Biology subjects

Anthony, R.

Publications and source records attributed to Anthony, R..

6 recordsLinked to original sources

bioRxiv2025

Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples

Oxford Nanopore adaptive sampling (NAS) is a method by which the long-read sequencing flowcell accepts or rejects DNA molecules that are actively being sequenced based on their initial [~]500bp sequences, selectively increasing target data output. NAS promises up to 5-10x enrichment of target sequencing yield without additional sample preparation, but this optimal performance is dependent on ideal sample parameters which may be difficult to achieve under many real-world use-cases. We evaluated the use of NAS with the current R10.4.1 flowcell chemistry for profiling clinical sputum metagenomes, achieving at best 3.1x enrichment of bacterial sequence output due to the shorter read lengths ([~]2.5kb) from the PCR amplification necessary to compensate for low DNA extraction yields. More critically, we encountered rapid pore loss during our runs that reduced total sequencing yield by an estimated 80%. We were unable to mitigate the pore loss despite extensive attempts to reduce contaminant carry-over, and we could not determine its cause but ruled out NAS and pore underloading as contributing factors. We conclude that the utility of NAS is often limited by the characteristics of the metagenomic sample studied, and that the factors contributing to pore loss need to be resolved before ONT sequencing can be reliably applied to long-read metagenomics.

microbiology↗

bioRxiv2025

Verification of emerging genomic mutations in Mycobacterium tuberculosis allows transmission chains to be distinguished in an epidemiological typing cluster extending over thirty years.

Whole genome sequencing (WGS) is able to identify epidemiological links between Mycobacterium tuberculosis isolates. Recent clustering can be ruled out using a pre-defined single nucleotide polymorphism (SNP) threshold. If WGS clusters grow significantly over time limited genetic variability hampers epidemiological investigations. Newly emerging (informative) SNPs in isolates of an extended cluster growing for more than 30 years to >150 cases in the Netherlands were analysed. WGS data was analyzed from 61 sequencing files from 54 patients. Genomic positions that varied within the cluster isolates were carefully screened for minority populations in other isolates from the cluster. A transmission scheme was generated on the basis of WGS data alone then compared to the epidemiological information available. Fifty-two informative SNPs were identified, eight of which were also detected as mixed variants. One emerging SNP in dnaA (1199G>A R400H) has been observed in other transmitted strains and may be under selection. There was high concordance between the transmission chains suggested on basis of the newly emerging SNPs and scenarios identified using classical epidemiological cluster investigations. Analysis of filtered SNPs accumulating in the genome of M. tuberculosis in large clusters contains information on transmission dynamics and can be used to support epidemiological investigations.

microbiology↗

bioRxiv2024

Understanding the epidemiology and pathogenesis of Mycobacterium tuberculosis with non-redundant pangenome and population genetics

Tuberculosis is a major public health threat demanding more than one million lives every year. Many challenges exist to defeat this deadly infectious disease which address the importance of a thorough understanding of the biology of the causative agent Mycobacterium tuberculosis (MTB). We generated a non-redundant pangenome of 420 epidemic MTB strains from China. We estimate that MTB strains have a pangenome of 4,278 genes encoding 4,183 proteins, of which 3,438 of which are core genes. However, due to 99,694 interruptions in 2,447 coding genes, only 1,651 may be translated in all samples, which dramatically reduces the number of active core genes. Of these interruptions, 67,315 (67.52%) could be classified by various genetic variations detected by currently available tools, and more than half of them are due to structure variations, mostly small indels. We further describe differential evolutionary patterns of genes under the influences of selective pressure, population structure and background selection. While selective pressure is ubiquitous among these coding genes, evolutionary adaptations primarily occur in 1,313 genes. Genes located in the cell wall and membrane region are under the strongest selective pressure, while biological processes including regulation of transcription, translation and regulation of growth are under strongest background selection in MTB. The metabolism of fatty acids may be an outstanding example of evolutionary adaption for MTB under current selective pressure. This study provides a comprehensive view on the genetic diversity and evolution patterns of coding genes in MTB which may deepen our understanding of its epidemiology and pathogenicity.

microbiology↗

bioRxiv2023

Microbiota-dependent indole production is required for the development of collagen-induced arthritis

Altered tryptophan catabolism has been identified in inflammatory diseases like rheumatoid arthritis (RA) and spondyloarthritis (SpA), but the causal mechanisms linking tryptophan metabolites to disease are unknown. Using the collagen-induced arthritis (CIA) model we identify alterations in tryptophan metabolism, and specifically indole, that correlate with disease. We demonstrate that both bacteria and dietary tryptophan are required for disease, and indole supplementation is sufficient to induce disease in their absence. When mice with CIA on a low-tryptophan diet were supplemented with indole, we observed significant increases in serum IL-6, TNF, and IL-1{beta}; splenic ROR{gamma}t+CD4+ T cells and ex vivo collagen-stimulated IL-17 production; and a pattern of anti-collagen antibody isotype switching and glycosylation that corresponded with increased complement fixation. IL-23 neutralization reduced disease severity in indole-induced CIA. Finally, exposure of human colon lymphocytes to indole increased expression of genes involved in IL-17 signaling and plasma cell activation. Altogether, we propose a mechanism by which intestinal dysbiosis during inflammatory arthritis results in altered tryptophan catabolism, leading to indole stimulation of arthritis development. Blockade of indole generation may present a novel therapeutic pathway for RA and SpA.

immunology↗

bioRxiv2022

Positive effects of tree diversity on tropical forest restoration in a field-scale experiment

Experiments under controlled conditions have established that ecosystem functioning is generally positively related to levels of biodiversity, but it is unclear how widespread these effects are in real-world settings and whether they can be harnessed for ecosystem restoration. We used a long-term, field-scale tropical restoration experiment to test how the diversity of planted trees affected recovery measured across a 500 ha area of selectively logged forest using multiple sources of satellite data. Replanting with species rich mixtures of tree seedlings that had higher phylogenetic and functional diversity accelerated restoration rates. Our results are consistent with a positive relationship between biodiversity and ecosystem functioning in the lowland dipterocarp rainforests of SE Asia and demonstrate that using diverse mixtures of species can enhance initial recovery after logging.

ecology↗

bioRxiv2020

Functional modulation of T follicular cells in vivo enhances antigen-specific humoral immunity

Generation of high-affinity IgG is essential for defense against infections and cancer, is the intended consequence of many vaccines, but can cause autoimmune and inflammatory diseases when inappropriately directed against self (Wang et al., 2018, Ludwig et al., 2017, Chinen et al., 2010). The interplay and balance of T follicular helper cells (TFH) and T follicular regulatory cells (TFR) is critical for production of high-affinity IgG (Wing et al., 2018). Here, we empowered TFH cells and improve antigen-specific IgG responses with two interventions intended to transiently diminish TFR influence. First, adult mice were administered an antibiotic cocktail (ABX) for an extended period to deplete the immunoregulatory intestinal microbiota (Belkaid and Harrison, 2017, Thaiss et al., 2016, Rooks and Garrett, 2016, Honda and Littman, 2016, Perruzza et al., 2017, Teng et al., 2016, Block et al., 2016, Proietti et al., 2014, Slack et al., 2014). This treatment skewed T follicular cell ratios, with increased TFH and reduced TFR numbers. TNP-KLH immunization resulted in higher affinity TNP-specific IgG in ABX mice compared to controls. In a model of IgG-driven inflammatory nephritis, ABX mice had significantly worse nephritis accompanied by higher affinity antigen-specific IgG, and enriched TFH cells compared to controls. Second, we sought to functionally manipulate TFH and TFH cells, which both express the checkpoint inhibitory molecule, PD-1 (Sage et al., 2013), by administration of -PD-1 during immunization. This intervention enhanced the affinity of antigen-specific IgG and increased in TFH following TNP-KLH immunization and nephritis induction. These results suggest that altering TFH and TFR ratio during immunization is an appealing strategy to qualitatively improve IgG responses.

immunology↗