Biology subjects

Floyd, R.

Publications and source records attributed to Floyd, R..

9 recordsLinked to original sources

bioRxiv2026

Chromatin remodelling enables enhancer resetting to facilitate the ERK transcriptional response

During development, cellular identity is ultimately determined by transcriptional output: lineage-specific genes must be activated, while genes associated with alternative fates must be repressed. This process depends on the activity of chromatin remodelling complexes, which regulate the accessibility of transcription factors to chromatin regulatory elements. In addition, cellular identity is shaped by exposure to intercellular signals. Understanding the mechanisms by which extracellular signals are translated into changes in the transcriptional program is essential for understanding cell fate decisions during development, as well as in disease conditions such as cancer. Here we describe a rapid and widespread enhancer resetting event in response to ERK signalling in mouse ES cells. This process occurs in two distinct phases: an immediate, genome-wide alteration in transcription factor binding dynamics at regulatory regions which is dependent on the release of paused RNA Polymerase II, followed by the re-establishment of a context appropriate, stable chromatin state. We demonstrate that the chromatin remodelling complex NuRD is required for this reestablishment phase and for the appropriate transcriptional response to ERK signalling. We propose that enhancer resetting places genomic regulatory regions in a state which is permissive to the exchange of transcription factors in order to establish a new, stable enhancer topology enabling rapid yet precise transcriptional response to extracellular signals.

molecular biology↗

bioRxiv2025

Incidence and attributes of chimeric COI and 18S sequences derived from nematode-infected arthropods

High-throughput sequencing is speeding the discovery of new species and making it possible to quantify the species richness of bulk samples. However, chimeric sequences can lead to both type I errors (true species mistakenly rejected) and type II errors (chimeras incorrectly viewed as valid species). This study employed nanopore sequencing to examine the incidence and nature of chimeric sequences recovered from 531 arthropod specimens infected with nematodes. Specifically, it examined chimera formation in two gene regions: the 658 bp segment of mitochondrial COI employed as the barcode region for the animal kingdom, and a 900 bp segment of nuclear 18S often employed to discriminate lineages of nematodes. This work revealed chimeras for both gene regions despite the deep sequence divergences between members of these two phyla. However, the incidence of chimeric molecules was higher for 18S than COI, with chimera formation correlating with local variation in DNA stability and conserved regions between parent sequences. Aside from demonstrating that chimeras can arise from distantly related organisms, this study provides insights into the mechanisms underlying their formation.

molecular biology↗

bioRxiv2025

Factors Influencing Emerald Ash Borer Ecological Interactions

Emerald ash borer beetles (Agrilus planipennis) in North America are a destructive invasive species that increase tree mortality continent-wide, resulting in major ecological and economic impacts. Trees that are infested experience mortality rates which can exceed 99%, disrupting ecological communities and threatening the $218 billion forestry industry in North America. Given the ecological and economic impact of these pests, we seek to identify biological interactions and gain a better understanding of what ecological factors might influence these relationships. We use DNA metabarcoding from multiple markers to analyze the fungal, parasitic, plant, and microbial interactions of these beetles, and assess the relative importance of life stage (e.g., larvae, pupae, and adults), collection location, habitat, and date on the detection of ecological interactions. We detected 30 different taxonomic orders including 29 order-level interactions in larva1-stage individuals (3 animal, 17 bacteria, and 9 fungi), 64 in larva2-stage individuals (8 animal, 24 bacteria, and 32 fungi), 10 in larva3-stage individuals (2 animal, 3 bacteria, and 5 fungi), 74 in the pupae (5 animal, 31 bacteria, and 38 fungi), and 82 in the adult beetles (4 animal, 48 bacteria, 29 fungi, and 1 parasitic alveolate). These detections include several likely agents of biocontrol including the known commercially available Beauveria fungus, and several potential parasites including Wolbachia and ichneumonid wasps. A random forest model suggests the detection of interactions is best predicted by collection date and life stage, with interactions more likely to be detected in pupal samples which may be the ideal target for future analysis, where cost and time constraints prevent the more thorough analysis of all life stages.

ecology↗

bioRxiv2024

Sex Hormones Alter Pseudomonas aeruginosa Iron Acquisition and Virulence Factors

Urinary Tract Infections (UTI) are one of the most widespread infections in healthcare and community settings worldwide. Pseudomonas aeruginosa is the third most common pathogen associated with catheter-associated UTI (CAUTI). P. aeruginosa infections are highly resistant and difficult to treat and it is currently classified as priority 1 by the World Health Organisation. In vitro studies of microbes typically employ laboratory media. The inadequacy of nutrient-rich media in simulating the physiological environment has led to the development of multiple media that mimic human body fluids, including Artificial Urine Medium (AUM). By studying growth and in vitro biofilm assays along with proteomics, we sought to establish whether UTI P. aeruginosa respond differently in laboratory media, AUM and urine. To further probe the impact of environmental influences, sex hormones estradiol, progesterone and testosterone were added at physiologically relevant concentrations. The proteomic profiles were then compared between hormone supplemented AUM and urine. Our findings indicate that bacterial responses in standard laboratory media, AUM and urine were distinct. Increased proteins associated with iron acquisition mechanisms were similar in both AUM and urine. However, differences were observed in other virulence and iron pathways, such as phenazine production. Treatment with hormones decreased the abundance of P. aeruginosa proteins involved in iron acquisition. Individual hormones exhibited specific bacterial alterations. The presence of estradiol increased protein abundance of the Pseudomonas Quinolone Signal (PQS) quorum sensing system. This study suggests that P. aeruginosa pathogenesis in UTI infections may be influenced by the presence of specific hormones in the host. Understanding the individual role of host factors could contribute to a personalised treatment approach based on the potential impact on infection susceptibility and outcome.

microbiology↗

bioRxiv2023

Genotypic and Phenotypic Analyses of Two Distinct Sets of Pseudomonas aeruginosa Urinary Tract Isolates

Urinary tract infections (UTIs) are associated with a high burden of morbidity, mortality, and cost. Pseudomonas aeruginosa employs a myriad of virulence factors, including biofilm formation and motility mechanisms, to cause infections including persistent UTIs. P. aeruginosa is highly resistant to antibiotics and the World Health Organization has identified it as a pathogen for which novel antimicrobials are urgently required. Genotypic and phenotypic characterization of P. aeruginosa from UTIs are underreported. In addition, the rise of antimicrobial resistance (AMR) is a cause for concern, particularly in many countries where surveillance is severely lacking. 22 P. aeruginosa UTI isolates were sourced from the United Kingdom (UK) and Kuwait. To establish the phenotypes of UK isolates, growth analysis, biofilm formation assays, motility assays, and antibiotic disc diffusion assays were performed. Whole genome sequencing, antimicrobial susceptibility assays, and in silico detection of AMR-associated genes were conducted on both sets of isolates. In terms of their phenotypic characteristics and genomic composition, the UTI isolates varied. Multiple resistance genes associated with resistance to various classes of antibiotics, such as aminoglycosides, fluoroquinolones, and {beta}-lactams, particularly in isolates from Kuwait. Extreme antibiotic resistance was detected in the isolates obtained from Kuwait, indicating that the country may be an antibiotic resistance hotspot. This study highlights that isolates from UTIs are diverse and can display extremely high resistance. Surveillance in countries such as Kuwait are currently limited and this study suggest the need for greater surveillance.

microbiology↗

bioRxiv2023

Barcode 100K Specimens: In a Single Nanopore Run

It is a global priority to better manage the biosphere, but action needs to be informed by monitoring shifts in the abundance and distribution of species across the domains of life. The acquisition of such information is currently constrained by the limited knowledge of biodiversity. Among the 20 million or more species of eukaryotes, just a tenth have scientific names. DNA barcoding can speed the registration of unknown animal species, the most diverse kingdom of eukaryotes, as the BIN system automates their recognition. However, inexpensive analytical protocols are critical as the census of all animal species will require processing a billion or more specimens. Barcoding involves DNA extraction followed by PCR and sequencing with the last step dominating costs until 2017. By recovering barcodes from highly multiplexed samples, the Sequel platforms from Pacific BioSciences slashed costs by 90%, but these instruments are only deployed in core facilities because of their expense. Sequencers from Oxford Nanopore Technologies provide an escape from high capital and service costs, but their low sequence fidelity has, until now, kept analytical cost above Sequel. However, the improved performance of its latest flow cells (R10.4.1) might erase this differential. This study demonstrates that a regular MinION flow cell can characterize an amplicon pool derived from 100,000 specimens while a Flongle flow cell can process one derived from several thousand. At $0.01 per specimen, DNA sequencing is now the least expensive step in the barcode workflow. By coupling simplified protocols for DNA extraction with ultra-low volume PCRs, it will be possible to move from specimen to DNA barcode for $0.10, a price point that will enable the census of all species within two decades.

molecular biology↗

bioRxiv2020

Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics

Enhancer-promoter dynamics are crucial for the spatiotemporal control of gene expression, but it remains unclear whether these dynamics are controlled by chromatin regulators, such as the nucleosome remodelling and deacetylase (NuRD) complex. The NuRD complex binds to all active enhancers to modulate transcription and here we use Hi-C experiments to show that it blurs TAD boundaries and increases the proximity of intermediate-range (~1 Mb) genomic sequences and enhancer-promoter interactions. To understand whether NuRD alters the dynamics of 3D genome structure, we developed an approach to segment and extract key biophysical parameters from 3D single-molecule trajectories of the NuRD complex determined using live-cell imaging. Unexpectedly, this revealed that the intact NuRD complex decompacts chromatin structure and makes NuRD-bound enhancers move faster, increasing the overall volume of the nucleus that these key regulatory regions explore. Interestingly, we also uncovered a rare fast-diffusing state of NuRD bound enhancers that exhibits directed motion. The NuRD complex reduces the amount of time that enhancers remain in this fast-diffusing state, which we propose might otherwise re-organise enhancer-promoter proximity. Thus, we uncover an intimate connection between a chromatin remodeller and the spatial dynamics of the local regions of the genome to which it binds.

cell biology↗

bioRxiv2018

MTA proteins act redundantly within the NuRD complex to ensure fidelity of ES cell lineage commitment

Multiprotein chromatin remodelling complexes show remarkable conservation of function amongst metazoans, even though components present in invertebrates are often present as multiple paralogous proteins in vertebrate complexes. In some cases these paralogues specify distinct biochemical and/or functional activities in vertebrate cells. Here we set out to define the biochemical and functional diversity encoded by one such group of proteins within the mammalian Nucleosome Remodelling and Deacetylation (NuRD) complex: Mta1, Mta2 and Mta3. We find that, in contrast to what has been described in somatic cells, MTA proteins are not mutually exclusive within ES cell NuRD and, despite subtle differences in chromatin binding and biochemical interactions, serve largely redundant functions. Nevertheless, ES cells lacking all three MTA proteins represent a complete NuRD null and are viable, allowing us to identify a previously undetected function for NuRD in maintaining differentiation trajectory during early stages of lineage commitment.

developmental biology↗

bioRxiv2017

The Nucleosome Remodelling and Deacetylation complex restricts Mediator access to enhancers to control transcription

A number of different chromatin remodelling complexes in mammalian cells are implicated in the control of gene expression. The genetic requirements for many such complex components have been described, and the biochemical activities of complex components characterised in vitro, yet the molecular mechanisms by which these biochemical activities impact transcriptional regulation in vivo remain ill-defined. Using an inducible system with fine temporal resolution, we show that the Nucleosome Remodelling and Deacetylation (NuRD) complex directly regulates chromatin architecture at enhancer regions in ES cells, in turn influencing the activity of RNA polymerase II via Mediator. Through this mechanism NuRD restricts Mediator access to enhancer chromatin during lineage commitment, thereby enabling appropriate transcriptional regulation. In contrast, acetylation levels of histone H3 lysine 27 are not immediately impacted by NuRD activity, correlating with transcriptional response only after expression levels have changed. These findings provide a detailed, molecular picture of genome-wide modulation of lineage-specific transcription by an abundant chromatin remodelling complex.

molecular biology↗