Biology subjects

Wood, K.

Publications and source records attributed to Wood, K..

15 recordsLinked to original sources

bioRxiv2026

Post-loading ribonucleic acid into lipid nanoparticle carriers

Lipid nanoparticles (LNPs) are effective carriers for messenger ribonucleic acid (mRNA) delivery in vaccines; however, their reliance on extreme cold-chain storage limits global manufacturing and distribution. Conventional LNPs are formed by rapidly mixing four lipids with mRNA through electrostatic interactions between cationic ionizable lipids and negatively charged nucleic acids, facilitating nucleation and precipitation of mRNA-loaded LNPs. However, this binding also accelerates mRNA degradation, requiring stringent cold storage which limits widespread vaccine deployment. To overcome this limitation, we introduce a post-loading strategy in which empty LNPs (eLNPs) are first fabricated and RNA is subsequently loaded at a later stage. Using scalable confined impinging jet (CIJ) mixers, we optimized pH, buffer composition, lipid concentration, and ethanol content to produce colloidally stable eLNPs. Controlled adjustment of ethanol content and pH enabled efficient incorporation of four distinct RNA payloads while maintaining loaded LNP diameters below 100 nm. Post-loaded LNPs demonstrated mRNA delivery efficiencies in HeLa cells comparable to those of conventionally co-precipitated LNPs. Consistent size distributions and zeta potentials further confirmed comparable surface properties. Structural characterization by x-ray and neutron scattering revealed similar internal architectures for post-loaded and co-precipitated LNPs without compromising RNA loading efficiency. Together, these results demonstrate equivalent cellular delivery performance between the two formulations. This post-loading approach enables decentralized assembly of mRNA LNPs at the point of administration, with both eLNPs and mRNA stored under mild refrigeration, thereby improving vaccine accessibility. Moreover, eLNPs function as modular laboratory reagents, facilitating the translation of mRNA research toward clinical applications.

bioengineering↗

bioRxiv2026

Insulin preservatives trigger neutrophil extracellular trap formation through SYNE1-mediated nuclear disassembly

Neutrophil extracellular traps (NETs) are critical effector molecules in sterile inflammation, yet the molecular mechanisms by which xenobiotic chemical exposures trigger NETosis remain poorly defined. Here, using phenolic preservatives present in all FDA-approved insulin formulations as a discovery platform, we show that these compounds induce NETosis in primary human neutrophils (34.3 {+/-} 5.0% vs. 2.8 {+/-} 0.9% for preservative-free insulin; p < 0.001) via a mechanism distinct from canonical PKC- and calcium-dependent pathways. Data-independent acquisition mass spectrometry (n = 6 donors) reveals that preservatives prompt coordinated dephosphorylation of SYNE1 (nesprin-1) at Ser8724 and Ser8727 (log2FC = -4.41 and -4.01, respectively; both q-value < 0.0001), disrupting LINC complex-mediated nuclear-cytoskeletal anchoring, through a phosphatase-dependent pathway distinct from canonical PKC- and calcium-dependent NETosis. In a porcine subcutaneous catheter model, preservative-containing formulations drive progressive NET accumulation, neutrophil infiltration, and early fibrotic changes over 7 days, whereas removing preservatives reduces the histological inflammation score by 40% (P < 0.001). These findings establish phenolic preservatives as non-pathogen triggers of NETosis, identify disruption of the SYNE1-LINC complex as the underlying mechanism, and demonstrate that preservative-free formulations lessen device-related inflammation, offering a translatable strategy for safer implantable drug delivery systems.

immunology↗

bioRxiv2025

UC Irvine Brain Initiative Cell Atlas Network (BICAN) Brain Procurement Program for the Center for Multiomic Human Brain Cell Atlas Project

High-quality neurotypical postmortem human brain tissue is essential but difficult to obtain for constructing comprehensive human brain cell atlases. Here we describe the establishment of UC Irvines Brain Procurement Program, a coordinated initiative to collect and process neurotypical donor brains for multiomic mapping studies within the NIH BRAIN Initiative Cell Atlas Network (BICAN) consortium. Through partnerships with the Orange County Coroners Office, the UC Irvine Willed Body Program, UCI Medical Center, and the Childrens Hospital of Orange County, we have developed standardized workflows encompassing donor identification, postmortem brain recovery and processing, region-of-interest dissection, neurotypical donor selection, and data management. Our experience demonstrates the feasibility of a community-based, multi-institutional procurement framework while highlighting challenges in recruiting neurotypical donors and ensuring demographic representation reflective of Southern California. We further identify opportunities to strengthen outreach and donation pathways. This program provides a scalable model for advancing population-reflective, high-quality human brain cell atlas efforts. HighlightsO_LIEstablish a multi-site pipeline for procuring high-quality neurotypical human brains. C_LIO_LIDemonstrate feasibility of donor collection across childhood to adulthood. C_LIO_LIIdentify barriers and propose strategies to improve broad donor recruitment. C_LI

neuroscience↗

bioRxiv2025

The Goldilocks effect drives plant diversification on middle-aged Hawaiian islands

Islands are natural laboratories for studying dispersal, speciation, and extinction, yet the historical dynamics of many insular radiations remain poorly understood because of the difficulty aligning the tempo and mode of diversification with paleogeography during phylogenetic inference. We introduce a phylogenetic modeling framework, named TimeFIG, that combines data about species ranges and genetic variation with paleogeographic information to simultaneously infer divergence times, ancestral ranges, and historical diversification rates, without relying on fossils to time-calibrate the phylogeny. Applying TimeFIG to the spectacular radiation of Hawaiian Kadua (Rubiaceae) points to colonization of either modern Kaua'i or ancient now-eroded islands, with island isolation as the strongest correlate of dispersal, and with a tendency for net diversification to be highest on "middle-aged" islands. Modeling diversification within an explicit spatiotemporal context, while accounting for historical uncertainty regarding the timing and placement of phylogenetic and biogeographic events, enables the rigorous testing of foundational hypotheses in island biology and evolutionary theory for clades beyond Kadua.

evolutionary biology↗

bioRxiv2024

A real-time forecasting framework for emerging infectious diseases affecting animal populations

Infectious disease forecasting has become increasingly important in public health, as demonstrated during the COVID-19 pandemic. However, forecasting tools for emergency animal diseases, particularly those offering real-time decision support when parameters governing disease dynamics are unknown, remain limited. We introduce a generalised modelling framework for near-real-time forecasting of the temporal and spatial spread of infectious livestock diseases using data from the early stages of an outbreak. We applied the framework to the 2007 equine influenza outbreak in Australia, generating prediction targets at three timepoints across four regional clusters. Our targets included future daily case counts, outbreak size, peak timing and duration, and spatial distributions of future spread. We evaluated how well the forecasts predicted daily cases and the spatial distribution of case counts, using skill scores as a benchmark for future model improvements. Forecast accuracy, certainty, and skill improved significantly after the outbreaks peak, while early predictions were more variable, suggesting that pre-peak forecasts should be interpreted with caution. Spatial forecasts maintained positive skill throughout the outbreak, supporting their use in guiding response priorities. This framework provides a tool for real-time decision-making during livestock disease outbreaks and establishes a foundation for future refinements and applications to other animal diseases.

bioinformatics↗

bioRxiv2024

Linking spatial drug heterogeneity to microbial growthdynamics in theory and experiment

Diffusion and migration play pivotal roles in microbial communities - shaping, for example, colonization in new environments and the maintenance of spatial structures of biodiversity. While previous research has extensively studied free diffusion, such as range expansion, there remains a gap in understanding the effects of biologically or physically deleterious confined environments. In this study, we examine the interplay between migration and spatial drug heterogeneity within an experimental meta-community of E. faecalis, a Gram-positive opportunistic pathogen. When the community is confined to spatially-extended habitats ( islands) bordered by deleterious conditions, we find that the population level response depends on the trade-off between the growth rate within the island and the rate of transfer into regions with harsher conditions, a phenomenon we explore by modulating antibiotic concentration within the island. In heterogeneous islands, composed of spatially patterned patches that support varying levels of growth, the populations fate depends critically on the specific spatial arrangement of these patches - the same spatially averaged growth rate leads to diverging responses. These results are qualitatively captured by simple simulations, and analytical expressions which we derive using first-order perturbation approximations to reaction-diffusion models with explicit spatial dependence. Among all possible spatial arrangements, our theoretical and experimental findings reveal that the arrangement with the highest growth rates at the center most effectively mitigates population decline, while the arrangement with the lowest growth rates at the center is the least effective. Extending this approach to more complex experimental communities with varied spatial structures, such as a ring-structured community, further validates the impact of spatial drug arrangement. Our findings suggest new approaches to interpreting diverging clinical outcomes when applying identical drug doses and inform the possible optimization of spatially-explicit dosing strategies. Author summaryIn this study, we develop an automated platform to experimentally investigate short-term population growth and migration dynamics under spatial drug heterogeneity. Our findings reveal that the collective spatial response of the population can vary significantly, even with the same migration rate and averaged drug dose, due to different spatial drug arrangements. By constructing a simple reaction-diffusion model, we observed that simulated short-term spatial growth rate closely matches the experimental data. Furthermore, this short-term spatial growth rate aligns well with the long-term spatial growth rate, defined by the largest eigenvalue, as the spatial system quickly enters the equilibrium growth state. Using concepts from perturbation theory, we derived an analytical relationship between the boundary diffusion effect, homogeneous growth effect, and heterogeneous effect. Our results highlight that in spatially-extended habitats, the spatial growth response is an emergent property. The bacterial population quickly enters equilibrium growth, suggesting that the spatial growth rate measured at an ecological scale may be used to predict resistance evolutionary behavior.

biophysics↗

bioRxiv2023

Small molecule nitroalkenes inhibit RAD51-mediated homologous recombination and amplify triple-negative breast cancer cell killing by DNA-directed therapies.

Nitro fatty acids (NO2-FAs) are endogenously generated lipid signaling mediators from metabolic and inflammatory reactions between conjugated diene fatty acids and nitric oxide or nitrite-derived reactive species. NO2-FAs undergo reversible Michael addition with hyperreactive protein cysteine thiolates to induce posttranslational protein modifications that can impact protein function. Herein, we report a novel mechanism of action of natural and non-natural nitroalkenes structurally similar to (E) 10-nitro-octadec-9-enoic acid (CP-6), recently de-risked by preclinical Investigational New Drug-enabling studies and Phase 1 and Phase 2 clinical trials and found to induce DNA damage in a TNBC xenograft by inhibiting homologous-recombination (HR)-mediated repair of DNA double-strand breaks (DSB). CP-6 specifically targets Cys319, essential in RAD51-controlled HR-mediated DNA DSB repair in cells. A nitroalkene library screen identified two structurally different nitroalkenes, a non-natural fatty acid [(E) 8-nitro- nonadec-7-enoic acid (CP-8)] and a dicarboxylate ester [dimethyl (E)nitro-oct-4-enedioate (CP- 23)] superior to CP-6 in TNBC cells killing, synergism with three different inhibitors of the poly ADP-ribose polymerase (PARP) and {gamma}-IR. CP-8 and CP-23 effectively inhibited {gamma}-IR-induced RAD51 foci formation and HR in a GFP-reported assay but did not affect benign human epithelial cells or cell cycle phases. In vivo, CP-8 and CP-23s efficacies diverged as only CP-8 showed promising anticancer activities alone and combined with the PARP inhibitor talazoparib in an HR-proficient TNBC mouse model. As preliminary preclinical toxicology analysis also suggests CP-8 as safe, our data endorse CP-8 as a novel anticancer molecule for treating cancers sensitive to homologous recombination-mediated DNA repair inhibitors. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=172 SRC="FIGDIR/small/552990v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1dcec56org.highwire.dtl.DTLVardef@1202a09org.highwire.dtl.DTLVardef@a7e7b6org.highwire.dtl.DTLVardef@15d8925_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2022

The PREGCARE study: Personalized recurrence risk assessment following the birth of a child with a pathogenic de novo mutation

Next-generation sequencing has led to a dramatic improvement in molecular diagnoses of serious pediatric disorders caused by apparently de novo mutations (DNMs); by contrast, clinicians ability to counsel the parents about the risk of recurrence in a future child has lagged behind. Owing to the possibility that one of the parents could be mosaic in their germline, a recurrence risk of 1-2% is frequently quoted, but for any specific couple, this figure is usually incorrect. We present a systematic approach to providing individualized recurrence risk stratification, by combining deep-sequencing of multiple tissues in the mother-father-child trio with haplotyping to determine the parental origin of the DNM. In the first 58 couples analysed (total of 59 DNMs in 49 different genes), the risk for 35 (59%) DNMs was decreased below 0.1% but for 6 (10%) couples it was increased owing to parental mosaicism - that could be quantified in semen (recurrence risks of 5.6-12.1%) for the paternal cases. Deep-sequencing of the DNM efficiently identifies couples at greatest risk for recurrence and may qualify them for additional reproductive technologies. Haplotyping can further reassure many other couples that their recurrence risk is very low, but its implementation is more technically challenging and will require better understanding of how couples respond to information that reduces their risks.

genetics↗

bioRxiv2021

Cooperation between CYB5R3 and NOX4 via coenzyme Q mitigates endothelial inflammation

NADPH oxidase 4 (NOX4) regulates endothelial inflammation by producing reactive oxygen species. Since coenzyme Q (CoQ) mimics affect NOX4 activity, we hypothesize that cytochrome b5 reductase 3 (CYB5R3), a CoQ reductase abundant in vascular endothelial cells, modulates inflammatory activation. Mice lacking endothelial CYB5R3 (R3 KO), under lipopolysaccharides (LPS) challenge, showed exacerbated hypotension, decreased acetylcholine-induced vasodilation, and elevated vascular adhesion molecule 1 (Vcam-1) mRNA in aorta. In vitro, silencing Cyb5r3 enhanced LPS-induced VCAM-1 protein in a NOX4 dependent manner. APEX2- based electron microscopy and proximity biotinylation demonstrated CYB5R3s localization on the mitochondrial outer membrane and its interaction with NOX4, which was further confirmed by the proximity ligation assay. Notably, Cyb5r3 silenced HAECs had less total H2O2 but more mitochondrial O2*-. Using inactive or non-membrane bound active CYB5R3, we found CYB5R3 activity and membrane translocation were needed for optimal generation of H2O2 by NOX4. Lastly, CoQ deficient cells showed decreased NOX4-derived H2O2, indicating a requirement for endogenous CoQ in NOX4 activity. In conclusion, CYB5R3 mitigates endothelial inflammatory activation by assisting in NOX4-dependent H2O2 generation via CoQ. NOVELTY AND SIGNIFICANCEO_ST_ABSWhat Is Known?C_ST_ABSNADPH oxidase 4 (NOX4) reportedly produces primarily hydrogen peroxide (H2O2) and, to a lesser extent, superoxide (O2*-) and has been shown to have both beneficial and deleterious effects in the cardiovascular system. NOX4 activity can be affected by NAD(P)H quinone oxidoreductase 1 (NQO1), a CoQ reductase, and synthetic quinone compounds used to mimic CoQ. Cytochrome b5 reductase 3 (CYB5R3) is known to reduce CoQ and is highly expressed in endothelial cells. What New Information Does This Article Contribute?In vivo, the lack of endothelial CYB5R3 causes exacerbated lipopolysaccharides (LPS)-induced inflammatory signaling, endothelial dysfunction, and hypotension. Endothelial CYB5R3 mitigates inflammatory signaling by LPS and tumor necrosis factor (TNF-) in a NOX4 dependent manner. In endothelial cells, CYB5R3 and NOX4 reside in close proximity on the mitochondrial outer membrane. NOX4s ability to generate H2O2 depends on the membrane translocation and activity of CYB5R3 and the presence of endogenous CoQ. NONSTANDARD Abbreviations and Acronyms [Table 1] Protein names are abbreviated as capital letters (e.g., CYB5R3), while the corresponding gene names are annotated as in italic lower cases (e.g., Cyb5r3).

cell biology↗

bioRxiv2021

TREM2 impacts brain microglia, oligodendrocytes and endothelial co-expression modules revealing genes and pathways important in Alzheimer s disease

A microglia response to pathogenic signals in diseases such as Alzheimers disease (AD) has long been recognised, but recent genetic findings have cemented their direct causal contribution to AD and thus the potential to target them or their effector pathways as a possible treatment strategy. TREM2 is a highly penetrant microglia risk gene for AD, which appears central to the coordination of the damage response by microglia in AD. Its absence has a negative impact on Tau and amyloid symptoms and pathologies. Full knowledge of its pathway and relationships with other brain cells in AD has not been fully characterised, but will be essential to fully evaluate the impact of manipulating this pathway for treatment development and to establish the best targets for achieving this. We used whole genome RNA sequencing of hippocampus and cortical brain samples from control, AD, and AD TREM2 risk carriers to identify TREM2-dependent genes driving changes in pathways, processes and cell types in AD. Through highly influential intra and intermodular hub genes and overall changes in the levels of gene expression, TREM2-DAP12 was found to strongly influence a number of other microglia, oligodendrocyte and endothelial genes, notably those involved in complement and Fc{gamma} receptor function, microglia-associated ribosomal genes and oligodendrocyte genes, particularly proteosomal subunits. These strong TREM2 centred co-expression relationships were significantly disrupted in AD cases with a TREM2 risk variant, revealing for the first time genes and pathways directly impacted by TREM2 in the brains of AD patients. Consistent with its function as a lipid sensor, our data supports a role for TREM2 in mediating oligodendrocyte and/or myelin clearance in AD which may be essential not only for preserving healthy tissue homeostasis but may also serve to minimise the persistence of antigenic peptides and lipids which may lead to detrimental pro-inflammatory sequelae. Further work should expand our knowledge of TREM2 on complement and Fc{gamma} receptor function and its impact on oligodendcrotye and myelin integrity and further evaluate the genes and pathways we have identified as possible treatment targets for AD.

neuroscience↗

bioRxiv2019

Engineered niches support the development of human dendritic cells in humanized mice

Classical dendritic cells (cDCs) are rare sentinel cells specialized in the regulation of adaptive immunity. Modeling cDC development is both crucial to study cDCs and harness their potential in immunotherapy. Here we addressed whether cDCs could differentiate in response to trophic cues delivered by mesenchymal components of the hematopoietic niche where they physiologically develop and maintain. We found that expression of the membrane bound form of human FLT3L and SCF together with CXCL12 in a bone marrow mesenchymal stromal cell line is sufficient to induce the contact-dependent specification of both type 1 and type 2 cDCs from CD34+ hematopoietic stem and progenitor cells (HSPCs). Engraftment of these engineered mesenchymal stromal cells (eMSCs) together with CD34+ HSPCs creates an in vivo synthetic niche in the dermis of immunodeficient mice. Cell-to-cell contact between HSPCs and stromal cells within these organoids drive the local specification of cDCs and CD123+AXL+CD327+ pre/AS-DCs. cDCs generated in vivo display higher levels of resemblance with human blood cDCs unattained by in vitro generated subsets. Altogether, eMSCs provide a novel and unique platform recapitulating the full spectrum of cDC subsets enabling their functional characterization in vivo.

immunology↗

bioRxiv2018

Loss of Trem2 in microglia leads to widespread disruption of cell co-expression networks in mouse brain

Rare heterozygous coding variants in the Triggering Receptor Expressed in Myeloid cells 2 (TREM2) gene, conferring increased risk of developing late-onset Alzheimer's disease, have been identified. We examined the transcriptional consequences of the loss of Trem2 in mouse brain to better understand its role in disease using differential expression and coexpression network analysis of Trem2 knockout and wild-type mice. We generated RNA-Seq data from cortex and hippocampus sampled at 4 and 8 months. Using brain cell type markers and ontology enrichment, we found subnetworks with cell type and/or functional identity. We primarily discovered changes in an endothelial-gene enriched subnetwork at 4 months, including a shift towards a more central role for the Amyloid Precursor Protein (App) gene, coupled with widespread disruption of other cell-type subnetworks, including a subnetwork with neuronal identity. We reveal an unexpected potential role of Trem2 in the homeostasis of endothelial cells that goes beyond its known functions as a microglial receptor and signalling hub, suggesting an underlying link between immune response and vascular disease in dementia.

systems biology↗

bioRxiv2017

Pervasive and diverse collateral sensitivity profiles inform optimal strategies to limit antibiotic resistance

Evolved resistance to one antibiotic may be associated with \"collateral\" sensitivity to other drugs. Here we provide an extensive quantitative characterization of collateral effects in Enterococcus faecalis, a gram-positive opportunistic pathogen. By combining parallel experimental evolution with high-throughput dose-response measurements, we measure phenotypic profiles of collateral sensitivity and resistance for a total of 900 mutant-drug combinations. We find that collateral effects are pervasive but difficult to predict, as independent populations selected by the same drug can exhibit qualitatively different profiles of collateral sensitivity as well as markedly different fitness costs. Using whole-genome sequencing of evolved populations, we identified mutations in a number of known resistance determinants, including mutations in several genes previously linked with collateral sensitivity in other species. While phenotypic drug sensitivity profiles show significant diversity, they cluster into statistically similar groups characterized by selecting drugs with similar mechanisms. To exploit the statistical structure in these resistance profiles, we develop a simple mathematical model based on a stochastic control process and use it to design optimal drug policies that assign a unique drug to every possible resistance profile. Stochastic simulations reveal that these optimal drug policies outperform intuitive cycling protocols by maintaining long-term sensitivity at the expense of short-term periods of high resistance. The approach reveals a new conceptual strategy for mitigating resistance by balancing short-term inhibition of pathogen growth with infrequent use of drugs intended to steer pathogen populations to a more vulnerable future state. Experiments in laboratory populations confirm that model-inspired sequences of four drugs reduce growth and slow adaptation relative to naive protocols involving the drugs alone, in pairwise cycles, or in four-drug uniform cycles.

evolutionary biology↗

bioRxiv2017

Interplay between antibiotic efficacy and drug-induced lysis underlie enhanced biofilm formation at subinhibitory drug concentrations

Subinhibitory concentrations of antibiotics have been shown to enhance biofilm formation in multiple bacterial species. While antibiotic exposure has been associated with modulated expression in many biofilm-related genes, the mechanisms of drug-induced biofilm formation remain a focus of ongoing research efforts and may vary significantly across species. In this work, we investigate antibiotic-induced biofilm formation in E. faecalis, a leading cause of nosocomial infections. We show that biofilm formation is enhanced by subinhibitory concentrations of cell wall synthesis inhibitors, but not by inhibitors of protein, DNA, folic acid, or RNA synthesis. Furthermore, enhanced biofilm is associated with increased cell lysis, an increase in extracellular DNA (eDNA), and an increase in the density of living cells in the biofilm. In addition, we observe similar enhancement of biofilm formation when cells are treated with non-antibiotic surfactants that induce cell lysis. These findings suggest that antibiotic-induced biofilm formation is governed by a trade-off between drug toxicity and the beneficial effects of cell lysis. To understand this trade-off, we developed a simple mathematical model that predicts changes to antibiotic-induced biofilm formation due to external perturbations, and we verify these predictions experimentally. Specifically, we demonstrate that perturbations that reduce eDNA (DNase treatment) or decrease the number of living cells in the planktonic phase (a second antibiotic) decrease biofilm induction, while chemical inhibitors of cell lysis increase relative biofilm induction and shift the peak to higher antibiotic concentrations. Overall, our results offer experimental evidence linking cell wall synthesis inhibitors, cell lysis, increased eDNA, and biofilm formation in E. faecalis while also providing a predictive, quantitative model that sheds light on the interplay between cell lysis and antibiotic efficacy in developing biofilms.

microbiology↗

bioRxiv2017

Integration of visual information in auditory cortex promotes auditory scene analysis through multisensory binding

How and where in the brain audio-visual signals are bound to create multimodal objects remains unknown. One hypothesis is that temporal coherence between dynamic multisensory signals provides a mechanism for binding stimulus features across sensory modalities. Here we report that when the luminance of a visual stimulus is temporally coherent with the amplitude fluctuations of one sound in a mixture, the representation of that sound is enhanced in auditory cortex. Critically, this enhancement extends to include both binding and non-binding features of the sound. We demonstrate that visual information conveyed from visual cortex, via the phase of the local field potential, and is combined with auditory information within auditory cortex. These data provide evidence that early cross-sensory binding provides a bottom-up mechanism for the formation of cross-sensory objects and that one role for multisensory binding in auditory cortex is to support auditory scene analysis.

neuroscience↗