Biology subjects

Thomas, K. N.

Publications and source records attributed to Thomas, K. N..

10 recordsLinked to original sources

bioRxiv2026

Telmisartan alters the transcriptomes of cancer associated fibroblasts and fibrocytes in a solid tumour model

Cancer associated fibroblasts (CAFs) are the main contributors to fibrosis in solid tumours. Fibrosis can lead to increased tumoural stiffness, immune cell exclusion, and poor response to cancer therapies. However, therapeutically depleting CAFs has been shown to increase tumour progression and metastasis in some pre-clinical tumour models. Targeted approaches to inhibit CAF activity and decrease fibrosis without abrogating CAFs altogether may improve the effect of existing cancer therapies. We have previously shown that the blood pressure medication telmisartan decreases tumoural collagen, resulting in improved vascular perfusion, decreased hypoxia, and improved radiation treatment efficacy. To understand how telmisartan influences CAF populations in solid tumours, we conducted single cell RNA sequencing analyses of host cells isolated from tumours in mice treated with telmisartan. Telmisartan modified the transcriptomes of CAF populations, promoting the expression of chemokine signaling while decreasing the expression of extracellular matrix components in myCAFs. Telmisartan decreased expression of collagen transcripts in myCAFs and fibrocytes, indicating that telmisartan does not remove myCAFs but changes the myCAF transcriptome to become less fibrillar. Our work provides further support for using telmisartan to manipulate CAF populations in the solid tumour microenvironment to decrease collagen deposition and render tumours more responsive to current cancer therapies.

cancer biology↗

bioRxiv2025

Eyes wide open: Frogs with reduction of auditory communication ability show lower eye, but higher corneal, investment

Vocal communication is the primary mechanism of mate attraction in frogs, but some species have lost the auditory structures needed to hear airborne sounds, raising the question of how they communicate in their absence. We hypothesized that frog species with auditory system reductions have compensated through enhanced visual ability, including through enlarged eyes. To test this trade-off hypothesis, we estimated relative eye and corneal investment across 264 species and tested for correlations with auditory reduction. Contrary to our expectations, we found that species with auditory reductions had smaller eye size and lower eye investment. Instead, we found that non-fossorial species with auditory reductions had significantly greater corneal investment, after controlling for habitat-based variation. Enlarged corneas enhance light sensitivity but are expected to have a lower metabolic cost than larger eyes. Relatively larger corneas may, in combination with other changes, allow frogs with auditory reductions to rely more on vision for communication, while at the same time minimizing energetic costs in small animals that are already metabolically constrained. Our findings suggest that the visual system plays an adaptive role in response to the reduction of auditory communication and highlights the condition of sensory systems as an important factor shaping frog evolution.

evolutionary biology↗

bioRxiv2025

Evolutionary and ontogenetic shifts from aquatic to terrestrial light environments in frogs provide new insights into the vertebrate phototransduction cascade

Evolutionary studies of vertebrate vision have mainly focused on the light-sensitive opsins neglecting the downstream phototransduction cascade. Here, we investigate patterns of gene loss and expression across jawed vertebrates, providing clarity on the evolution of phototransduction. We next focus on an ecologically diverse sample of frogs represented by whole-eye transcriptomes and genomes from 113 species. We tested the hypothesis that phototransduction genes were lost in the common ancestor of frogs due to nocturnality and that functional differences in phototransduction are driven by variation in habitat, activity pattern, and life history. Across frogs, we recovered 38 of 39 vertebrate phototransduction genes, with all but one of these (GUCA1B2) consistently expressed in frog eyes. This contrasts the high level of gene loss found in other ancestrally nocturnal tetrapods (e.g., mammals and snakes) and is more similar to ray-finned fishes. More than other ecological traits, we found that loss of the larval aquatic life stage (direct development) and inhabiting aquatic and semiaquatic habitats as adults were most strongly associated with shifts in selective strength, with widespread signals of both positive and relaxed selection across frog phototransduction genes. These findings suggest that phototransduction is under different functional constraints in aquatic versus terrestrial light environments and that shifts in the use of these environments have played a strong role in frog visual evolution. Collectively, these results reinforce that frogs are of particular interest for vertebrate visual evolution because they span both an evolutionary and an ontogenetic transition from vision underwater to vision on land.

evolutionary biology↗

bioRxiv2025

Assay for Rapid Quantification of Capped and Tailed Intact mRNA

The rapid development of mRNA vaccines since the COVID-19 pandemic has highlighted the potential of mRNA technology for vaccine and therapeutic applications. However, evaluating mRNA quality, including its integrity, 5' capping efficiency, and 3' poly(A) tailing, remains complex and challenging. Current analytical methods provide detailed insights, but are often limited by long analysis times, complex sample preparation, and the need for specialized expertise. The 5 CapQ assay addresses these challenges and provides a novel, rapid, and straightforward method that offers a single, unique measurement of intact mRNA with both a 5'cap and 3'poly(A) tail. This 2-hour benchtop-based assay provides quantitative or relative analysis, with high accuracy and precision without extensive sample processing. The 5 CapQ assay offers a significant advancement in mRNA analytics to alleviate bottlenecks in applications including in vitro transcription (IVT) reaction optimization, post-transcriptional capping optimization, and assessment of batch-to-batch IVT bioprocess consistency.

molecular biology↗

bioRxiv2022

Molecular evolution of non-visual opsin genes across environmental, developmental, and morphological adaptations in frogs

Non-visual opsins are transmembrane proteins expressed in the eyes, skin, and brain of many animals. When paired with a light-sensitive chromophore, non-visual opsins form photopigment systems involved in various non-visual, light-detection functions, including circadian rhythm regulation, light-seeking behavior, and detection of seasonality. Previous research has primarily explored the diversity and function of non-visual opsins in model organisms, with few studies investigating their molecular evolution in non-model species. Here we explored molecular evolution of non-visual opsin genes in anuran amphibians (frogs and toads). With diverse lifestyles ranging from fossorial to aquatic, anurans inhabit a diverse array of light environments, which makes them a compelling system for studying the evolution of light detection mechanisms. Using whole-eye transcriptomes from 79 anuran species, as well as genomes and multi-tissue transcriptomes from an additional 15 species, we 1) identify which non-visual opsin genes are expressed in the eyes of anurans; 2) compare selective constraint ({omega}, or dN/dS) among non-visual opsin genes; and 3) test for potential adaptive evolution by comparing selection between discrete ecological classes in anurans (e.g. diurnal versus non-diurnal). We consistently recovered 14 non-visual opsin genes from anuran eye transcriptomes, compared to 18 genes that we recovered genome wide, and detected positive selection in a subset of these genes. We also found variation in selective constraint between discrete ecological and life-history classes, which may reflect functional adaptation in non-visual opsin genes. Although non-visual opsins remain poorly understood, these findings provide insight into their molecular evolution and set the stage for future research on their potential function across taxa with diverse environmental, developmental, and morphological adaptations.

evolutionary biology↗

bioRxiv2022

30-Minute Highly Multiplexed VaxArray Immunoassay for Pneumococcal Vaccine Antigen Characterization

Pneumonia accounts for over 20% of deaths worldwide in children aged 1 to 5 years, disproportionately affecting lower- and middle-income countries. Effective, highly multivalent pneumococcal vaccines are available to decrease disease burden, with numerous new vaccines currently under development to serve a variety of worldwide markets. However, pneumococcal conjugate vaccines are among the hardest biologics to manufacture and characterize due to their complexity and heterogeneity. Current characterization methods are often inherently singleplex, requiring separate tests for each serotype present. In addition, identity and quantity are often determined with separate methods. We have developed the VaxArray Pneumococcal Assay for applications in identity, quantity, and stability testing of pneumococcal polysaccharide and pneumococcal conjugate vaccines. The VaxArray Pneumococcal Assay has a time to result of less than 30 minutes and is an off-the-shelf multiplexed, microarray-based immunoassay kit that can identify and simultaneously quantify 23 pneumococcal polysaccharide serotypes common to many on-market and in-development vaccines. Here, we highlight the potential of the assay for identity testing by showing high reactivity and serotype-specificity to a wide variety of native polysaccharides, CRM197-conjugated polysaccharides, and drug product. The assay also has vaccine-relevant lower limits of quantification in the low to mid ng/mL range and can be used for accurate quantification even in adjuvanted vaccines. Excellent correlation to the anthrone assay is demonstrated, with VaxArray resulting in significantly improved precision over this antiquated chemical method.

immunology↗

bioRxiv2021

VaxArray Immunoassay for the Multiplexed Quantification of Poliovirus D-Antigen

Next generation poliovirus vaccines are critical to reaching global poliovirus eradication goals. Recent efforts have focused on creating inactivated vaccines using attenuated Sabin strains that maintain patient safety benefits and immunogenicity of conventional inactivated vaccines while increasing manufacturing safety and lowering production costs, and on developing novel oral vaccines using modified Sabin strains that provide critical mucosal immunity but are further attenuated to minimize risk of reversion to neurovirulence. In addition, there is a push to improve the analytical tools for poliovirus vaccine characterization. Conventional and Sabin inactivated poliovirus vaccines typically rely on standard plate-based ELISA as in vitro D-antigen potency assays in combination with WHO international standards as calibrants. While widely utilized, the current D-antigen ELISA assays have a long time to result (up to 72 hours), can suffer from lab-to-lab inconsistency due to non-standardized protocols and reagents, and are inherently singleplex. For D-antigen quantitation, we have developed the VaxArray Polio Assay Kit, a multiplexed, microarray-based immunoassay that uses poliovirus-specific human monoclonal antibodies currently under consideration as standardized reagents for characterizing inactivated Sabin and Salk vaccines. The VaxArray assay can simultaneously quantify all 3 poliovirus serotypes with a time to result of less than 3 hours. Here we demonstrate that the assay has limits of quantification suitable for both bioprocess samples and final vaccines, excellent reproducibility and precision, and improved accuracy over an analogous plate-based ELISA. The assay is suitable for adjuvanted combination vaccines, as common vaccine additives and crude matrices do not interfere with quantification, and is intended as a high throughput, standardized quantitation tool to aid inactivated poliovirus vaccine manufacturers in streamlining vaccine development and manufacturing, aiding the global polio eradication effort.

immunology↗

bioRxiv2021

Diversity and evolution of amphibian pupil shapes

Pupil constriction has important functional consequences for animal vision, yet the evolutionary mechanisms underlying diverse pupil sizes and shapes, often among animals that occupy optically similar environments, are poorly understood. We aimed to quantify the diversity and evolution of pupil shapes among amphibians and test for potential correlations to ecology based on functional hypotheses. Using photographs, we surveyed pupil shape and the orientation of the constricted pupil across adults of 1293 amphibian species, 72 families, and 3 orders, and additionally for larval life stages for all families of frogs and salamanders with a biphasic ontogeny. Pupil shape is exceptionally diverse in amphibians with evolutionary transitions throughout the amphibian tree of life. For amphibians with a biphasic life history, we found that pupils change in many species that occupy distinct habitats before and after metamorphosis. Finally, we found that non-elongated (round or diamond) constricted pupils were correlated with species inhabiting consistently dim light environments (burrowing and aquatic species) and that elongated pupils (vertical and horizontal) were more common in species with larger absolute eye sizes. We propose that amphibians provide a valuable group within which to explore the anatomical, physiological, optical, and ecological mechanisms underlying the evolution of pupil shape.

evolutionary biology↗

bioRxiv2021

Multiplexed VaxArray Immunoassay for Rapid Antigen Quantification in Measles and Rubella Vaccine Manufacturing

Measles-containing vaccines (MCV), specifically vaccines against measles and rubella (MR), are extremely effective and critical for the eradication of measles and rubella diseases. In developed countries, vaccination rates are high and vaccines are readily available, but continued high prevalence of both diseases in developing countries and surges in measles deaths in recent years have highlighted the need to expand vaccination efforts. To meet demand for additional vaccines at a globally affordable price, it is highly desirable to streamline vaccine production thereby reducing cost and speeding up time to delivery. MR vaccine characterization currently relies on the 50% cell culture infectious dose (CCID50) assay, an endpoint assay with low reproducibility that requires 10-14 days to complete. For streamlining bioprocess analysis and improving measurement precision relative to CCID50, we developed the VaxArray Measles and Rubella assay kit, which is based on a multiplexed microarray immunoassay with a 5-hour time to result. Here we demonstrate vaccine-relevant sensitivity ranging from 345 - 800 IFU/mL up to 100,000 IFU/mL and specificity that allows simultaneous analysis in bivalent vaccine samples. The assay is sensitive to antigen stability and has minimal interference from common vaccine additives. The assay exhibits high reproducibility and repeatability, with 15% CV, much lower than the typical 0.3 log10 error (~65%) observed for the CCID50 assay. The intact protein concentration measured by VaxArray is reasonably correlated to, but not equivalent to, CCID50 infectivity measurements for harvest samples. However, the measured protein concentration exhibits equivalency to CCID50 for more purified samples, including concentrated virus pools and monovalent bulks, making the assay a useful new tool for same-day analysis of vaccine samples for bioprocess development, optimization, and monitoring.

immunology↗

bioRxiv2021

Genomic and Spectral Visual Adaptation in Southern Leopard Frogs during the Ontogenetic Transition from Aquatic to Terrestrial Light Environments

Many animals have complex life cycles where larval and adult forms have distinct ecologies and habitats that impose different demands on their sensory systems. While the adaptive decoupling hypothesis predicts reduced genetic correlations between life stages, how sensory systems adapt across life stages at the molecular level is not well understood. Frogs are a compelling system to study this question in because most species rely on vision as both aquatic tadpoles and terrestrial adults, but these habitats present vastly different light environments. Here we used whole eye transcriptome sequencing to investigate differential expression between aquatic tadpoles and terrestrial juveniles of the southern leopard frog (Lithobates sphenocephalus). Because visual physiology changes with light levels, we also tested how constant light or dark exposure affected gene expression. We found 42% of genes were differentially expressed in the eyes of tadpoles versus juveniles, versus 5% for light/dark exposure. Analyses targeting a curated set of visual genes revealed significant differential expression between life stages in genes that control aspects of visual function and development, including spectral sensitivity and lens composition. Light/dark exposure had a significant effect on a smaller set of visual genes. Finally, microspectrophotometry of photoreceptors confirmed shifts in spectral sensitivity predicted by the expression results, consistent with adaptation to distinct light environments. Overall, we identified extensive expression-level differences in the eyes of tadpole and juvenile frogs related to observed morphological and physiological changes through metamorphosis, and corresponding adaptive shifts to optimize vision in aquatic versus terrestrial environments.

genomics↗