Biology subjects

Fernandes, K.

Publications and source records attributed to Fernandes, K..

7 recordsLinked to original sources

bioRxiv2026

Temporal persistence of vertebrate airborne environmental DNA in a natural open-air setting

Airborne environmental DNA (eDNA) is a promising tool for detecting a wide range of terrestrial taxa, including threatened and invasive species, from trace genetic material shed into the air. Yet, application of this technique in species management is constrained by a limited understanding of airborne eDNA ecology, including temporal persistence of signals in open-air environments. We investigated the temporal persistence of airborne eDNA in a natural outdoor setting, using the invasive Bennetts wallaby Notamacropus rufogriseus as a case study. We captured airborne eDNA from a single Bennetts wallaby carcass, deployed in an area where wallabies are otherwise not present. A total of 180 samples were collected, spanning the period before deploying the carcass, the 11 days it was on site, and for 32 days after its removal, at distances of 1, 10, and 100 metres using both active (fan-assisted) and passive (no fan) collection methods. Although overall detection rates were low, wallaby DNA was detectable up to 100 metres away shortly after the wallaby was introduced to the site and for up to three days after its removal. These findings indicate that airborne eDNA persists only briefly. Actively sampling air using battery-powered fans significantly improved detection rates relative to passive sampling. We demonstrate that airborne eDNA can detect individual organisms in outdoor environments, but reliable detection requires robust sampling and replication to capture rare, transient signals. By revealing how these signals persist over time, our findings provide a framework for optimizing field deployment and for distinguishing remnant DNA from new incursions.

molecular biology↗

bioRxiv2025

Targeted Airborne eDNA Detection of Pest Wallabies: Effects of Sampler Type and Distance

Bennetts wallabies Notamacropus rufogriseus, introduced to New Zealand from Australia in the late 1800s, strongly exemplify the detection challenges posed by invasive terrestrial species that are rare, cryptic, and highly mobile. Across their invasive range, N. rufogriseus occupy large landscapes at low densities, making their surveillance challenging. Recent research has demonstrated that airborne environmental DNA (eDNA) can rapidly identify terrestrial vertebrate diversity in an area. Leveraging these findings, we investigate the utility of airborne eDNA for the targeted monitoring of N. rufogriseus, using a novel, probe-based quantitative PCR assay. The effects of filtration material, collection method (active versus passive), distance from the source, and environmental conditions were examined for their effects on airborne detection probability, using a captive population of wallabies in a controlled park setting. A total of 110 airborne samples were collected, 55 with active (battery-powered fan) samplers and 55 passive (non-powered) samplers, across six distinct experimental periods at distances of 0, 10, 100, and 1000 metres from the closest known source of wallaby DNA. Filters designed to capture coarse particles (>10 {micro}m) significantly improved detection rates and DNA recovery for actively collected samples, compared to filters targeting finer particles (1-10 {micro}m). Active samplers significantly outperformed passive samplers in overall detection rates, particularly at shorter ranges from the target. Distance from the source had a significant negative effect on detection probability. Detection rates declined sharply beyond 10 metres but remained possible up to 1 kilometre from the source for both collection methods. These findings demonstrate that airborne eDNA can detect terrestrial vertebrate species at ecologically relevant distances, supporting its potential for landscape-scale surveillance. Notably, these results underscore the importance of optimising sampler design when applying airborne eDNA for targeted species monitoring.

genetics↗

bioRxiv2025

In vivo inhibition of stearoyl-CoA desaturase modulates the hippocampal fatty acid profile and restores density of dendritic spines in the aggressive 5xFAD model of Alzheimer s disease

While alterations in brain lipids are a central feature of Alzheimers disease (AD), therapeutic strategies targeting brain lipid metabolism are still lacking. Prior preclinical work has shown that pharmacological inhibition of the fatty acid desaturase, stearoyl-CoA desaturase (SCD), leads to recovery of hippocampal synapses with associated improvements in learning and memory in the slow-progressing 3xTg AD mouse model. Here, we used the rapidly progressing, highly amyloidogenic 5xFAD AD model to further delve into the effect of the SCD inhibitor (SCDi) on AD-associated fatty acid alterations and synapse loss. Hippocampus, cortex and plasma samples were collected from male and female 5xFAD and non-carrier control mice for fatty acid profiling and assessment of disease hallmarks. Plaque pathology, gliosis, and fatty acid alterations that included an increase in the C16:1/C16:0 desaturation index, a measure of SCD enzymatic activity, were apparent in the female hippocampus at 5 months of age, with similar fatty acid changes appearing in males by 8 months. Intracerebroventricular infusion of SCDi via osmotic pump for 28 days in 5 months old female 5xFAD and NC mice modulated the SCD-related fatty acid disturbances as well as PUFA concentrations. Quantification of Golgi staining revealed an SCDi-induced recovery of dendritic spine density. The beneficial effects of SCDi treatment on fatty acid balance and hippocampal dendritic spines in this more aggressive amyloidogenic 5xFAD model further support SCD inhibition as a promising therapeutic avenue for AD.

neuroscience↗

bioRxiv2025

Ketogenic interventions prevent alterations of the gut microbiome in transgenic Alzheimer Disease mice

Alterations in the gut microbiome constitute a feature of aging and therefore represent a therapeutic target for aging-related diseases. In this study, we investigated the impact of ketogenic interventions on the microbiome of mice genetically predisposed to Alzheimers disease (AD). AD mice exhibited several microbial alterations, notably increased levels of Bifidobacterium and decreased levels of Bacteroidetes. Ketogenic interventions, either a medium-chain triglyceride-enriched diet (MCT) or carbohydrate-free high-fat diet (CFHF), administered for 1 month restored the levels of more than 50% of the bacteria altered in AD mice, including a strong reduction in Bifidobacterium levels. Ketogenic interventions induced a shift in the gut microbiome associated with increased levels of short-chain fatty acid-producing bacteria, such as Lachnospiraceae and Muribaculaceae. MCT and CFHF also triggered diet-specific microbial changes, which may contribute to the distinct physiological effects of these diets. In conclusion, ketogenic interventions may influence AD pathophysiology by modulating the gut microbiome.

neuroscience↗

bioRxiv2024

tombRaider - improved species and haplotype recovery from metabarcoding data through artefact and pseudogene exclusion.

Environmental DNA metabarcoding has revolutionized ecological surveys of natural systems. By amplifying and sequencing small gene fragments from environmental samples containing complex DNA mixtures, scientists are now capable of exploring biodiversity patterns across the tree of life in a time-efficient and cost-effective manner. However, the accuracy of species and haplotype identification can be compromised by sequence artefacts and pseudogenes. Despite various strategies developed over the years, effective removal of artefacts remains challenging and inconsistent data reporting standards hinder reproducibility in eDNA metabarcoding experiments. To address these issues, we introduce tombRaider, an open-source command line software program (https://github.com/gjeunen/tombRaider) and R package (https://github.com/gjeunen/tombRaider_R) to remove artefacts and pseudogenes from metabarcoding data post clustering and denoising. tombRaider features a modular algorithm capable of evaluating multiple criteria, including sequence similarity, co-occurrence patterns, taxonomic assignment, and the presence of stop codons. We validated tombRaider using various published data sets, including mock invertebrate communities, air eDNA from a zoo, and salmon haplotypes from aquatic eDNA. Our results demonstrate that tombRaider effectively removed a higher proportion of artefacts while retaining authentic sequences, thus enhancing the accuracy and reliability of eDNA-derived diversity metrics. This user-friendly software program not only improves data quality in eDNA metabarcoding studies, but also contributes to standardised reporting practices, an aspect currently lacking in this emerging research field.

bioinformatics↗

bioRxiv2024

Electrocorticographic and Astrocytic Signatures of Stearoyl-CoA Desaturase Inhibition in the Triple Transgenic Mouse Model of Alzheimer's Disease

The symptomatology of Alzheimers disease (AD) includes cognitive deficits and sleep disturbances. Recent findings suggest the involvement of dysfunctions in lipid metabolism, such as oleic acid build-up, in the brain of AD patients and animal models. In addition, the inhibition of stearoyl-CoA desaturase (SCD), a lipid-converting enzyme, was shown to restore memory in triple transgenic (3xTg)-AD mice. In the brain, astrocytes regulate the synthesis of specific lipids. Alterations in astrocytes and their function were reported in AD patients and animal models, and astrocytes have been implicated in the regulation of sleep. However, the relationship between sleep disturbances, astrocytes and lipid metabolism remains to be explored in AD. This project thus aimed at assessing whether the inhibition of SCD restores sleep in 3xTg-AD mice, and whether this associated with modifications in astrocytic function. Wild-type (WT) and 3xTg-AD female mice (4-months old) received intracerebroventricular infusion of a SCD inhibitor (SCDi) or vehicle for 28 days, and a 24-hour electrocorticographic (ECoG) recording was conducted post-treatment. Post-mortem brain slices were stained for the astrocytic markers glial fibrillary acidic protein (GFAP) and 10-formyltetrahydrofolate dehydrogenase (ALDH1L1) to perform cell counting and/or morphological evaluation in the hippocampus, lateral hypothalamus and thalamus. The results indicate that the reduced time spent awake and increased time spent in slow wave sleep (SWS) in 3xTg-AD mice was not restored by the SCDi treatment. Similar observations were made concerning the increased number of wake and SWS bouts in 3xTg-AD mice. Rhythmic and scale-free ECoG activity were markedly altered in 3xTg-AD mice for all wake/sleep states, and SCDi significantly altered these phenotypes in a different manner in mutant mice in comparison to WT mice. GFAP- and ALDH1L1-positive cell densities were elevated in the hippocampus and lateral hypothalamus/thalamus of 3x-Tg-AD mice, respectively, and SCDi rescued the increase in the CA1 region in particular. Overall, these findings suggest that the multiple wake/sleep alterations in 3xTg-AD mice are not substantially restored by targeting lipid metabolism using SCD inhibition, at least for the targeted age window, but that this treatment can revert hippocampal changes in astrocytes. This work will benefit the understanding of the pathophysiology related to AD and associated sleep disturbances.

neuroscience↗

bioRxiv2023

Impact of in vivo cyclic reprogramming on the choroid plexus

In vivo reprogramming using the transient expression of Oct3/4, Sox2, Klf4 and c{square}Myc (OSKM) transcription factors can be used to induce tissue regeneration. A cyclic regime for short{square}term OSKM expression has been shown to promote regeneration of several organs however its impact on the brain remains largely unknown. We investigated the effects of a cyclic short-term OSKM expression on the choroid plexus (CP), a highly vascularized tissue found within the brain ventricles which is responsible for producing the cerebrospinal fluid (CSF). Transient reprogramming was done on 8-week-old mice carrying the polycistronic OSKM cassette under tetracycline operator (tetO) and confirmed the successful transient reprogramming. We then performed the analysis of the CP at cellular and molecular levels. The CP tissue exhibited minor morphological changes in height and area of epithelial cells. We did not observe any significant differences in the integrity of the brain-CSF barrier but noticed an increase of NKCC1 expression, a protein involved in CSF production. A whole transcriptome analysis (RNA-seq) was also carried on the tissue and showed no difference in gene expression after the transient reprogramming, at the exception of blood-related genes. Our results indicate that surprisingly the CP mainly remains insensible to in vivo transient reprogramming as only morphological and protein changes were observed in the tissue, suggesting that translational changes might be at stake during the reprogramming process but are not present at the transcriptomic level. Our results also highlight that more tailored strategies need to be developed for exploring the potential of CP reprogramming in regenerative medicine.

neuroscience↗