Biology subjects

Carr, E.

Publications and source records attributed to Carr, E..

8 recordsLinked to original sources

bioRxiv2026

Viral impacts on plankton standing stocks, primary productivity, and biogeochemistry in a model ocean

Viral lysis fuels the microbial loop by enhancing organic matter recycling (via the viral shunt) and can redirect organic matter toward export (via the viral shuttle). However, the global impact of viral infection mediated by shunt and shuttle pathways remains unclear. Here, we implemented viral infection and lysis processes in a global ocean ecosystem model, including a single phytoplankton (representing Prochlorococcus), virus (representing cyanophage), and nanozooplankton. Despite low but plausible levels of viral infection, high shunt efficiencies generated enhanced-productivity regions covering up to approximately one-half of the global ocean. For lower viral shunt efficiencies, the enhanced-productivity regions contracted abruptly, accompanied by steady declines in productivity. Viral-mediated increases in primary productivity reduced the extent of tropical oligotrophic regions at high shunt efficiencies, while lower efficiencies expanded oligotrophic areas. These results provide a path forward to developing predictive models of how viral infection and the fate of cellular lysates shape global ocean ecosystems.

ecology↗

bioRxiv2025

A Shot in the Dark: Comparative Morphology of the Bioluminescent Tube Organs in Tubeshoulders (Platytroctidae)

Bioluminescence, light produced by a living organism, is a key innovation in the diversification of deep-sea fishes. It is useful for a myriad of behaviors and interactions in deep sea organisms, including communication, predation, camouflage via counterillumination, and predator avoidance. In this study, we investigate the deep-sea tubeshoulders (Platytroctidae), fishes that possess a unique postcleithral tube organ associated with their shoulder girdle that excretes bioluminescent fluid, a feature that unites all members of this poorly studied family. Many tubeshoulders also possess additional bioluminescent structures and luminescent tissues, including a series of tube organs on the caudal peduncle unique to Platytroctes apus that are hypothesized to be similar in structure and function to the postcleithral tube organ. Herein, we present the first histological analysis of the caudal tube organs in P. apus and use histological methods to investigate the morphological diversity in postcleithral tube organ structure across 14 species of platytroctids, representing 10 of 13 valid genera. We show that the postcleithral tube organ generally exhibits a conserved morphology across genera and species, however, several species-specific anatomical differences are noted. In some individuals, we observe the presence of luminescent-fluid cells within the tube organ in various stages of development, which may provide evidence for inferring the type of secretory gland found in this novel bioluminescent light organ. We also show that the structure of the caudal tube organs in P. apus are similar to the postcleithral tube organ present in all members of Platytroctidae, likely indicating a similar luminescent fluid emission function.

evolutionary biology↗

bioRxiv2025

Coexistence of Photosynthetic Marine Microorganisms, Viruses, and Grazers: Toward Integration in Ocean Ecosystem Models

Photosynthetic microorganisms are responsible for primary production at the base of the marine food web that impacts ocean biogeochemistry and ecological interactions. The growth of these microorganisms is balanced by mortality processes, including top-down losses from zooplankton grazing and infection and lysis by viruses. Multiple types of grazers and viruses often coexist despite apparent competition for the same (or similar) microorganisms. Here, we develop a community model of photosynthetic microorganisms, grazers, and viruses that accounts for molar cell and virion elemental quotas suitable for incorporation into ocean ecosystem models. Our aim is to investigate mechanisms that enable coexistence of a virus and a grazer with a single phytoplankton type. To do so, we evaluate the extent to which coexistence is facilitated by: (i) infected phytoplankton, potentially subject to non-preferential intraguild predation, where grazers feed on virally infected microorganisms; (ii) heterogeneity in susceptibility to infection, where microorganisms vary in their resistance to the virus either intracellularly or extracellularly; and (iii) the inclusion of higher-order mortality terms for the predators. We find evidence for a trade-off between the virus latent period and virulence in facilitating a coexistence regime. The inclusion of an explicit latent period can generate oscillations of all populations that facilitate coexistence by reducing the growth rate of the free virus, or lead to system collapse when oscillations become too large. Heterogeneity in phage susceptibility promotes coexistence through resource partitioning between the predators, while higher-order mortality terms widen the coexistence regime by stabilizing the system. We observe strong sensitivity of model outcomes to viral life history traits, including shifts in infected cell percentages and the balance between virally and zooplankton-induced mortality. Finally, taking advantage of algebraic calculation of model equilibria, we identify life history trait parameter combinations that yield realistic ecological properties in simplified oligotrophic and mesotrophic epipelagic environments. Importantly, our ecological models suggest that ongoing efforts to embed virus dynamics in large-scale ocean ecosystem models should likely include phytoplankton types that are moderately to strongly resistant to viral infection and lysis.

ecology↗

bioRxiv2025

Towards Precision Functional Brain Network Mapping in Parkinsons Disease

BackgroundParkinsons disease (PD) is a complex neurodegenerative condition that leads to widespread disruption of large-scale brain networks and is further complicated by substantial individual variability in symptomology, progression rates, and treatment response. Consequently, the investigation of individual differences in networks measured via resting state functional connectivity (RSFC) may provide insight. However, most RSFC studies are unable to identify interindividual differences due to poor reliability and group average network definitions. "Precision" RSFC addresses these shortcomings through extended data collection, strict denoising, and individual network definition, but remains untested in PD. ObjectivesTo evaluate the feasibility and reliability of precision RSFC studies in PD. MethodsWe collected >100 minutes of RSFC data from 20 PD and 6 healthy controls participants. We evaluated the level of motion, reliability and stability of RSFC measures in each participant and contrasted these measures between the PD and HC groups, as well as compared to a conventional 5 minutes of RSFC data. In addition, we created individualized brain network measures in PD participants to establish feasibility in this population. ResultsUsing precision methods, the PD group produced reliable and stable RSFC measures of brain networks of similar quality to healthy controls and substantially better than conventional methods. Individualized network maps from individuals with PD demonstrate differences from group averages and from each other, including in key motor systems. ConclusionPrecision RSFC is feasible and reliable in individuals with PD. This approach holds promise for advancing personalized diagnostics and identifying brain-based biomarkers underlying clinical variability in PD.

neuroscience↗

bioRxiv2024

Marine fishes exhibit exceptional variation in biofluorescent emission spectra

Biofluorescence is a phylogenetically widespread phenomenon among marine fishes, yet the phenotypic diversity in fluorescent emission wavelengths (e.g., green, red) remains poorly studied across the broad diversity of marine teleosts. In this study we investigate the fluorescent emission spectra from a diverse array of 18 teleost families and record fluorescent emission peaks over multiple body regions. Our results show that fluorescent emission spectra are remarkably diverse among teleost families, as well as within genera. Fluorescent emissions also varied across different body regions within some individuals. We show that members of the families Gobiidae, Oxudercidae, and Bothidae, exhibit at least six distinct, non-overlapping fluorescent emission peaks. Nine of the 18 families examined in this study were found to have at least four distinct and non-overlapping fluorescent emission peaks. Further, we find that several families exhibit multiple discrete emission peaks for a single fluorescent color (i.e., wavelength range), including multiple distinct peaks within the green and red portions of the spectrum. This exceptional degree of phenotypic variation in fluorescent emissions highlights the potential for a diverse, even species-specific, fluorescent signaling system in certain teleost families. The interplay between different fluorescent emission wavelengths and notable variation in the distribution of fluorescence on the body could allow for a wide array of fluorescent patterns to be produced by an individual or among closely related species. Our results reveal far more diversity in both fluorescent emission wavelengths (colors) and in the distribution of fluorescent molecules on the body than had previously been reported in the literature. We characterize this novel variation in fluorescent emissions across an array of teleost families that exhibit biofluorescence and discuss the potential functional implications of this exceptional phenotypic variability.

ecology↗

bioRxiv2020

Severe dysregulation of TNF expression leads to multiple inflammatory diseases and embryonic death

Post-transcriptional regulation mechanisms regulate mRNA stability or translational efficiency via ribosomes and recent evidence indicates that it is a major determinant of the accurate levels of cytokine mRNAs. While transcriptional regulation of Tnf has been well studied and found to be important for the rapid induction of Tnf mRNA and regulation of the acute phase of inflammation, study of its post-transcriptional regulation has been largely limited to the role of the AU-rich element (ARE), and to a lesser extent, that of the constitutive decay element (CDE). We have identified a new regulatory element (NRE) in the 3 untranslated region (3UTR) of Tnf, and demonstrate that ARE, CDE and NRE cooperate to efficiently down regulate Tnf expression and prevent autoimmune inflammatory diseases. We also show for the first time that excessive TNF may lead to embryonic death.

immunology↗

bioRxiv2018

Parameterising continuum models of heat transfer in heterogeneous living skin using experimental data

In this work we consider a recent experimental data set describing heat conduction in living porcine tissues. Understanding this novel data set is important because porcine skin is similar to human skin. Improving our understanding of heat conduction in living skin is relevant to understanding burn injuries, which are common, painful and can require prolonged and expensive treatment. A key feature of skin is that it is layered, with different thermal properties in different layers. Since the experimental data set involves heat conduction in thin living tissues of anesthetised animals, an important experimental constraint is that the temperature within the living tissue is measured at one spatial location within the layered structure. Our aim is to determine whether this data is sufficient to reliably infer the heat conduction parameters in layered skin, and we use a simplified two-layer mathematical model of heat conduction to mimic the generation of experimental data. Using synthetic data generated at one location in the two-layer mathematical model, we explore whether it is possible to infer values of the thermal diffusivity in both layers. After this initial exploration, we then examine how our ability to infer the thermal diffusivities changes when we vary the location at which the experimental data is recorded, as well as considering the situation where we are able to monitor the temperature at two locations within the layered structure. Overall, we find that our ability to parameterise a model of heterogeneous heat conduction with limited experimental data is very sensitive to the location where data is collected. Our modelling results provide guidance about optimal experimental design that could be used to guide future experimental studies.\n\nNomenclatureA brief description of all variables used in the document are given in Table 1.\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@121864aorg.highwire.dtl.DTLVardef@1f789c8org.highwire.dtl.DTLVardef@76c62corg.highwire.dtl.DTLVardef@1cca220org.highwire.dtl.DTLVardef@1a82158_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1:C_FLOATNO O_TABLECAPTIONVariable nomenclature and description.\n\nC_TABLECAPTION C_TBL

biophysics↗

bioRxiv2017

Quantifying the efficacy of first aid treatments for burn injuries using mathematical modelling and in vivo porcine experiments

First aid treatment of burn injuries reduces scarring and improves healing. Here, we quantify the efficacy of various first aid treatments by using a mathematical model to describe a suite of experimental data from a series of in vivo porcine experiments. We study a series of consistent burn injuries that are subject to first aid treatments that vary in both the temperature and duration of the first aid treatment. Calibrating the mathematical model to the experimental data provides estimates of the in vivo thermal diffusivity, the rate at which thermal energy is lost to the blood (perfusion), and the heat transfer coefficient controlling the loss of thermal energy at the interface of the fat and muscle layers. A limitation of working with in vivo animal experiments is the difficulty of resolving spatial variations in temperature across the tissues. Here, we use the solution of the calibrated mathematical model to predict and visualise the temperature distribution across the thickness of the tissue during the creation of the burn injury and the application of various first aid treatments. Using this information we propose, and report values for, a novel measure of the potential for tissue damage. This measure quantifies two important aspects that are thought to be related to thermal injury: (i) the volume of tissue that rises above the threshold temperature associated with the accumulation of tissue damage; and, (ii) the duration of time that the tissue remains above this threshold temperature. We conclude by discussing the clinical relevance of our findings.

biophysics↗