Biology subjects

Fernandes, K.

Publications and source records attributed to Fernandes, K..

3 recordsLinked to original sources

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↗