Biology subjects

Charles, R.

Publications and source records attributed to Charles, R..

7 recordsLinked to original sources

bioRxiv2026

A nicotine biosensor derived from microbial screening

Physiologically relevant biosensors are in increasingly high demand, yet existing ones are severely limited in the number and type of biomarkers that are detected. The lack of biorecognition elements for most medically relevant biomarkers restricts the development of next generation single and continuous use monitors. Over billions of years, microbes have evolved a vast array of proteins to sense and metabolize small molecules, including those pertinent to human health. Of particular interest to us is the identification and subsequent integration of new microbial redox enzymes into electronic biosensors building off the established electrochemical technology of the continuous glucose monitor. Here we deploy genomic screening to identify analyte specific redox enzymes for biosensor development. As a proof of concept, we report the first electrochemical enzyme-based nicotine biosensor from a novel microbial enzyme, and use a variant with improved catalytic performance to enhance sensor performance. The biosensor detects nicotine over 0.4-100 M, a range relevant to nicotine concentrations present in active smoker sweat, saliva, gastric juice, and urine. This microbial mining approach for discovering redox enzymes expands the sensing parts toolbox available over conventional antibodies and aptamers.

bioengineering↗

bioRxiv2025

Wearable sweat nicotine biosensor based on a nicotineoxidoreductase and its natural electron acceptor

The advent of wearable biosensors is empowering clinical and lifestyle decision making. Nicotine is a drug of significant negative impact on public health given the prevalence of smoking and vaping. Yet noninvasive, continuous monitoring of nicotine is challenging due to lack of specific and sensitive biosensing elements. Here, we report a wearable highly sensitive nicotine biosensor and demonstrate on-body deployment of the sensor in a first-in-human study. The biosensor comprises nicotine oxidoreductase (NicA2) with its natural cytochrome c electron acceptor (CycN) as mediator: both proteins play a key role in the nicotine-degrading bacterium, Pseudomonas putida S16. The biosensor detects nicotine over four-orders of magnitude (0.1-100 M) with nanomolar sensitivity (LOD [~]33.6 nM), performs in the physiological pH range (pH 6-9), and is highly selective against common interferants and the major human nicotine metabolite, cotinine. Incorporation of the biosensor in a custom wearable device enables real-time measurement of nicotine from locally induced sweat on volunteer subjects and demonstrates higher analytical accuracy than gold-standard mass spectrometry.

bioengineering↗

bioRxiv2024

Two distinct durable human class-switched memory B cell populations are induced by vaccination and infection

Memory lymphocytes are durable cells that persist in the absence of antigen, but few human B cell subsets have been characterized in terms of durability. The relative durability of eight non-overlapping human B cell sub-populations covering 100% of all human class-switched B cells was interrogated. Only two long-lived B cell populations persisted in the relative absence of antigen. In addition to canonical germinal center-derived switched-memory B cells with an IgD-CD27+ CXCR5+ phenotype, a second, non-canonical, but distinct memory population of IgD-CD27- CXCR5+ DN1 B cells was also durable, exhibited a unique TP63-linked transcriptional and anti-apoptotic signature, had low levels of somatic hypermutation, but was more clonally expanded than canonical switched-memory B cells. DN1 B cells likely evolved to preserve immunological breadth and may represent the human counterparts of rodent extrafollicular memory B cells that, unlike canonical memory B cells, can enter germinal centers and facilitate B cell and antibody evolution. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/624972v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@169c77forg.highwire.dtl.DTLVardef@1a872f5org.highwire.dtl.DTLVardef@1360cforg.highwire.dtl.DTLVardef@38d7ed_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2021

recount3: summaries and queries for large-scale RNA-seq expression and splicing

We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to the data, we provide the recount3 and snapcount R/Bioconductor packages as well as complementary web resources. Using these tools, data can be downloaded as study-level summaries or queried for specific exon-exon junctions, genes, samples, or other features. Monorail can be used to process local and/or private data, allowing results to be directly compared to any study in recount3. Taken together, our tools help biologists maximize the utility of publicly available RNA-seq data, especially to improve their understanding of newly collected data. recount3 is available from http://rna.recount.bio.

genomics↗

bioRxiv2018

ASCOT identifies key regulators of neuronal subtype-specific splicing

Public archives of next-generation sequencing data are growing exponentially, but the difficulty of marshaling this data has led to its underutilization by scientists. Here we present ASCOT, a resource that allows researchers to summarize, visualize, and query alternative splicing patterns in public RNA-Seq data. ASCOT enables rapid identification of splice-variants across tens of thousands of bulk and single-cell RNA-Seq datasets in human and mouse. To demonstrate the utility of ASCOT, we first focused on the nervous system and identified many alternative exons used only by a single neuronal subtype. We then leveraged datasets from the ENCODE and GTEx consortiums to study the unique splicing patterns of rod photoreceptors and found that PTBP1 knockdown combined with overexpression of MSI1 and PCBP2 activates rod-specific exons in HepG2 liver cancer cells. Furthermore, we observed that MSI1 targets intronic UAG motifs proximal to the 5 splice site and interacts synergistically with PTBP1 downregulation. Finally, we show that knockdown of MSI1 in the retina abolishes rod-specific splicing. This work demonstrates how large-scale analysis of public RNA-Seq datasets can yield key insights into cell type-specific control of RNA splicing and underscores the importance of considering both annotated and unannotated splicing events. ASCOT splicing and gene expression data tables, software, and interactive browser are available at http://ascot.cs.jhu.edu.

neuroscience↗

bioRxiv2018

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots

Root-associated microbes play a key role in plant performance and productivity, making them important players in agroecosystems. So far, very few studies have assessed the impact of different farming systems on the root microbiota and it is still unclear whether agricultural intensification influences network complexity of microbial communities. We investigated the impact of conventional, no-till and organic farming on wheat root fungal communities using PacBio SMRT sequencing on samples collected from 60 farmlands in Switzerland. Organic farming harboured a much more complex fungal network than conventional and no-till farming systems. The abundance of keystone taxa was the highest under organic farming where agricultural intensification was the lowest. The occurrence of keystone taxa was best explained by soil phosphorus levels, bulk density, pH and mycorrhizal colonization. The majority of keystone taxa are known to form arbuscular mycorrhizal associations with plants and belong to the orders Glomerales, Paraglomerales, and Diversisporales. Supporting this, the abundance of mycorrhizal fungi in roots and soils was also significantly higher under organic farming. To our knowledge, this is the first study to report mycorrhizal keystone taxa for agroecosystems, and we demonstrate that agricultural intensification reduces network complexity and the abundance of keystone taxa in the root microbiota.

microbiology↗

bioRxiv2017

Scaling read aligners to hundreds of threads on general-purpose processors

General-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads, genomics software must contend with new and subtle computer architecture issues. We discuss some of these and propose methods for improving thread scaling in tools that analyze each read independently, such as read aligners. We implement these methods in new versions of Bowtie, Bowtie 2 and HISAT. We greatly improve thread scaling in many scenarios, including on the recent Intel Xeon Phi architecture. We also highlight how bottlenecks are exacerbated by variable-record-length file formats like FASTQ and suggest changes that enable superior scaling.

bioinformatics↗