Biology subjects

Miller, C. T.

Publications and source records attributed to Miller, C. T..

13 recordsLinked to original sources

bioRxiv2026

Development, dimorphism, and divergence of the oral dentition in threespine sticklebacks (Gasterosteus aculeatus)

How morphology forms during development and changes during evolution remain major questions in biology. In vertebrates, teeth have long served as model systems to address these questions. In threespine stickleback fish (Gasterosteus aculeatus), repeated and convergent increases in pharyngeal tooth number in derived freshwater sticklebacks occur, suggesting increased tooth number is adaptive in freshwater environments, likely due to a diet of larger prey in freshwater. Whether changes in oral tooth patterning also occur in freshwater sticklebacks was unknown. Here we describe oral tooth number and patterning in a dense developmental time course of lab-reared ancestral marine and derived freshwater fish. We address three major questions. First, is the spatial sequence of early oral tooth formation invariant as we previously described for the pharyngeal dentition? Second, is oral tooth patterning in the upper and lower jaw sexually dimorphic, and if so, when during development does this dimorphism arise? Third, have freshwater fish evolved increases in oral tooth number? We find that (1) unlike the pharyngeal dentition, the oral jaw early spatial sequence is variable, especially in the lower jaw (2) sexual dimorphism in both oral jaws arises at the late juvenile stage with males having more teeth and (3) freshwater fish have evolved more oral teeth similar to the evolved tooth gain in the pharyngeal jaw. Together our morphological descriptions advance the stickleback oral jaw as a model system to study how morphology forms during development and evolves in nature.

developmental biology↗

bioRxiv2026

Active gaze behavior organizes V1 activity in freely-moving marmosets

Human and nonhuman primates rely heavily on vision to actively explore and navigate their environment. Although primate visual cortex has been studied extensively in head-fixed animals, little is known about how the primate visual system supports natural, active vision in freely moving animals. Here, we address this gap in the primary visual cortex (V1) by leveraging a head-mounted eye-tracking system while simultaneously recording the activity of ensembles of single V1 neurons in freely moving marmosets. Our results reveal that primate neural activity is tightly driven by visual input and organized by the temporal structure of natural gaze behavior, and these gaze-related responses are largely abolished in the absence of visual input. We further show that distinct phases of gaze movement, i.e. rapid redirection (gaze shift) and subsequent stabilization (fixation), engage separable suppression and enhancement of the V1 responses. The enhancement during fixation was clearly linked to visual input. Moreover, the amplitudes of naturally-occurring gaze shifts organize RF input across successive fixations, and adaptively shapes fixation-associated enhancement. These findings define the dynamics in V1 that link natural gaze behavior and stimulus-driven responses in freely moving primates. The work opens a previously inaccessible but fundamental regime of primate vision and establishes freely moving paradigms as a foundation for understanding real-world visual processing during ethologically relevant behaviors.

neuroscience↗

bioRxiv2025

Ectodysplasin overexpression reveals spatiotemporally dynamic tooth formation competency in stickleback and zebrafish

Organ initiation is often driven by extracellular signals that activate precursor cells competent to receive and respond to the signal, yet little is known about how dynamic competency is in space and time during development. Teeth are excellent organs to study organ initiation competency because they can be activated with the addition of a single signaling ligand, Ectodysplasin (Eda). Eda, a Tumor Necrosis Factor (TNF) ligand, is a critical regulator of ectodermal organ development, including teeth, acting through TNF receptors, like Edar, to activate NF-{kappa}B signaling in tooth precursor cells. While Eda is both necessary for normal tooth formation and sufficient for ectopic tooth formation, the spatial and temporal dynamics of competency for ectopic tooth initiation and maintenance remains unknown. To investigate the role of Eda in tooth specification, we generated transgenic sticklebacks and zebrafish with heat shock-inducible Eda overexpression. We find that stickleback Eda can drive de novo tooth formation in at least eight distinct oropharyngeal and cranial domains. Both zebrafish and stickleback exhibit maximal responsiveness to Eda overexpression during the critical window of pioneer tooth initiation, highlighting that the precursors of ectopic pharyngeal teeth likely follow a similar developmental trajectory as endogenous tooth precursors. Furthermore, we observe that some induced dental fields often undergo tooth regeneration to maintain themselves, allowing them to persist for months after the cessation of transgene activation. Finally, analysis of TNF receptor expression in sticklebacks reveals that ectopic tooth formation in the pharynx correlates with Edar and Troy expression, while in the region where teeth can form on the face, only Troy expression was detected, providing a possible molecular mechanism of competency involving spatially restricted receptor expression. These findings underscore the latent developmental potential, i.e. competency, of the vertebrate dentition and provide insights into organ competency during embryonic and post-embryonic development.

developmental biology↗

bioRxiv2022

Modulation of tooth regeneration through opposing responses to Wnt and BMP signals in teleosts

Most vertebrate species undergo tooth replacement throughout adult life. This process is marked by the shedding of existing teeth and the regeneration of tooth organs. However, little is known about the genetic circuitry regulating tooth replacement. Here we tested whether fish orthologs of genes known to regulate mammalian hair regeneration have effects on tooth replacement. Using two fish species that demonstrate distinct modes of tooth regeneration, threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio), we found that transgenic overexpression of four different genes changed tooth replacement rates in direction predicted by a hair regeneration model: Wnt10a and Grem2a increased tooth replacement rate, while Bmp6 and Dkk2 strongly inhibited tooth formation. Thus, similar to known roles in hair regeneration, Wnt and BMP signals promote and inhibit regeneration, respectively. Regulation of total tooth number was separable from regulation of replacement rates. RNA-seq on stickleback dental tissue showed that Bmp6 overexpression resulted in an upregulation of Wnt inhibitors. Together these data support a model where different epithelial organs like teeth and hair share genetic circuitry driving organ regeneration.

developmental biology↗

bioRxiv2022

Evolution of spatial and temporal cis-regulatory divergence between marine and freshwater sticklebacks

Cis-regulatory changes are thought to play a major role in adaptation. Threespine sticklebacks have repeatedly colonized freshwater habitats in the Northern Hemisphere, where they have evolved a suite of phenotypes that distinguish them from marine populations, including changes in physiology, behavior, and morphology. To understand the role of gene regulatory evolution in adaptive divergence, here we investigate cis-regulatory changes in gene expression between marine and freshwater ecotypes through allele-specific expression (ASE) in F1 hybrids. Surveying seven ecologically relevant tissues, including three sampled across two developmental stages, we identified cis-regulatory divergence affecting a third of genes, nearly half of which were tissue-specific. Next, we compared allele-specific expression in dental tissues at two timepoints to characterize cis-regulatory changes during development between marine and freshwater fish. Applying a genome-wide test for selection on cis-regulatory changes, we find evidence for lineage-specific selection on several processes, including the Wnt signaling pathway in dental tissues. Finally, we show that genes with ASE, particularly those that are tissue-specific, are enriched in genomic regions associated with marine-freshwater divergence, supporting an important role for cis-regulatory differences in adaptive evolution of sticklebacks. Altogether, our results provide insight into the cis-regulatory landscape of divergence between stickleback ecotypes and supports a fundamental role for cis-regulatory changes in rapid adaptation to new environments.

evolutionary biology↗

bioRxiv2022

Site pleiotropy of a stickleback tooth and fin enhancer

Development and regeneration are orchestrated by gene regulatory networks that operate in part through transcriptional enhancers. Although many enhancers are pleiotropic and are active in multiple tissues, little is known about whether enhancer pleiotropy is due to 1) site pleiotropy, in which individual transcription factor binding sites (TFBS) are required for activity in multiple tissues, or 2) multiple distinct sites that regulate expression in different tissues. Here, we investigated the pleiotropy of an intronic enhancer of the stickleback Bone morphogenetic protein 6 (Bmp6) gene. This enhancer was previously shown to regulate evolved changes in tooth number and tooth regeneration, and is highly pleiotropic, with robust activity in both fins and teeth throughout embryonic, larval, and adult life. We tested the hypothesis that the pleiotropy of this enhancer is due to site pleiotropy of an evolutionarily conserved predicted Foxc1 TFBS. Transgenic analysis and site-directed mutagenesis experiments both deleting and scrambling this predicted Foxc1 TFBS revealed that the binding site is required for enhancer activity in both teeth and fins throughout embryonic, larval, and adult development. Collectively these data support a model where the pleiotropy of this Bmp6 enhancer is due to site pleiotropy and this putative binding site is required for enhancer activity in multiple anatomical sites from the embryo to the adult.

developmental biology↗

bioRxiv2022

Ultraviolet Dosage and Decontamination Efficacy was Widely Variable Across 14 UV Devices after Testing a Dried Enveloped Ribonucleic Acid Virus Surrogate for SARS-CoV-2

AbstractO_ST_ABSAimsC_ST_ABSThe dosages and efficacy of 14 ultraviolet (UV) decontamination technologies were measured against a SARS-CoV-2 surrogate virus that was dried on to different materials for lab and field testing. Methods and ResultsA live enveloped, ribonucleic acid (RNA) virus surrogate for SARS- CoV-2 was dried on stainless steel 304 (SS304), Navy Top Coat-painted SS304 (NTC), cardboard, polyurethane, polymethyl methacrylate (PMMA), and acrylonitrile butadiene styrene (ABS) at > 8.0 log10 plaque-forming units (PFU) per test coupon. The coupons were then exposed to UV radiation during both lab and field testing. Commercial and prototype UV- emitting devices were measured for efficacy: 4 handheld devices, 3 room/surface-disinfecting machines, 5 air-disinfection devices, and 2 larger custom-made machines. UV device dosages ranged from 0.01-729 mJ cm-2. Anti-viral efficacy among the different UV devices ranged from no decontamination up to nearly achieving sterilization. Importantly, cardboard required far more dosage than SS304. ConclusionsEnormous variability in dosage and efficacy was measured among the different UV devices. Porous materials limit the utility of UV decontamination. Significance and Impact of the StudyUV devices have wide variability in dosages, efficacy, hazards, and UV output over time indicating that each UV device needs independent technical measurement and assessment for product development, prior to, and during use.

microbiology↗

bioRxiv2021

Behavioral context affects social signal representations within single primate prefrontal cortex neurons

We tested whether social signal processing in more traditional, head-restrained contexts is representative of the putative natural analog - social communication - by comparing responses to vocalizations within individual neurons in marmoset prefrontal cortex (PFC) across a series of behavioral contexts ranging from traditional to naturalistic. Although vocalization responsive neurons were evident in all contexts, cross-context consistency was notably limited. A response to these social signals when subjects were head-restrained was not predictive of a comparable neural response to the identical vocalizations during natural communication, even within the same neuron. Neural activity at the population level followed a similar pattern, as PFC activity could be reliably decoded for the context in which vocalizations were heard. This suggests that neural representations of social signals in primate PFC are not static, but highly flexible and likely reflect how nuances of the dynamic behavioral contexts affect the perception of these signals and what they communicate.

neuroscience↗

bioRxiv2021

Evolved Bmp6 enhancer alleles drive spatial shifts in gene expression during tooth development in sticklebacks

Mutations in enhancers have been shown to often underlie natural variation but the evolved differences between enhancer activity can be difficult to identify in vivo. Threespine sticklebacks (Gasterosteus aculeatus) are a robust system for studying enhancer evolution due to abundant natural genetic variation, a diversity of evolved phenotypes between ancestral marine and derived freshwater forms, and the tractability of transgenic techniques. Previous work identified a series of polymorphisms within an intronic enhancer of the Bone morphogenetic protein 6 (Bmp6) gene that are associated with evolved tooth gain, a derived increase in freshwater tooth number that arises late in development. Here we use a bicistronic reporter construct containing a genetic insulator and a pair of reciprocal two-color transgenic reporter lines to compare enhancer activity of marine and freshwater alleles of this enhancer. In older fish the two alleles drive partially overlapping expression in both mesenchyme and epithelium of developing teeth, but the freshwater enhancer drives a reduced mesenchymal domain and a larger epithelial domain relative to the marine enhancer. In younger fish these spatial shifts in enhancer activity are less pronounced. Comparing Bmp6 expression by in situ hybridization in developing teeth of marine and freshwater fish reveals similar evolved spatial shifts in gene expression. Together, these data support a model in which the polymorphisms within this enhancer underlie evolved tooth gain by shifting the spatial expression of Bmp6 during tooth development, and provide a general strategy to identify spatial differences in enhancer activity in vivo.

genetics↗

bioRxiv2020

Mechanisms for Communicating in a Marmoset "Cocktail Party"

A fundamental challenge for audition is parsing the voice of a single speaker amid a cacophony of other voices known as the Cocktail Party Problem (CPP). Despite its prevalence, relatively little remains known about how our simian cousins solve the CPP for active, natural communication. Here we employed an innovative, multi-speaker paradigm comprising five computer-generated Virtual Monkeys (VM) whose respective vocal behavior could be systematically varied to construct marmoset cocktail parties and tested the impact of specific acoustic scene manipulations on vocal behavior. Results indicate that marmosets not only employ auditory mechanisms - including attention - for speaker stream segregation, but also selectively change their own vocal behavior in response to the dynamics of the acoustic scene to overcome the challenges of the CPP. These findings suggest notable parallels between human and nonhuman primate audition and highlight the active role that speakers play to optimize communicative efficacy in complex real-world acoustic scenes.

neuroscience↗

bioRxiv2020

Distinct tooth regeneration systems deploy a conserved battery of genes

BackgroundVertebrate teeth exhibit a wide range of regenerative systems. Many species, including most mammals, reptiles, and amphibians, form replacement teeth at a histologically distinct location called the successional dental lamina, while other species do not employ such a system. Notably, a lamina-less tooth replacement condition is found in a paraphyletic array of ray-finned fishes, such as stickleback, trout, cod, medaka, and bichir. Furthermore, the position, renewal potential, and latency times appear to vary drastically across different vertebrate tooth regeneration systems. The progenitor cells underlying tooth regeneration thus present highly divergent arrangements and potentials. Given the spectrum of regeneration systems present in vertebrates, it is unclear if morphologically divergent tooth regeneration systems deploy an overlapping battery of genes in their naive dental tissues. ResultsIn the present work, we aimed to determine whether or not tooth progenitor epithelia could be composed of a conserved cell type between vertebrate dentitions with divergent regeneration systems. To address this question, we compared the tooth regeneration processes in two ray-finned fishes: zebrafish (Danio rerio) and threespine stickleback (Gasterosteus aculeatus). These two teleost species diverged approximately 250 million years ago, and demonstrate some stark differences in dental morphology and regeneration. Here we find that the successional dental lamina in zebrafish sharply upregulates Wnt signaling and Lef1 expression during early morphogenesis stages of tooth development. Additionally, the naive zebrafish successional dental lamina expresses a battery of nine genes (Bmpr1a, Bmp6, CD34, Gli1, Igfbp5a, Lgr4, Lgr6, Nfatc1, and Pitx2). We also find that, despite the absence of a histologically distinct successional dental lamina in stickleback tooth fields, new tooth germs also sharply upregulate Wnt signaling and Lef1 expression, and additionally express the same battery of nine genes in the basalmost endodermal cell layer from which replacement tooth epithelia arise. Thus, two fish systems that either have an organized successional dental lamina (zebrafish) or lack a morphologically distinct successional dental lamina (sticklebacks) deploy similar genetic programs during tooth regeneration. ConclusionsWe propose that the expression domains described here delineate a highly conserved "successional dental epithelium" (SDE). Furthermore, a set of orthologous genes is known to mark hair follicle epithelial stem cells in mice, suggesting that regenerative systems in other epithelial appendages may utilize a related epithelial progenitor cell type, despite the highly derived nature of the resulting functional organs.

developmental biology↗

bioRxiv2020

Hot, humid air decontamination of aircraft confirmed that high temperature and high humidity are critical for inactivation of infectious, enveloped ribonucleic acid (RNA) virus

AimsTo develop infectious (live/dead) enveloped virus test indicators and Response Surface Methodology (RSM) models that evaluate survival of an enveloped ribonucleic acid (RNA) virus on contaminated aircraft materials after exposure to hot, humid air (HHA). Methods and ResultsEnveloped RNA bacteriophage Phi6 ({Phi}6) was dried on wiring insulation, aircraft performance coating (APC), polypropylene, and nylon at [≥] 8 log10 plaque-forming units (PFU) test coupon-1. Only 2.4 log10 inactivation was measured on APC at 70{degrees}Celsius ({degrees}C), 5% relative humidity (RH) after 24 h. In contrast, HHA RSM models showed a 90% probability of a 7-log10 inactivation at [≥]63{degrees}C, 90% RH after 1 h, and decontamination kinetics were similar across different materials. HHA decontamination of C-130 and C-17 aircraft showed >7 log10 and [≥]5.9 log10 inactivation of enveloped virus on 100 and 110 test indicators, respectively, with a 1-h treatment, excluding ramp-up and ramp-down times. ConclusionsEnveloped RNA virus test indicators were successfully developed, lab tested for HHA decontamination, analyzed for RSM, and field-tested in aircraft demonstrations. Significance and Impact of the StudyThe utility of HHA decontamination was demonstrated after inactivating enveloped RNA virus on aircraft with a 1-h HHA treatment within aircraft temperature and RH limits.

microbiology↗

bioRxiv2018

Convergent evolution of gene expression in two high-toothed stickleback populations

Changes in developmental gene regulatory networks enable evolved changes in morphology. These changes can be in cis regulatory elements that act in an allele-specific manner, or changes to the overall trans regulatory environment that interacts with cis regulatory sequences. Here we address several questions about the evolution of gene expression accompanying a convergently evolved constructive morphological trait, increases in tooth number in two independently derived freshwater populations of threespine stickleback fish (Gasterosteus aculeatus). Are convergently evolved cis and/or trans changes in gene expression associated with convergently evolved morphological evolution? Do cis or trans regulatory changes contribute more to the evolutionary gain of a morphological trait? Transcriptome data from dental tissue of ancestral low-toothed and two independently derived high-toothed stickleback populations revealed significantly shared gene expression changes that have convergently evolved in the two high-toothed populations. Comparing cis and trans regulatory changes using phased gene expression data from F1 hybrids, we found that trans regulatory changes were predominant and more likely to be shared among both high-toothed populations. In contrast, while cis regulatory changes have evolved in both high-toothed populations, overall these changes were distinct and not shared among high-toothed populations. Together these data suggest that a convergently evolved trait can occur through genetically distinct regulatory changes that converge on similar trans regulatory environments.\n\nAuthor SummaryConvergent evolution, where a similar trait evolves in different lineages, provides an opportunity to study the repeatability of evolution. Convergent morphological evolution has been well studied at multiple evolutionary time scales ranging from ancient, to recent, such as the gain in tooth number in freshwater stickleback fish. However, much less is known about the accompanying evolved changes in gene regulation during convergent evolution. Here we compared evolved changes in gene expression in dental tissue of ancestral low-toothed marine fish to fish from two independently derived high-toothed freshwater populations. We also partitioned gene expression changes into those affecting a genes regulatory elements (cis), and those affecting the overall regulatory environment (trans). Both freshwater populations have evolved similar gene expression changes, including a gain of expression of putative dental genes. These similar gene expression changes are due mainly to shared changes to the trans regulatory environment, while the cis changes are largely population specific. Thus, during convergent evolution, overall similar and perhaps predictable transcriptome changes can evolve despite largely different underlying genetic bases.

genomics↗