Biology subjects

Foo, A.

Publications and source records attributed to Foo, A..

3 recordsLinked to original sources

bioRxiv2023

Fluorescent Peptide-based Probe for the Detection of Alpha-synuclein Aggregates in the Gut

BackgroundParkinsons disease (PD) is diagnosed clinically by motor symptoms, with no molecular diagnostic test currently available. By the time motor symptoms manifest, significant irreversible neurodegeneration has already occurred, limiting the effectiveness of neuroprotective therapies and drug interventions. Recent identification of pathological alpha-synuclein (-syn) aggregates in the gastrointestinal (GI) tract of prodromal PD patients offer a potential avenue for early disease diagnosis. This study aims to explore specific fluorescence labelling of -syn aggregates in the GI tract using a peptide-based probe for early diagnosis of PD. MethodsWe used primary hippocampal neuronal cells and wild-type mouse tissues with the addition of pre-formed -syn fibrils to identify the most suitable peptide fluorescent probe (P1) for staining -syn aggregates in cells and tissues. We validated the probe labelling in GI tract tissues from three mouse models, including PFF-injected mice and two transgenic PD mouse strains. We quantified labelling accuracy by confocal imaging and protein analysis. ResultsWe found that P1 labelled -syn aggregates with high accuracy (87% in comparison to Serine129-phosphorylated -syn antibody) and high specificity for labelling their aggregated forms over monomeric forms. In GI tract tissues, P1 labelled -syn aggregates across tissue layers (mucosa, sub-mucosa, muscularis externa) and achieved comparable performance to antibody staining. Higher degree of probe labelling was found in older mice due to increased accumulation of -syn aggregates with ageing. Notably, -syn aggregates were readily detectable in the colonic mucosae using P1, indicating the potential use of this probe for early PD diagnosis during colonic examinations like colonoscopy. ConclusionWe have developed a peptide-based fluorescent probe and demonstrated its rapid and specific labelling of -syn aggregates. We highlight the probes ability to label these aggregates rapidly over -syn monomers and survey the abundance of -syn aggregates throughout the entire length of the GI tract. These support the further development of P1 as a specific fluorescent imaging biomarker for colonic -syn aggregates for the early detection of PD.

neuroscience↗

bioRxiv2023

Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates -- MosAIC (Mosquito-Associated Isolate Collection)

Mosquitoes transmit medically important human pathogens, including viruses like dengue virus and parasites such as Plasmodium spp., the causative agent of malaria. Mosquito microbiomes are critically important for the ability of mosquitoes to transmit disease-causing agents. However, while large collections of bacterial isolates and genomic data exist for vertebrate microbiomes, the vast majority of work in mosquitoes to date is based on 16S rRNA gene amplicon data that provides limited taxonomic resolution and no functional information. To address this gap and facilitate future studies using experimental microbiome manipulations, we generated a bacterial Mosquito-Associated Isolate Collection (MosAIC) consisting of 392 bacterial isolates with extensive metadata and high-quality draft genome assemblies that are publicly available for use by the scientific community. MosAIC encompasses 142 species spanning 29 bacterial families, with members of the Enterobacteriaceae comprising 40% of the collection. Phylogenomic analysis of three genera, Enterobacter, Serratia, and Elizabethkingia, reveal lineages of mosquito-associated bacteria isolated from different mosquito species in multiple laboratories. Investigation into species pangenomes further reveals clusters of genes specific to these lineages, which are of interest for future work to identify functions underlying mosquito host association. Altogether, we describe the generation of a physical collection of mosquito-associated bacterial isolates, their genomic data, and analyses of selected groups in context of genome data from closely related isolates, providing a unique, highly valuable resource to investigate factors for bacterial colonisation and adaptation within mosquito hosts. Future efforts will expand the collection to include broader geographic and host species representation, especially from individuals collected from field populations, as well as other mosquito-associated microbes, including fungi, archaea, and protozoa.

microbiology↗

bioRxiv2022

MINUUR: Microbial INsight Using Unmapped Reads

BackgroundOngoing research of the mosquito microbiome aims to uncover novel strategies to reduce pathogen transmission. Sequencing costs, especially for metagenomics, are however still significant. A resource that is increasingly used to gain insights into host-associated microbiomes is the large amount of publicly available genomic data based on whole organisms like mosquitoes, which includes sequencing reads of the host-associated microbes and provides the opportunity to gain additional value of these initially host-focused sequencing projects. MethodsTo analyse non-host reads from existing genomic data, we developed a snakemake workflow called MINUUR (Microbial INsights Using Unmapped Reads). Within MINUUR, reads derived from the host-associated microbiome were extracted and characterised using taxonomic classifications and metagenome assembly followed by binning and quality assessment. We applied this pipeline to five publicly available Aedes aegypti genomic datasets, consisting of 62 samples with a broad range of sequencing depths. ResultsWe demonstrate that MINUUR recovers previously identified phyla and genera and is able to extract bacterial metagenome assembled genomes (MAGs) associated to the microbiome. Of these MAGS, 42 are high-quality representatives with >90% completeness and <5% contamination. These MAGs improve the genomic representation of the mosquito microbiome and can be used to facilitate genomic investigation of key genes of interest. Furthermore, we show that samples with a high number of KRAKEN2 assigned reads produce more MAGs. ConclusionsOur metagenomics workflow, MINUUR, was applied to a range of Aedes aegypti genomic samples to characterise microbiome-associated reads. We confirm the presence of key mosquito-associated symbionts that have previously been identified in other studies and recovered high-quality bacterial MAGs. In addition, MINUUR and its associated documentation are freely available on GitHub (https://github.com/aidanfoo96/MINUUR) and provide researchers with a convenient workflow to investigate microbiome data included in the sequencing data for any applicable host genome of interest.

bioinformatics↗