary success depends on the ability to seek and consume foods while avoiding environmental threats. However, how evolutionarily conserved threat detection circuits modulate feeding is unknown. In mammals, feeding and threat assessment are strongly influenced by the parabrachial nucleus (PBN), a structure that responds to threats and inhibits feeding. Here, we report that the PBN receives dense inputs from the bed nucleus of the stria terminalis (BNST), an extended amygdala structure that encodes affective information. Using a series of complementary approaches, we identify opposing BNST-PBN circuits that modulate a genetically-defined population of PBN neurons to control feeding. This previously unrecognized neural circuit integrates threat assessment with the intrinsic drive to eat.

neuroscience↗

bioRxiv2018

Impending regeneration failure of the IUCN Vulnerable Borneo ironwood (Eusideroxylon zwageri)

The regeneration of many climax species in tropical forest critically depends on adequate seed dispersal and seedling establishment. Here we report the decreased abundance and increased spatial aggregation of younger trees of the Borneo ironwood (Eusideroxylon zwageri) in a protected forest in Sabah Malaysia. We observed a high level of seedling herbivory with strong density dependence, likely exacerbated by local aggregation and contributing to the progressively shrinking size-distribution. We also note the largely undocumented selective herbivory by sambar deer on E. zwageri seedlings. This study highlights the combined impact of altered megafauna community on a tree population through interlinked ecological processes and the need for targeted conservation intervention for this iconic tropical tree species.

ecology↗

bioRxiv2017

Do early life non-cognitive skills matter?A systematic review and meta-analysis of early life effects on academic achievement, psychosocial, language and cognitive, and health outcomes

BackgroundSuccess in school and the labour market is due to more than just high intelligence. Associations between traits such as attention, self-regulation, and perseverance in childhood, and later outcomes have been investigated by psychologists, economists, and epidemiologists. Such traits have been loosely referred to as \"non-cognitive\" skills. There has been no attempt to systematically assess the relative importance of non-cognitive skills in early life on later outcomes.\n\nMethodsThe systematic review protocol was registered with the International Prospective Register for Systematic Reviews (PROSPERO, CRD42013006566) in December 2013. We systematically reviewed electronic databases covering psychology, education, health and economics for articles published from database conception until September 2015. Titles and abstracts were screened for eligibility, and from eligible articles data was extracted on study design, sample type and size, age of participants at exposure and outcome, loss to follow up, measurement of exposure and outcome, type of intervention and comparison group, confounding adjustment and results. Where possible we extracted a standardised effect size. We reviewed all studies and rated their evidence quality as better, weak, or poor on the basis of study design and potential for confounding, selection and measurement bias.\n\nResultsWe reviewed 375 studies and provided interpretation of results from 142 (38%) better quality studies comprising randomised controlled trials, quasi-experimental, fixed effects including twin studies, longitudinal and some cross-sectional designs that made reasonable attempts to control confounding. In the academic achievement category outcomes were reported in 78 publications of better quality studies which were consistent with 0.1-0.2 SD effects.\n\nPsychosocial outcomes were reported in 65 better quality studies consistent with effects of 0.3-0.4 SD. For the language and cognitive category there were 42 publications reporting better quality studies consistent with effects of 0.3-0.4 SD. For physical health, results across only eight better quality studies were inconsistent but centred around zero. Analysis of funnel plots consistently showed asymmetric distributions, raising the potential of small study bias which may inflate these observed effects.\n\nConclusionsThe evidence under-pinning the importance of non-cognitive skills for life success is diverse and inconsistent. Nevertheless, there is tentative evidence from published studies that non-cognitive skills associate with modest improvements in academic achievement, psychosocial, and language and cognitive outcomes with effects in the range of 0.2-0.4 SD. The quality of evidence under-pinning this field is generally low with more than a third of studies making little or no attempt to control even the most basic confounding (endogeneity) bias. The evidence could be improved by adequately powering studies, and using procedures and tools that improve the conduct and reporting of RCTs and observational studies. Interventions designed to develop childrens non-cognitive skills could potentially improve opportunities, particularly for disadvantaged children. The inter-disciplinary researchers interested in these skills should take a more rigorous approach to determine which interventions are most effective.

epidemiology↗