Biology subjects

Farrell, J.

Publications and source records attributed to Farrell, J..

7 recordsLinked to original sources

bioRxiv2025

Quantifying antibiotic susceptibility and inoculum effects using transient dynamics of Pseudomonas aeruginosa

Antibiotics are a cornerstone of modern medicine, targeting pathogen cells by disrupting essential cellular processes. However, standard antibiotic susceptibility metrics (e.g. MIC) and textbook models neglect transient dynamics and density-dependent effects, despite their ubiquity in nature. In clinical infections, where bacterial populations are the units we treat, this can increase the risk of under treatment. To address this gap, we generate high resolution optical density time series data for Pseudomonas aeruginosa (3 antibiotics, 12 doses, 7 inoculum sizes, 4x replication), enabling gradient estimation and gradient-based model parameterization. We develop a dynamics-led computational pipeline that (1) evaluates population scale ordinary differential equation models in the context of estimated time derivative data, and (2) classifies transient dynamics in dose-inoculum space using unsupervised clustering. Applied to our data, the pipeline identifies an ordinary differential equation model with a saturating antibiotic-loss term and a threshold-dependent weak Allee term that recapitulates and quantifies classic rate, yield, and inoculum effects of antibiotics. In addition, our model and clustering approach suggest a set of novel metrics, defining thresholds separating distinct dynamical regimes. Beyond antibiotic data sets, our approach utilizing a derivative-based fitting algorithm and clustering of derivative trajectories is applicable to any biological time series with controlled perturbations and variable initial conditions. Author summaryWe show that standard math models and antibiotic susceptibility metrics fail to capture the regimes of dynamical behavior that result from combined antibiotic and inoculum effects when Pseudomonas aeruginosa (PAO1) is exposed to antibiotics. Using iterations of forward and data-driven modeling, we highlight the importance of transient dynamics, derivative-based model fitting, and higher-order nonlinearities in quantifying bacterial dynamics under perturbation. We identify an ordinary differential equation-based model that describes the observed inoculum effect as a type of weak Allee effect (positive density-dependence) and also captures antibiotic effects on population growth rate and yield governed by a saturating loss function. We show that these results generalize across antibiotic mechanisms of action and highlight the importance of fitting models using dynamics-based algorithms. Finally, we explore a clustering method for bacterial dynamics that, in combination with our mathematical model, advises a set of novel metrics for measuring antibiotic susceptibility.

microbiology↗

bioRxiv2023

Novel Imaging Guidance for Cholesteatoma Surgery usingTissue Autofluorescence

SignificanceCholesteatoma is an expansile destructive lesion of the middle ear and mastoid, which can result in significant complications by eroding adjacent bony structures. Currently, there is an inability to accurately distinguish cholesteatoma tissue margins from middle ear mucosa tissue, causing a high recidivism rate. Accurately differentiating cholesteatoma and mucosa will enable a more complete removal of the tissue. AimDevelop an imaging system to enhance the visibility of cholesteatoma tissue and margins during surgery. ApproachCholesteatoma and mucosa tissue samples were excised from the inner ear of patients and illuminated with 405, 450, and 520 nm narrowband lights. Measurements were made with a spectroradiometer equipped with a series of different longpass filters. Images were obtained using a red-green-blue (RGB) digital camera equipped with a long pass filter to block reflected light. ResultsCholesteatoma tissue fluoresced under 405 and 450 nm illumination. Middle ear mucosa tissue did not fluoresce under the same illumination and measurement conditions. All measurements were negligible under 520 nm illumination conditions. All spectroradiometric measurements of cholesteatoma tissue fluorescence can be predicted by a linear combination of emissions from keratin and flavin adenine dinucleotide (FAD). We built a prototype of a fluorescence imaging system using a 495 nm longpass filter in combination with an RGB camera. The system was used to capture calibrated digital camera images of cholesteatoma and mucosa tissue samples. The results confirm that cholesteatoma emits light when it is illuminated with 405 and 450 nm, whereas mucosa tissue does not. ConclusionsWe prototyped an imaging system that is capable of measuring cholesteatoma tissue autofluorescence.

bioengineering↗

bioRxiv2021

AKT1 is Required for a Complete Palbociclib-induced Senescence Phenotype in BRAF-V600E-Driven Human Melanoma

Cellular senescence is a carefully regulated process of proliferative arrest accompanied by numerous functional and morphologic changes. Senescence allows damaged cells to avoid neoplastic proliferation, however induction of the senescence-associated secretory phenotype (SASP) can promote tumor growth. The complexity of the senescence response may limit the efficacy of anti-neoplastic agents, such as CDK4/6 inhibitors (Cdk4/6i), that induce a senescence-like, non-proliferative state in tumor cells. The AKT kinase family plays an important role in cellular growth and division, and is commonly hyperactive in many cancers including melanoma. AKT activity has also been implicated in regulation of senescence. The three AKT isoforms play both redundant and unique roles in tumorigenesis and cancer progression. To interrogate the role of AKT isoforms in the induction of cellular senescence by Cdk4/6i, we generated isoform specific AKT knockout human BRAF-V600E mutated melanoma cell lines. We found that the CDK4/6i Palbociclib induced a form of senescence in these cells that was dependent on AKT1. As a potential mechanism, we evaluated the activity of the cGAS-STING pathway, recently implicated in cellular senescence. While we showed cGAS-STING function to be dependent on AKT1, pharmacologic inhibition of either cGAS or STING had little effect on senescence. However, we found SASP factors to require NF-kB function, in part dependent on a stimulatory phosphorylation of IKK by AKT1 previously reported in other models. In summary, we provide the first evidence of a novel, isoform specific role for AKT1 in therapy-induced senescence in human melanoma cells acting through NF-kB but independent of cGAS-STING.

cancer biology↗

bioRxiv2021

Simulations of fluorescence imaging in the oral cavity

We describe an end-to-end image systems simulation that models a device capable of measuring fluorescence in the oral cavity. Our software includes a 3D model of the oral cavity and excitation-emission matrices of endogenous fluorophores that predict the spectral radiance of oral mucosal tissue. The predicted radiance is transformed by a model of the optics and image sensor to generate expected sensor image values. We compare simulated and real camera data from tongues in healthy individuals and show that the camera sensor chromaticity values can be used to quantify the fluorescence from porphyrins relative to the bulk fluorescence from multiple fluorophores (elastin, NADH, FAD, and collagen). Validation of the simulations supports the use of soft-prototyping in guiding system design for fluorescence imaging. (C) 2021 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

bioengineering↗

bioRxiv2020

Mutational, transcriptional and viral shedding dynamics of the marine turtle fibropapillomatosis tumor epizootic

Sea turtle populations are directly and indirectly under threat from a range of anthropogenic processes. Perhaps the most visibly apparent of these is the disfiguring tumor disease epizootic (animal epidemic) known as fibropapillomatosis. Fibropapillomatosis continues to spread geographically, with prevalence of the disease also growing at a number of affected sites globally. Environmental exposures seem key to inducing tumor development, possibly through weakening host immune systems to the point of enabling pathogen-induced tumor formation. However, we do not yet understand the precise molecular and mutational events driving fibropapillomatosis tumor formation and progression. Similarly, many open questions remain about the role of the herpesvirus (chelonid herpesvirus 5, ChHV5) associated with the disease as a potential co-trigger, and whether its occurrence within tumors is causative or opportunistic. Without improved understanding of the basic biology of this disease epizootic, treatment, containment and mitigation options are severely hampered. To address fundamental questions relating to the oncogenic signaling, mutational spectrum, viral load, viral transcriptional status (lytic or latent) and spread, we employed transcriptomic profiling, whole genome sequencing, immunohistochemistry and environmental (e)DNA-based monitoring of viral shedding. In particular we focused on the mutational landscape of tumors and assessing the transcriptional similarity of external (skin) and internal (visceral organs) tumors, and the oncogenic signaling events driving early stage tumor growth and post-surgical tumor regrowth. These analyses revealed that internal fibropapillomatosis tumors are molecularly distinct from the more common external tumors. However, our molecular analyses also revealed that there are a small number of conserved potentially therapeutically targetable molecular vulnerabilities in common between internal and external tumors, such as the MAPK, Wnt, TGF{beta} and TNF oncogenic signaling pathways. We also determined that the tumor genomes can harbor copy number gains, indicating potentially viral-independent oncogenic processes. Genes within such mutated genomic regions have known roles in human skin cancer, including MAPK-associated genes. Turtles attempt to mount an immune response, but in some animals this appears to be insufficient to prevent tumor development and growth. ChHV5 was transcriptionally latent in all tumor stages sequenced, including early stage and recurrent tumors. We also revealed that the tumors themselves are the primary source of viral shedding into the marine environment and, if they are surgically removed, the level of ChHV5 in the water column drops. Together, these results offer an improved understanding of fibropapillomatosis tumorigenesis and provide insights into the origins, therapeutic treatment, and appropriate quarantine responses for this wildlife epizootic. Furthermore, they provide insights into human pathogen-induced cancers, particularly mechanisms which are difficult to study in the human and terrestrial context, such as time-course quantification-based monitoring of viral shedding.

cancer biology↗

bioRxiv2018

Combining population genomics and forward simulations to investigate stocking impacts: A case study of Muskellunge (Esox masquinongy) from the St. Lawrence River basin

Understanding the genetic and evolutionary impacts of fish stocking on wild populations has long been of interest as negative consequences such as reduced fitness and loss of genetic resources are commonly reported. Nearly five decades of extensive stocking of over a million Muskellunge (Esox masquinongy) in the Lower St. Lawrence River (Quebec, Canada) was implemented by managers in an attempt to sustain a fishery. We investigated the effect of stocking on this native species genetic structure and allelic diversity in the St. Lawrence river and its tributaries as well as several stocked inland lakes. Using Genotype-By-Sequencing (GBS), we genotyped 643 individuals representing 22 sampling sites and combined this information with forward simulations to investigate the genetic consequences of stocking. Individuals native to the St. Lawrence watershed were genetically divergent from the sources used for stocking and both the St. Lawrence tributaries and inland lakes were also naturally divergent from the main stem. Empirical data and simulations revealed weak effects of stocking on admixture patterns within the St. Lawrence despite intense stocking in the past, whereas footprints of admixture were higher in the smaller stocked populations from tributaries and lakes. Altogether, our data suggests that selection against introgression has been relatively efficient within the large St. Lawrence River. In contrast, the smaller populations from adjacent tributaries and lakes still displayed stocking related admixture which apparently resulted in higher genetic diversity, suggesting that, while stocking stopped at the same time, its impact remained higher in these populations. Finally, the origin of populations from inland lakes that were established by stocking confirmed their close affinity with these source populations. This study illustrates the benefit of combining extensive genomic data with forward simulations for improved inferences regarding outcomes of population enhancement by stocking, as well as its relevance for fishery management decision making.

evolutionary biology↗

bioRxiv2017

Simulating retinal encoding: factors influencing Vernier acuity

Humans resolve the spatial alignment between two visual stimuli at a resolution that is substantially finer than the spacing between the foveal cones. In this paper, we analyze the factors that limit the information at the cone photoreceptors that is available to make these acuity judgments (Vernier acuity). We use open-source software, ISETBIO1 to quantify the stimulus and encoding stages in the front-end of the human visual system, starting with a description of the stimulus spectral radiance and a computational model that includes the physiological optics, inert ocular pigments, eye movements, photoreceptor sampling and absorptions. The simulations suggest that the visual system extracts the information available within the spatiotemporal pattern of photoreceptor absorptions within a small spatial (0.12 deg) and temporal (200 ms) regime. At typical display luminance levels, the variance arising from the Poisson absorptions and small eye movements (tremors and microsaccades) both appear to be critical limiting factors for Vernier acuity.

neuroscience↗