Biology subjects

Forbes, M.

Publications and source records attributed to Forbes, M..

6 recordsLinked to original sources

bioRxiv2026

Characterising recent antimalarial resistance in West Africa: Insights from amplicon sequencing of 17,384 Plasmodium falciparum infection samples

Plasmodium falciparum (P. falciparum) infection remains a significant public health threat in West Africa, where chemoprevention and first-line therapies are key interventions against malaria. However, the development and spread of resistance to commonly used antimalarials poses a growing threat to the efficacy of these strategies. This study characterises the recent landscape of antimalarial resistance in West Africa by analysing targeted amplicon sequences from 17,384 P. falciparum infection samples. Across countries, the prevalence of the pyrimethamine resistance-associated dhfr triple mutant allele (51I/59R/108N) exceeded 80%, while its combination with the sulphadoxine resistance-associated dhps 437G exceeded 60% of infections. Unlike the parasite genotypes in East Africa, the prevalence of the dhps 540E mutant was low (1.5%), whereas dhps 436A was common (43.8%). The chloroquine resistance marker crt 76T showed greatest geographic heterogeneity, ranging from low prevalence in Ghana (1.3%) to very common in The Gambia (64.9%). Non-synonymous mutants of kelch13 were uncommon, most with unknown relevance to artemisinin resistance and observed for the first time in Africa. However, mutants that are artemisinin resistance-associated elsewhere were detected in three infection samples from Ghana (574L, 561H, 469Y), and one in Cameroon (538V). This large-scale genomic surveillance of P. falciparum infections highlights the need for ongoing monitoring of drug resistance and for data integration throughout the region.

genomics↗

bioRxiv2025

Benchmarking of Human ReadRemoval Strategies for Viral andMicrobial Metagenomics

Human reads are a key contaminant in microbial metagenomics and enrichment-based studies, requiring removal for computational efficiency, biological analysis, and privacy protection. Various in silico methods exist, but their effectiveness depends on the parameters and reference genomes used. Here, we assess different methods, including the impact of the updated T2T-CHM13 human genome versus GRCh38. Using a synthetic dataset of viral and human reads, we evaluated performance metrics for multiple approaches. We found that the usage of high-sensitivity configuration of Bowtie2 with the T2T-CHM13 reference assembly significantly improves human read removal with minimal loss of specificity, albeit at higher computational cost compared to other methods investigated. Applying this approach to a publicly available microbiome dataset, we effectively removed sex-determining SNPs with little impact on microbial assembly. Our results suggest that our high-sensitivity Bowtie2 approach with the T2T-CHM13 is the best method tested to minimise identifiability risks from residual human reads.

genomics↗

bioRxiv2024

Optimal Phylogenetic Reconstruction of Insertion and Deletion Events

Insertions and deletions (indels) influence the genetic code in fundamentally distinct ways from substitutions, significantly impacting gene product structure and function. Despite their influence, the evolutionary history of indels is often neglected in phylogenetic tree inference and ancestral sequence reconstruction, hindering efforts to comprehend biological diversity determinants and engineer variants for medical and industrial applications. We frame determining the optimal history of indel events as a single Mixed-Integer Programming (MIP) problem, across all nodes in a phylogenetic tree adhering to topological constraints, and all sites implied by a given set of aligned, extant sequences. By disentangling the impact on ancestral sequences at each branch point, this approach identifies the minimal indel events that jointly explain the diversity in sequences mapped to the tips of that tree. MIP can recover alternate optimal indel histories, if available. We evaluated MIP for indel inference on a dataset comprising 15 real phylogenetic trees associated with protein families ranging from 165 to 2000 extant sequences, and on 60 synthetic trees at comparable scales of data and reflecting realistic rates of mutation. Across relevant metrics, MIP outperformed alternative parsimony-based approaches and reported the fewest indel events, on par or below their occurrence in synthetic datasets. MIP offers a rational justification for indel patterns in extant sequences; importantly, it uniquely identifies global optima on complex protein data sets without making unrealistic assumptions of independence or evolutionary underpinnings, promising a deeper understanding of molecular evolution and aiding novel protein design.

bioinformatics↗

bioRxiv2023

L-glyceraldehyde inhibits neuroblastoma cell growth via a multi-modal mechanism on metabolism and signaling

Glyceraldehyde (GA) is a 3-carbon monosaccharide that can be present in cells as a by-product of fructose metabolism. Bruno Mendel and Otto Warburg showed that the application of GA to cancer cells inhibits glycolysis and their growth. This phenomenon was extensively studied up until the 1970s. However, the molecular mechanism by which this occurred was not clarified. We describe a novel multi-modal mechanism by which the L-isomer of GA (L-GA) inhibits cancer cell growth. L-GA induces significant changes in the metabolic profile, promotes oxidative stress and hinders nucleotide biosynthesis. GC-MS and 13C-labelling was employed to measure the flow of carbon through glycolytic intermediates under L-GA treatment. It was found that L-GA is a potent inhibitor of glycolysis due to its proposed targeting of NAD(H)-dependent reactions. This results in growth inhibition, apoptosis and a redox crisis in the cancer cell. It was confirmed that the redox mechanisms were modulated via L-GA by proteomic analysis. This elucidated a specific subset of proteins harbouring oxidoreductase and antioxidant activity. Analysis of nucleotide pools in L-GA treated cells depicted a remarkable and previously unreported phenotype. Nucleotide biosynthesis in neuroblastoma cells is significantly inhibited upon L-GA treatment. Through the application of the antioxidant N-acetyl-cysteine in conjunction with L-GA, metabolic inhibition was partially relieved. We present novel evidence for the multi-modal mechanism of L-GA action in neuroblastoma cells. Specifically, a simple sugar that inhibits the growth of cancer via dysregulating the fragile homeostatic environment inherent to the cancerous cell.

biochemistry↗

bioRxiv2023

A high-throughput screen identifies RNA binding proteins that affect fertility in Caenorhabditis elegans and reveals a functional relationship between ADR-2 and SQD-1

RNA binding proteins play essential roles in coordinating germline gene expression and development in all organisms. Here, we report that loss of ADR-2, a member of the Adenosine DeAminase acting on RNA (ADAR) family of RNA binding proteins and the sole adenosine-to-inosine RNA editing enzyme in C. elegans, can improve fertility in multiple genetic backgrounds. First, we show that loss of RNA editing by ADR-2 restores normal embryo production to subfertile animals that transgenically express a vitellogenin (yolk protein) fusion to green fluorescent protein. Using this phenotype, a high-throughput screen was designed to identify RNA binding proteins that when depleted yield synthetic phenotypes with loss of adr-2. The screen uncovered a genetic interaction between ADR-2 and SQD-1, a member of the heterogenous nuclear ribonucleoprotein (hnRNP) family of RNA binding proteins. Microscopy, reproductive assays, and high-throughput sequencing reveal that sqd-1 is essential for the onset of oogenesis and oogenic gene expression in young adult animals, and that loss of adr-2 can counteract the effects of loss of sqd-1 on gene expression and rescue the switch from spermatogenesis to oogenesis. Together, these data demonstrate that ADR-2 can contribute to the suppression of fertility and suggest novel roles for both RNA editing-dependent and independent mechanisms in regulating embryogenesis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/565157v2_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@14a3449org.highwire.dtl.DTLVardef@aead7dorg.highwire.dtl.DTLVardef@1fff947org.highwire.dtl.DTLVardef@46d487_HPS_FORMAT_FIGEXP M_FIG Graphical AbstractFigure created with BioRender. C_FIG Article SummaryThe molecular information that controls early development is RNA. Interactions between RNA and RNA binding proteins (RBPs) are critical for successful reproduction across species. In this study, we uncovered two roles for the RBP ADR-2 in regulating reproduction. First, we demonstrate that the RNA editing activity of ADR-2 regulates fertility. Next, we screened over 250 other RBPs revealed a genetic interaction between ADR-2 and SQD-1. Further analysis revealed that sqd-1 is essential for the onset of oogenesis, and an editing-independent function of ADR-2 influences proper germline gene expression and oocyte fate in these animals.

genetics↗

bioRxiv2023

"Surviving and Thriving": Evidence for Cortical GABA Stabilization in Cognitively-Intact Oldest-Old Adults

Cortical GABA levels are reduced in older age; age-related differences in GABA may be associated with age-related cognitive change. The nature of age-related GABA differences in the highest-functioning stratum of the oldest-old (85+) population is not yet known. We extend our previously-reported Individual Participant Data Meta-Analysis of GABA levels (Porges et al., 2021) across the lifespan with four novel datasets sampling the cognitively-intact oldest-old. The slope of age-related GABA differences in cognitively-intact oldest-old adults flattens after roughly age 80. We interpret these findings as an effect of survivorship: inclusion in the study required intact cognition, and too great a reduction of GABA levels may not be compatible with neurophysiological function needed for intact cognition. This work contributes to a growing body of evidence suggesting that successful cognitive aging may require intact GABAergic function, as well as further characterizing successful aging amongst oldest-old adults.

neuroscience↗