Biology subjects

Edwards, B.

Publications and source records attributed to Edwards, B..

13 recordsLinked to original sources

bioRxiv2026

Regeneration-associated utrophin expression in skeletal muscle: implications for utrophin-targeted therapies

Duchenne muscular dystrophy (DMD) is a lethal, X-linked muscle-wasting disease caused by loss of dystrophin. Utrophin, a structural and functional paralogue of dystrophin, can compensate for dystrophin deficiency and represents a therapeutic target applicable to patients irrespective of their DMD mutation. However, utrophin is also naturally upregulated at the sarcolemma of regenerating myofibres, creating an important confounding factor when utrophin levels are used to evaluate therapeutic activity. Here, we defined the temporal relationship between utrophin expression and complementary markers of skeletal muscle regeneration in wild-type and dystrophic mdx muscle following cardiotoxin-induced injury. Utrophin protein and mRNA dynamics were assessed together with dystrophin, embryonic myosin (MyHC-emb), centronucleation, cross-sectional area (CSA), and minimal Ferets diameter (MinFeret). MyHC-emb and utrophin were strongly associated with the early regenerative phase, although MyHC-emb peaked before maximal utrophin protein expression. In contrast, CSA and MinFeret showed an inverse temporal relationship with utrophin, while centronucleation persisted after active regeneration and did not discriminate early from late regenerative stages. Utrophin also remained elevated at the dystrophic sarcolemma for longer than in wild-type muscle. These findings demonstrate that utrophin quantification cannot be interpreted independently of the regenerative state of muscle. Combining MyHC-emb with morphological indices such as CSA and MinFeret provides a complementary framework for contextualizing regeneration-associated utrophin and should improve interpretation of utrophin changes in preclinical evaluation of utrophin-targeted therapies.

genetics↗

bioRxiv2026

Oxylipins and Other Natural Products Produced by UV-sterilization Impact Commercial Oyster Larvae Production in a New England Estuary

Here, oyster larval developmental abnormalities within a New England hatchery were linked to a common UV sterilization technique that has been used for over 20 years. Because of the known link between phytoplankton oxylipins and egg mortality in copepods, we hypothesized that UV pretreatment of seawater results in the production of oxylipins that inhibit larval digestion of microalgae. We used lipidomics to observe changes in the organic compounds dissolved in estuarine seawater when filtered and when filtered and pretreated with UV. UV treatment resulted in an increase in the relative abundance of oxylipins associated with cyanobacteria, fungi, and macroalgae in 2020, whereas oxylipins typically produced by diatoms were more abundant in the UV treatments from 2021. Oxylipin concentrations were higher in 2020, when the hatchery reported the most severe problems with larval development. Removing the UV step allowed continued larval production in both years. However, the lack of UV sterilization led to an unidentified bacterial pathogen in 2021, which nearly decimated the overall seasonal production of oyster seed. To follow up in a more controlled environment, the larvae were exposed to exogenous oxidized lipids, which resulted in the same digestive syndrome and histological symptoms as the endogenous suite of compounds produced by UV. Further investigation of the lipidomes revealed that oxylipins were only one class of potentially harmful compounds linked to UV sterilization, and the dissolved concentrations of secondary metabolites associated with higher plants, a wide range of pharmaceuticals, and anthropogenic organic pollutants also increased under UV light. Future efforts will explore the sources of these compounds, the mechanisms by which they inhibit oysters, and whether this is an emerging environmental problem for other ecosystems and shellfish hatcheries. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/738347v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@1427dc0org.highwire.dtl.DTLVardef@4dcbf9org.highwire.dtl.DTLVardef@18a57faorg.highwire.dtl.DTLVardef@195e0ed_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2026

Atypical PI3Ks coordinate chemotaxis, signaling dynamics, and multicellular development in Dictyostelium

Phosphoinositide 3-kinase (PI3K) signaling regulates protrusion, polarity, membrane uptake, and multicellular development in Dictyostelium discoideum, but these functions have been interpreted largely through canonical Class I PI3Ks and PI(3,4,5)P production. This framework does not fully explain how PI3K-dependent pathways attenuate Ras activity, organize PI(3,4)P2-associated polarity states, support cAMP relay, or coordinate development. Here, we identify three atypical PI3K-family enzymes--PikF, PikG, and PikH--as functionally distinct regulators of these processes. PikF constrains Ras-phosphoinositide-actin signaling; pikF- cells show prolonged cAMP-stimulated Ras activation, extended PIP recruitment, delayed PI(3,4)P2 biosensor recovery, elevated peripheral actin activity, impaired chemotactic precision, and delayed abnormal development. PikG acts through a distinct relay-associated pathway: pikG- cells fail to generate endogenous cAMP oscillations, display disrupted ACA polarity, deposit spatially disorganized ACA-positive vesicle trails, and fail to aggregate. PikH, in contrast, supports efficient phagocytic uptake with little effect on acute chemotactic signaling. Kinase-dead rescue experiments show that conserved catalytic lysines are required for PikF- and PikG-dependent development and PikH-dependent uptake. Together, our results reveal that atypical PI3Ks diversify the Dictyostelium PI3K signaling toolkit, separating protrusive signal attenuation, cAMP relay organization, membrane uptake, and multicellular development into distinct kinase-dependent modules.

cell biology↗

bioRxiv2025

Optimized Lipid Extraction and Hybrid Annotation Pipeline for Individual Chitinous Mesozooplankton Using UPLC-HRMS

High-resolution lipidomics at the scale of individual mesozooplankton offers a powerful tool for understanding trophic interactions and carbon cycling in marine ecosystems, but chitinous exoskeletons present challenges for efficient lipid extraction. Here, we develop and validate an optimized Bligh and Dyer-based extraction protocol that incorporates in-line glass bead homogenization, yielding a 2.5-fold increase in lipid recovery. When combined with an increased injection volume, this protocol achieves a 4.4-fold gain in signal intensity. This workflow enables the robust detection of intact lipid species from single Calanus copepods, eliminating the need for additional homogenization equipment or extended extraction steps, thereby making it broadly accessible for analytical applications. To address the limitations of current annotation pipelines, we directly compared adduct-hierarchy (LOBSTAHS) and fragmentation-based (MS-DIAL) approaches, finding systematic biases that reshape lipidomic profiles depending on the computational strategy employed. Additionally, by integrating a wax ester-specific fragmentation library, we demonstrate improved annotation of marine-relevant lipid classes largely absent from conventional databases. Together, this extraction and hybrid annotation pipeline enables high-resolution, compound-specific lipidomics of individual mesozooplankton, capturing biological heterogeneity while remaining scalable to pooled samples. Our approach provides a critical methodological advance for tracing lipid metabolism across trophic levels and for quantifying the role of mesozooplankton lipids in marine biogeochemical cycles.

ecology↗

bioRxiv2025

Bioprospecting Native Oleaginous Microalgae for Wastewater Nutrient Remediation and Lipid Production

Subtropical climate in Florida offers a unique opportunity for sustainable biofuel production using native microalgae cultivated in untreated wastewater. This study bioprospected oleaginous microalgal consortia from a wastewater holding tank at the Thomas P. Smith Water Reclamation Facility in Tallahassee, Florida, aiming to identify strains capable of both nutrient remediation and lipid accumulation. Using Fluorescence Activated Cell Sorting (FACS), chlorophyll-containing cells were isolated and cultured on BG-11 media. Shotgun metagenomics revealed that the most robust consortia- labeled C3, C4, and C9, were dominated by Chlamydomonas, Acutodesmus, and Volvox spp., alongside diverse bacterial, fungal, and archaeal communities. Functional gene analysis indicated active pathways for photosynthesis, lipid biosynthesis, and nutrient assimilation. In microcosm experiments, these consortia achieved up to 100% ammonia, 95% phosphorus, and 89% nitrate removal, outperforming control treatments. Lipid screening confirmed significant accumulation, with consortium C9 showing the highest yield. These findings underscore the potential of native microalgal consortia for integrated wastewater treatment and biofuel production, advancing circular bioeconomy strategies for subtropical regions.

microbiology↗

bioRxiv2025

The CYP71A, NIT, AMI, and IAMH gene families are dispensable for indole-3-acetaldoxime-mediated auxin biosynthesis in Arabidopsis

Indole-3-acetic acid (IAA) is a crucial auxin governing plant development and environmental responses. While the indole-3-pyruvic acid (IPyA) pathway is the predominant IAA biosynthesis route, other pathways, like the indole-3-acetaldoxime (IAOx) pathway, have been proposed. The IAOx pathway has garnered attention due to its supposed activation in auxin-overproducing mutants (e.g., sur1, sur2, ugt74b1) and the auxin-like responses triggered by exogenous application of its proposed intermediates: IAOx, indole-3-acetonitrile (IAN), and indole-3-acetamide (IAM). However, despite supporting evidence for individual steps, conclusive physiological relevance of the IAOx pathway remains unproven. Using a comprehensive genetic approach combined with metabolic and phenotypic profiling, we demonstrate that mutating gene families proposed to function in the IAOx pathway does not result in prominent auxin-deficient phenotypes, nor are these genes required for high-auxin production in the sur2 mutant. Our findings also challenge the previously postulated linear IAOx pathway. While exogenously provided IAOx, IAN, and IAM can be converted to IAA in vivo, they do not act as precursors for each other. Finally, our findings question the physiological relevance of IAM and IAN as IAA precursors in plants and suggest the existence of a yet uncharacterized auxin biosynthetic route, likely involving IAOx as an intermediate, for the production of IAA in the sur2 mutant. Future identification of the metabolic steps and the corresponding genes in this new pathway may uncover the previously unknown way of synthesizing IAA in plants.

genetics↗

bioRxiv2024

Reducing flight time during running decreases tibial-fibular strains: a finite element analysis

PurposeReducing strains within the tibia and fibula during running may reduce the risk of stress fractures. We examined the effect of reduced flight time during running (i.e., grounded running) on finite-element predicted bone strains within the tibia-fibula complex. MethodsNine physically active males ran on an instrumented treadmill at 2.2 m/s using a preferred and reduced flight time technique in a randomized order. Three-dimensional force and motion capture data were recorded during running and a computed tomography image was subsequently acquired for the participants left leg. An inverse-dynamics-based musculoskeletal modeling workflow was used to calculate bone-on-bone contact and muscle forces during the stance phase of running. These forces served as inputs to a participant-specific finite-element model to estimate peak bone strains and strained volume (i.e., the volume of bone experiencing strains above a specific threshold) within the tibia-fibula complex. ResultsGuided attempts to reduce flight time was successful with an 18 ms (95% CI: 12 ms, 25 ms; p<0.001) reduction in flight time. Reducing flight time was associated with significant reductions in peak tibial/fibular strains (17% lower; 95% CI: -7.1%, -25.0%; p=0.002) and strained volume (35% lower; 95% CI: -13.57%, -50.87%; p=0.007). ConclusionWe conclude that guided attempts to reduce flight time significantly reduces strains in the tibia and fibula during treadmill running at a fixed speed. These results suggest that grounded running may be a viable technique to reduce musculoskeletal loading and stress fracture risk, particularly in slow runners and those runners coming back from injury.

bioengineering↗

bioRxiv2024

Camelina CircRNA Landscape: Implications for Gene Regulation and Fatty Acid Metabolism

Circular RNAs (circRNAs) are closed-loop RNAs forming a covalent bond between their 3 and 5 ends, the backsplice junction (BSJ), rendering them resistant to exonucleases and thus more stable compared to linear RNAs. Identification of circRNAs and distinction from its cognate linear RNA is only possible by sequencing the BSJ that is unique to the circRNA. CircRNAs are involved in regulation of their cognate RNAs by increasing transcription rates, RNA stability and alternative splicing. We have identified circRNAs from Camelina sativa that are associated with the regulation of germination, light response, and lipid metabolism. We sequenced light-grown and etiolated seedlings after 5 or 7 days post-germination and identified a total of 3,447 circRNAs from 2,763 genes. Most circRNAs originate from a single homeolog of the three subgenomes from allohexaploid camelina and correlates with higher ratios of alternative splicing of their cognate genes. A network analysis shows the interactions of select miRNA:circRNA:mRNAs for regulation of transcript stabilities where circRNA can act as a competing endogenous RNA. Several key lipid metabolism genes can generate circRNA and we confirmed the presence of KASII circRNA as a true circRNA. CircRNA in camelina can be a novel target for breeding and engineering efforts. Core ideasO_LIFirst discovery of 3,447 genic and 307 intergenic unique putative circRNAs from Camelina sativa. C_LIO_LIWe identified circRNAs that were regulated in response to seedling de-etiolation. C_LIO_LIMost circRNAs originate from only one homeolog of the three subgenomes in this allohexaploid Camelina. C_LIO_LIAlternative splicing of exon skipping and intron retention positively correlate with circRNA occurrence. C_LIO_LIValidation of KASII circRNAs as an example of lipid metabolism pathways potentially regulated by circRNA. C_LI

plant biology↗

bioRxiv2023

Re-engineering a lost trait: IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss

Arbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the model Arabidopsis thaliana. To explore why an apparently beneficial trait would be repeatedly lost, we generated Arabidopsis plants expressing a constitutively active form of Interacting Protein of DMI3, a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost from Arabidopsis along with the AM host trait. We characterize the transcriptomic effect of expressing IPD3 in Arabidopsis with and without exposure to the AM fungus (AMF) Rhizophagus irregularis, and compare these results to the AM model Lotus japonicus and its ipd3 knockout mutant cyclops-4. Despite its long history as a non-AM species, restoring IPD3 in the form of its constitutively active DNA-binding domain to Arabidopsis altered expression of specific gene networks. Surprisingly, the effect of expressing IPD3 in Arabidopsis and knocking it out in Lotus was strongest in plants not exposed to AMF, which is revealed to be due to changes in IPD3 genotype causing a transcriptional state which partially mimics AMF exposure in non-inoculated plants. Our results indicate that despite the long interval since loss of AM and IPD3 in Arabidopsis, molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.

plant biology↗

bioRxiv2022

Beyond energy balance in agrivoltaic food production: Emergent crop traits from color selective solar cells

The integration of semi-transparent organic solar cells (ST-OSCs) in greenhouses offers new agrivoltaic opportunities to meet the growing demands for sustainable food production. The tailored absorption/transmission spectra of ST-OSCs impacts the power generated as well as crop growth, development and responses to the biotic and abiotic environments. We grew lettuce and tomato, traditional greenhouse crops, under three ST-OSC filters that create different light spectra. Lettuce yield and early tomato development are not negatively affected by the modified light environment. Our genomic analysis reveals that lettuce production exhibits beneficial traits involving nutrient content and nitrogen utilization while select ST-OSCs impact regulation of flowering initiation in tomato. ST-OSCs integrated into greenhouses are not only a promising technology for energy-neutral, sustainable and climate-change protected crop production, but can deliver benefits beyond energy considerations.

plant biology↗

bioRxiv2022

Introduction of a condensed, reverse tricarboxylic acid cycle for additional CO2 fixation in plants

Plants employ the Calvin-Benson cycle (CBC) to fix atmospheric CO2 for the production of biomass. The flux of carbon through the CBC is limited by the activity and selectivity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Alternative pathways that do not use RuBisCO to fix CO2 exist but occur only in anaerobic microorganisms. Rather than modifying existing routes of carbon metabolism in plants, we have developed a synthetic carbon fixation cycle that does not exist in nature, but is inspired by metabolisms of bacterial autotrophs. This synthetic cycle uses endogenous plant metabolites to fix CO2 and yield glyoxylate as a product. In this work, we build and characterize a condensed, reverse tricarboxylic acid (crTCA) cycle in vitro and in planta. We demonstrate that a simple, synthetic cycle can be used to fix carbon in vitro under aerobic and mesophilic conditions and that these enzymes retain activity when expressed transiently in planta. We then evaluate stable transgenic lines of Camelina sativa that have both phenotypic and physiologic changes. Transgenic C. sativa are shorter than controls with increased rates of photosynthetic CO2 assimilation and changes in photorespiratory metabolism. This first iteration of a build-test-learn phase of the crTCA cycle provides promising evidence that this pathway can be used to increase photosynthetic capacity in plants.

plant biology↗

bioRxiv2022

Dogma and belief: the primary lesion in age-related hearing loss is old news

Presbycusis, or age-related hearing loss, is the most common sensory deficit globally, and the biggest modifiable risk factor for a later dementia diagnosis. Despite its ubiquity, however, the primary pathology contributing to presbycusis is reportedly contentious, particularly the relative role of damage to the sensory outer hair cells compared to the stria vascularis, an important inner ear structure that maintains the ionic concentration of inner ear fluids that surround it. To determine what might be the "dogma" of the field regarding the primary pathology in presbycusis, we conducted an online Google survey (https://forms.gle/GPreoePmRxBBkchc7) asking relevant respondents in the field their opinions on the matter. In Question (Q1), respondents were asked to rate in your opinion from least likely to most likely (on a scale 1 to 4 [being most likely]) what is the primary pathology contributing to presbycusis? in terms of damage to: i) the inner hair cells, ii) outer hair cells (OHCs), iii) spiral ganglion, iv) stria vascularis. The term dogma suggests that the proportion of people in the field who believe that the main cause of presbycusis is damage to the stria vascularis is at least 50%. The results of our survey estimated this proportion to be 19/101 = 0.188 (95% CI [0.124 0.275]) and a two-sided test of the null hypothesis that this proportion is at least 0.5 was rejected (p < 10-10). When it came to opining what other professionals in the field consider to be the primary pathology contributing to presbycusis (Q2), the tendency to rank damage to OHCs as being the primary pathology was 45%. Stria vascularis was least likely to be ranked 4 (11%) by professionals in the field opining about the beliefs of others. Even when noise damage was excluded as a factor (Q3), the most likely contributing factor to presbycusis was stated to be damage to the OHCs (42%). Our data suggest the dogma of the field is that damage to outer hair cells is the primary pathology in presbycusis.

neuroscience↗

bioRxiv2021

Dysregulation of the Tweak/Fn14 pathway in skeletal muscle of spinal muscular atrophy mice

Spinal muscular atrophy (SMA) is a childhood neuromuscular disorder caused by depletion of the survival motor neuron (SMN) protein. SMA is characterized by the selective death of spinal cord motor neurons, leading to progressive muscle wasting. Loss of skeletal muscle in SMA is a combination of denervation-induced muscle atrophy and intrinsic muscle pathologies. Elucidation of the pathways involved is essential to identify the key molecules that contribute to and sustain muscle pathology. The tumor necrosis factor-like weak inducer of apoptosis (TWEAK)/TNF receptor superfamily member fibroblast growth factor inducible 14 (Fn14) pathway has been shown to play a critical role in the regulation of denervation-induced muscle atrophy as well as muscle proliferation, differentiation and metabolism in adults. However, it is not clear whether this pathway would be important in highly dynamic and developing muscle. We thus investigated the potential role of the TWEAK/Fn14 pathway in SMA muscle pathology, using the severe Taiwanese Smn-/-;SMN2 and the less severe Smn2B/- SMA mice, which undergo a progressive neuromuscular decline in the first three post-natal weeks. Here, we report significantly dysregulated expression of the TWEAK/Fn14 pathway during disease progression in skeletal muscle of the two SMA mouse models. In addition, siRNA-mediated Smn knockdown in C2C12 myoblasts suggests a genetic interaction between Smn and the TWEAK/Fn14 pathway. Further analyses of SMA, Tweak-/- and Fn14-/- mice revealed dysregulated myopathy, myogenesis and glucose metabolism pathways as a common skeletal muscle feature, and providing further evidence in support of a relationship between the TWEAK/Fn14 pathway and Smn. Finally, a pharmacological intervention (Fc-TWEAK) to upregulate the activity of the TWEAK/Fn14 pathway improved disease phenotypes in the two SMA mouse models. Our study provides novel mechanistic insights into the molecular players that contribute to muscle pathology in SMA and into the role of the TWEAK/Fn14 pathway in developing muscle.

pathology↗