Biology subjects

Fletcher, D.

Publications and source records attributed to Fletcher, D..

6 recordsLinked to original sources

bioRxiv2025

Emergence of Artemisinin-based Combination Therapy Resistance Markers in Plasmodium falciparum from the Brazilian Tri-Border Region of the Guiana Shield

Plasmodium falciparum malaria remains a public health concern in the Brazilian Amazon, particularly among mobile and remote populations. Antimalarial drug resistance threatens elimination efforts, particularly in the Guiana Shield, which has historically been linked to the spread of resistant parasites. We analyzed 99 P. falciparum isolates collected in Roraima State, northern Brazil (2016-2020), using targeted deep sequencing. Variants were assessed in pfcrt, pfmdr1, and pfk13, and copy number variation in pfpm2 and pfpm3, including detection of the pfpm2/3 hybrid. High coverage enabled the detection of both dominant and minority alleles. Among the 99 isolates, the pfmdr1-NFD haplotype was found in 6% (6/99, all likely originating from Venezuela), pfcrt-C350R in 7% (7/99), and pfpm2 and pfpm3 amplifications in 5% (5/94) and 6% (6/97), respectively, and the pfpm2/3 hybrid in 4% (4/99). No validated or candidate pfk13 mutations associated with artemisinin partial resistance were detected. This study provides the first report of the pfpm2/3 hybrid and the pfmdr1-NFD haplotype in Brazil, and confirms the presence of pfcrt-C350R in isolates from the tri-border area. These variants, associated with reduced susceptibility to lumefantrine and piperaquine, suggest that parasites in northern Brazil already carry resistance markers that are prevalent in neighboring countries. These results highlight the need for continued genomic surveillance to detect early warning signals, guide treatment policies, and contain the spread of parasites with reduced susceptibility to ACT partner drugs.

microbiology↗

bioRxiv2024

The kinetics and optimality of influenza A virus locomotion

Influenza A viruses (IAVs) must navigate through a dense extracellular mucus to infect airway epithelial cells. The mucous layer, composed of glycosylated biopolymers (mucins), presents sialic acid that binds to ligands on the viral envelope and can be irreversibly cleaved by viral enzymes. It was recently discovered that filamentous IAVs exhibit directed persistent motion along their long axis on sialic acid-coated surfaces. This study demonstrates through stochastic simulations and mean-field theory, how IAVs harness a burnt-bridge Brownian ratchet mechanism for directed persistent translational motion. Importantly, our analysis reveals that equilibrium features of the system primarily control the dynamics, even out-of-equilibrium, and that ligand asymmetry allows for more robust directed transport. We show viruses occupy the optimal parameter range ( Goldilocks zone) for efficient mucous transport, possibly due to the evolutionary adaptation of enzyme kinetics. Our findings suggest novel therapeutic targets and provide insight into possible mechanisms of zoonotic transmission.

biophysics↗

bioRxiv2024

Effect of spatial overdispersion on confidence intervals for population density estimated by spatial capture-recapture

Spatially explicit capture-recapture models are used widely to estimate the density of animal populations. The population is represented by an inhomogeneous Poisson point process, where each point is the activity centre of an individual and density corresponds to the intensity surface. Estimates of density that assume a homogeneous model ( average density) are robust to unmodelled inhomogeneity, and the coverage of confidence intervals is good when the intensity surface does not change, even if it is quite uneven. However, coverage is poor when the intensity surface differs among realisations. Practical examples include populations with dynamic social aggregation, and the population in a region sampled using small detector arrays. Poor coverage results from overdispersion of the number of detected individuals; the number is Poisson when the intensity surface is static, but stochasticity leads to extra-Poisson variation. We investigated overdispersion from three point processes with a stochastic intensity surface (Thomas cluster process, random habitat mosaic and log-Gaussian Cox process). A previously proposed correction for overdispersion performed poorly. The problem is lessened by assuming population size to be fixed, but this assumption cannot be justified for common study designs. Rigorous correction for spatial overdispersion requires either prior knowledge of the generating process or replicated and representative sampling. When the generating process is known, variation in a new scalar measure of local density predicts overdispersion. Otherwise, overdispersion may be estimated empirically from the numbers detected on independent detector arrays.

ecology↗

bioRxiv2021

Using antibody synergy to engineer a high potency biologic cocktail against C. difficile

Here we show that transgenic spirulina may solve key challenges of developing effective monoclonal protein therapeutics for diseases afflicting gastrointestinal (GI) tissues. We describe, as a paradigm for this novel approach, LMN-201: an investigational four-component treatment for Clostridioides difficile (C. difficile) infection comprising four monoclonal protein therapeutics produced and delivered within spirulina biomass. Three antibody-like moieties within LMN-201 were rationally designed using a multiplicative potency framework, termed synthetic avidity, that increased in vitro toxin neutralization potency by >200-fold relative to the individual components. The fourth moiety, a lysin enzyme protein, adds direct, toxinotype-agnostic antibacterial activity. In rodent challenge models, species-relevant LMN-201-like cocktails reduced disease burden and mortality. In a human GI pharmacokinetic study, LMN-201 was present at concentrations 100- to 1,000-fold above the estimated minimally effective therapeutic threshold at the distal intestine. In a Phase 2 study in participants suffering from C. difficile infection (CDI), seven days of treatment with LMN-201 plus standard-of-care antibiotics achieved initial clinical cure in 21/21 (100%) participants, sustained clinical cure through four weeks in 19/21 (90.5%) participants, and had a favorable safety profile. These findings support LMN-201 with standard-of-care antibiotics as a viable treatment option for CDI, validate spirulina as a scalable platform for oral biologics, and establish a generalizable strategy for engineering high-potency combination protein therapeutics for diseases with a GI tissue nexus.

bioengineering↗

bioRxiv2021

Expression and Manufacturing of Protein Therapeutics in Spirulina

Arthrospira platensis (commonly known as spirulina) is a photosynthetic cyanobacterium1. It is a highly nutritious food that has been consumed for decades in the US, and even longer by indigenous cultures2. Its widespread use as a safe food source and proven scalability have driven frequent attempts to convert it into a biomanufacturing platform. But these were repeatedly frustrated by spirulinas genetic intractability. We report here efficient and versatile genetic engineering methodology for spirulina that allows stable expression of bioactive protein therapeutics at high levels. We further describe large-scale, indoor cultivation and downstream processing methods appropriate for the manufacturing of biopharmaceuticals in spirulina. The potential of the platform is illustrated by pre-clinical development and human testing of an orally delivered antibody therapeutic against campylobacter, a major cause of infant mortality in the developing world and a growing antibiotic resistance threat3,4. This integrated development and manufacturing platform blends the safety of food-based biotechnology with the ease of genetic manipulation, rapid growth rates and high productivity characteristic of microbial platforms. These features combine for exceptionally low-cost production of biopharmaceuticals to address medical needs that are unfeasible with current biotechnology platforms.

molecular biology↗

bioRxiv2018

A smartphone-based tool for rapid, portable, and automated wide-field retinal imaging

PurposeHigh-quality, wide-field retinal imaging is a valuable method to screen preventable, vision-threatening diseases of the retina. Smartphone-based retinal cameras hold promise for increasing access to retinal imaging, but variable image quality and restricted field of view can limit their utility. We developed and clinically tested a smartphone-based system that addresses these challenges with automation-assisted imaging.\n\nMethodsThe system was designed to improve smartphone retinal imaging by combining automated fixation guidance, photomontage, and multi-colored illumination with optimized optics, user-tested ergonomics, and touch-screen interface. System performance was evaluated from images of ophthalmic patients taken by non-ophthalmic personnel. Two masked ophthalmologists evaluated images for abnormalities and disease severity.\n\nResultsThe system automatically generated 100-degree retinal photomontages from five overlapping images in under 1 minute at full resolution (52.3 pixels per retinal degree) fully on-phone, revealing numerous retinal abnormalities. Feasibility of the system for DR screening using the retinal photomontages was performed in 71 diabetics by masked graders. DR grade matched perfectly with dilated clinical examination in 55.1% of eyes and within 1 severity level for 85.2% of eyes. For referral-warranted DR, average sensitivity was 93.3% and specificity 56.8%.\n\nConclusionsAutomation-assisted imaging produced high-quality, wide-field retinal images that demonstrate the potential of smartphone-based retinal cameras to be used for retinal disease screening.\n\nTranslational RelevanceEnhancement of smartphone-based retinal imaging through automation and software intelligence holds great promise for increasing the accessibility of retinal screening.

bioengineering↗