Biology subjects

Bedingfield, S. K.

Publications and source records attributed to Bedingfield, S. K..

4 recordsLinked to original sources

bioRxiv2026

Complementary Insights from Environmental DNA and Environmental RNA Metabarcoding for Marine Biodiversity Assessment Around San Andres Island, Colombia

Environmental DNA (eDNA) metabarcoding has become a cornerstone of marine biodiversity monitoring, yet it recovers genetic material irrespective of organism viability and may therefore conflate historical and contemporary community signals. Environmental RNA (eRNA), derived from less stable ribonucleic acid, is hypothesized to be biased toward metabolically active organisms and may provide a more temporally resolved snapshot of living communities. Here we present a paired eDNA/eRNA metabarcoding comparison across a tropical marine seascape, analyzing 19 co-sampled sites spanning coral reefs, mangroves, a seagrass bed, shipwrecks, a cenote, and coastal infrastructure around San Andres Island, Colombia. To our knowledge this is the first in situ, ecosystem-scale paired eDNA/eRNA survey of the broad eukaryotic community across multiple natural habitat types in a tropical marine system, extending mesocosm and freshwater work (e.g., Giroux et al., 2022) to a field setting. Using COI-region amplicon sequencing processed by NatureMetrics, we recovered 1,944 operational taxonomic units (OTUs) across the 19 paired sites. Of these, 1,015 (52.2%) were detected by both approaches, 305 (15.7%) were unique to eDNA, and 624 (32.1%) were unique to eRNA. The eRNA-unique fraction was taxonomically enriched for groups including diatoms (class Bacillariophyceae, phylum Ochrophyta), ciliates, and other protists. Paired Wilcoxon signed-rank tests showed that eRNA recovered significantly higher OTU richness (median 239 vs. 207; W = 36, p = 0.016) and Shannon diversity (median 3.64 vs. 3.38; W = 40, p = 0.026) than eDNA. The mean per-site Jaccard similarity between paired samples was 0.40, indicating substantial turnover in the rare-taxon composition recovered by each method. Principal coordinates analysis of Bray-Curtis dissimilarity showed that habitat type structured abundance-weighted community composition (PERMANOVA F = 2.49, p = 0.001) whereas molecular method did not (F = 1.37, p = 0.107). A PERMDISP test found homogeneous multivariate dispersion between methods (F = 0.01, p = 0.92), reinforcing the absence of a method effect, but significant dispersion heterogeneity among habitats (F = 24.0, p < 0.01), so the habitat result is interpreted with caution. Indicator species analysis identified 73 OTUs significantly associated with one template: eDNA indicators were dominated by dinoflagellates (Dinophyceae) and eRNA indicators by diatoms (Bacillariophyceae) and fungi, consistent with an eRNA bias toward metabolically active microbial eukaryotes. A read-weighted overlap analysis showed that although eRNA-unique OTUs outnumbered eDNA-unique OTUs roughly two to one, the large majority of reads (>95%) fell in shared OTUs, so method-unique detections are predominantly rare taxa. We discuss the complementary value of eRNA for marine monitoring, with the seagrass habitat -- where eRNA reduced masking by terrestrial plant material -- as the clearest use case, and propose, rather than prescribe, the integration of eRNA into routine programs.

genetics↗

bioRxiv2021

Galectin-anchored indoleamine 2,3-dioxygenase suppresses local inflammation

Summary paragraphChronic inflammation underlies the onset, progression and associated pain of numerous diseases.(1) Current anti-inflammatory treatments administered systemically are associated with moderate-to-severe side effects, while locally administered drugs have short-lived efficacy, and neither approach successfully modifies the underlying causality of disease.(2) We report a new way to locally modulate inflammation by fusing the enzyme indoleamine 2,3-dioxygenase 1 (IDO) to galectin-3 (Gal3). A general regulator of inflammation(3), IDO is immunosuppressive(4), catabolizing the essential amino acid tryptophan into kynurenine.(5) Recently we demonstrated that extracellular exogenous IDO regulates innate immune cell function(6), and envisioned delivering IDO into specific tissues would provide control of inflammation. However, proteins problematically diffuse away from local injection sites. Addressing this, we recently established that fusion to Gal3 anchors enzymes to tissues(7) via binding to extracellular glycans. Fusion protein IDO-Gal3 was retained in injected tissues and joints for up to a week or more, where it suppressed local inflammation in rodent models of endotoxin-induced inflammation, psoriasis, periodontal disease and osteoarthritis. Amelioration of local inflammation, disease progression and inflammatory pain were concomitant with homeostatic preservation of tissues without global immune suppression. Thus, IDO-Gal3 presents a new concept of anchoring immunomodulatory enzymes for robust control of focal inflammation in multiple disease settings.

bioengineering↗

bioRxiv2020

Kupffer Cell Release of Platelet Activating Factor Drives Dose Limiting Toxicities of Nucleic Acid Nanocarriers

In vivo nanocarrier-associated toxicity is a significant and poorly understood hurdle to clinical translation of siRNA nanomedicines. In this work, we demonstrate that platelet activating factor (PAF), an inflammatory lipid mediator, plays a key role in nanocarrier-associated toxicities, and that prophylactic inhibition of the PAF receptor (PAFR) completely prevents these toxicities. High-dose intravenous injection of siRNA-polymer nano-complexes (si-NPs) elicited acute, shock-like symptoms (vasodilation and vascular leak) in mice and caused a three-fold increase in blood PAF levels. PAFR inhibition completely prevented these toxicities, indicating PAF activity is a primary driver of systemic si-NP toxicity. Pre-treatment with clodronate liposomes fully abrogated si-NP-associated increases in blood PAF and consequent toxicities, suggesting that nanoparticle uptake by Kupffer macrophages is the source of PAF. Assessment of varied si-NP chemistries further confirmed that toxicity level correlated to relative uptake of the carrier by liver Kupffer cells and that this toxicity mechanism is dependent on the endosome disruptive function of the carrier. Finally, the PAF toxicity mechanism was shown to be generalizable to commercial delivery reagent in vivo-jetPEI(R) and an MC3 lipid nanoparticle formulated to match an FDA-approved siRNA nanomedicine. Greater sensitivity to the PAF mechanism occurs in 4T1 tumor-bearing mice, a mammary tumor model known to exhibit increased circulating leukocytes and potential to respond to inflammatory insult. These results establish Kupffer cell release of PAF as a key mediator of in vivo nucleic acid nanocarrier toxicity and identify PAFR inhibition as an effective prophylactic strategy to increase maximum tolerated dose and reduce nanocarrier-associated adverse events. SignificanceNon-viral nucleic acid nanocarriers can enable in vivo gene therapy, but their potential interaction with innate immune cells can cause dose-limiting toxicities. Nanoparticle toxicities are currently poorly understood, making it difficult to identify relevant design criteria for maximizing nanoparticle safety. This work connects nanoparticle-associated toxicities to the release of platelet activating factor (PAF) by liver Kupffer cells. Small molecule inhibition of the PAF receptor (PAFR) completely prevents severe adverse events associated with high doses of multiple polymer-based formulations and a lipid nanoparticle matching the composition of the first clinically-approved siRNA nanomedicine. This study identifies PAF as a toxicity biomarker for future nanomedicine discovery programs. Further, PAFR inhibition should be explored as a strategy to expand the therapeutic index of nanomedicines.

bioengineering↗

bioRxiv2020

Matrix-targeted Nanoparticles for MMP13 RNA Interference Blocks Post-Traumatic Osteoarthritis.

Osteoarthritis (OA) is a debilitating and prevalent chronic disease, but there are no approved disease modifying OA drugs (DMOADs), only pharmaceuticals for pain management. OA progression, particularly for post-traumatic osteoarthritis (PTOA), is associated with inflammation and enzymatic degradation of the extracellular matrix. In particular, Matrix Metalloproteinase 13 (MMP13) breaks down collagen type 2 (CII), a key structural component of cartilage extracellular matrix, and consequently, matrix degradation fragments perpetuate inflammation and a degenerative cycle that leads to progressive joint pathology. Here, we tested targeted delivery of endosome-escaping, MMP13 RNA interference (RNAi) nanoparticles (NPs) as a DMOAD. The new targeting approach pursued here deviates from the convention of targeting specific cell types (e.g., through cell surface receptors) and instead leverages a monoclonal antibody (mAbCII) that targets extracellular CII that becomes uniquely accessible at early OA focal defects. Targeted mAbCII-siNPs create an in situ NP depot for retention and potent activity within OA joints. The mAbCII-siNPs loaded with MMP13 siRNA (mAbCII-siNP/siMMP13) potently suppressed MMP13 expression (95% silencing) in TNF-stimulated chondrocytes in vitro, and the targeted mAbCII-siNPs had higher binding to trypsin-damaged porcine cartilage than untargeted control NPs. In an acute mechanical injury mouse model of PTOA, mAbCII-siNP/siMMP13 achieved 80% reduction in MMP13 expression (p = 0.00231), whereas a non-targeted control achieved only 55% silencing. In a more severe, PTOA model, weekly mAbCII-siNP/siMMP13 long-term treatment provided significant protection of cartilage integrity (0.45+/- .3 vs 1.6+/-.5 on the OARSI scale; p=0.0166), and overall joint structure (1.3+/-.6 vs 2.8+/-.2 on the Degenerative Joint Disease scale; p<0.05). Intra-articular mAbCII-siNPs better protected articular cartilage (OARSI score) relative to either single or weekly treatment with the clinical gold stand steroid treatment methylprednisolone. Finally, multiplexed gene expression analysis of 254 inflammation-related genes showed that MMP13 inhibition suppressed clusters of genes associated with tissue restructuring, angiogenesis (associated with synovial inflammation and thickening), innate immune response, and proteolysis. This work establishes the new concept of targeting unique local extracellular matrix signatures to sustain retention and increase delivery efficacy of biologics with intracellular activity and also validates the promise of MMP13 RNAi as a DMOAD in a clinically-relevant therapeutic context. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=148 SRC="FIGDIR/small/925321v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@1803795org.highwire.dtl.DTLVardef@c1254dorg.highwire.dtl.DTLVardef@78233eorg.highwire.dtl.DTLVardef@151d96f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOAbstract Figure:C_FLOATNO PTOA targeted delivery of MMP13 siRNA to block disease progressionThe top left schematic illustrates the progression (left to right) from healthy knee joint, through inflammation induction following traumatic injury, to cartilage loss and degenerative joint disease (including synovial response). Degradation of cartilage enhances inflammation, inducing a degenerative cycle (middle right). The bottom of the graphic illustrates the concept of the matrix targeted nanocarriers for enhanced retention and activity of MMP13 siRNA at sites of cartilage injury. C_FIG

bioengineering↗