Biology subjects

Sparks, N.

Publications and source records attributed to Sparks, N..

4 recordsLinked to original sources

bioRxiv2026

Physiological load via voluntary wheel running maintains Achilles tendon homeostasis by region-specific cellular responses

Physiological load is vital for maintaining tendon homeostasis, preserving the organized extracellular matrix that enables tendons to withstand extreme forces. Although tenocytes are regarded as the primary regulators of extracellular matrix production, precisely how cells facilitate the maintenance of homeostasis in response to physiological load is poorly understood. Here, we used Voluntary Wheel Running (VWR) as a model of physiological load to delineate the specific cellular contributions to mouse Achilles tendon homeostasis. Eight weeks of VWR led to a smaller cross-sectional area, increased mechanical and material properties at the midsubstance, which corresponded to a decreased proportion of small (0-60 nm) collagen fibrils and an increased proportion of larger (100-60 nm) collagen fibrils compared to sedentary controls. Using Visium HD spatial transcriptomics, we identified region-specific cell clusters (insertion vs. midsubstance). In response to physiological load, cells in the insertion and midsubstance upregulate distinct genes that reinforce the fibrocartilage interface and collagen-rich tendon matrix, respectively. Notably, Clu, Myoc, and Ccdc80 were upregulated with VWR in the midsubstance, with previously uncharacterized roles in tendon homeostasis. Together, our findings suggest that in response to physiological load, tendon cells maintain homeostasis by region-specific responses. Given that insertional and midsubstance tendinopathy is function-limiting and painful, defining the region-specific cellular responses will be key to advancing therapeutic prospects for tendon health. New and NoteworthyThis study is the first spatially rigorous characterization of the tendon response to physiological load using a Voluntary Wheel Running (VWR) model. VWR led to smaller, stronger, but not stiffer tendons at the midsubstance compared to sedentary controls. This corresponded with significant decreased proportion of small collagen fibrils and a shift toward an increased proportion of large collagen fibrils. Using Visium HD spatial transcriptomics, we identified region-specific transcriptional responses to physiological load that maintain homeostasis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=67 SRC="FIGDIR/small/722285v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@13aa717org.highwire.dtl.DTLVardef@1afe3f1org.highwire.dtl.DTLVardef@9e1137org.highwire.dtl.DTLVardef@17c47bc_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Cigarette Smoke and E-Cigarette Aerosol Extracts Induce Myelopoiesis and Suppress Inflammatory Cytokine Production

Tobacco and nicotine use remain the leading preventable drivers of cancer risk, and both direct and secondhand exposure to combustible cigarettes or electronic nicotine devices perturbs immune function and hematopoiesis. Here, we evaluate the impact of e-cigarette vapor and combustible cigarette smoke on in vitro cell inflammatory responses and in vivo long-term hematopoietic differentiation. In cell-based studies, cigarette smoke extract (CSE) and e-cigarette vapor extract (EVE) consistently suppress LPS-induced TNF- secretion across macrophage/monocyte models, including primary mouse and human cells and complementary cell lines, indicating a reproducible immunosuppressive effect on mature myeloid cells. Brief ex vivo exposure to CSE also alters myeloid subset composition and modifies the proliferative behavior of Tet2-knockout cells, suggesting that smoke-related cues can reshape competitive dynamics among mutant and wild-type myeloid progenitors. To assess consequences of smoking behavior in vivo, we used a custom nose-cone inhalation system to deliver controlled exposures to combustible cigarette smoke or e-cigarette aerosol to mice. Chronic exposure increased myeloid proliferation, consistent with smoking behavior inducing premature aging of the hematopoietic stem cell pool. Thus, these studies support a model in which tobacco exposures blunt innate immune responsiveness while simultaneously driving myeloid expansion conditions that accelerate hematopoietic aging.

cancer biology↗

bioRxiv2024

PrimalScheme: open-source community resources for low-cost viral genome sequencing

Viral genome sequencing using the ARTIC protocol has been a vital tool for understanding the spread of epidemics including Ebola, Zika, Covid-19 and Mpox and has seen widespread adoption due to its low cost and high sensitivity. Here, we describe PrimalScheme, an open-source toolkit and website that allows users to easily design primer schemes for amplicon sequencing of viruses, and has generated over 67,000 primer schemes for the global community since 2017. In January 2020, PrimalScheme was used to rapidly generate a primer scheme for SARS-CoV-2, with primer pools distributed to researchers from 44 countries to help scale-up genomic surveillance efforts. Overall, these primers were used to generate an estimated 18M genome sequences and the protocols were viewed online [~]250K times. To complement PrimalScheme, we have built PrimalScheme Labs, a scheme repository which allows users to find and share primer schemes as well as establishing a set of data standards. Through improvements to the primer design process, including the use of discrete primer clouds, we have expanded the use of amplicon sequencing to include diverse virus species. We demonstrate the utility of this approach through a high diversity pan-genotype Measles virus (MeV) scheme. We also demonstrate its use on a high sensitivity, short amplicon Monkeypox virus (MPXV) scheme with over 1000 primers, showing high genome recovery on low-titre clinical samples. These developments have implications for sequencing from samples such as wastewater, for genomic surveillance of endemic pathogens and in preparing for future pandemics.

genomics↗

bioRxiv2020

Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

Genome sequencing has been widely deployed to study the evolution of SARS-CoV-2 with more than 90,000 genome sequences uploaded to the GISAID database. We published a method for SARS-CoV-2 genome sequencing (https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w) online on January 22, 2020. This approach has rapidly become the most popular method for sequencing SARS-CoV-2 due to its simplicity and cost-effectiveness. Here we present improvements to the original protocol: i) an updated primer scheme with 22 additional primers to improve genome coverage, ii) a streamlined library preparation workflow which improves demultiplexing rate for up to 96 samples and reduces hands-on time by several hours and iii) cost savings which bring the reagent cost down to {pound}10 per sample making it practical for individual labs to sequence thousands of SARS-CoV-2 genomes to support national and international genomic epidemiology efforts.

genomics↗