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Biology subjects

Benson, E.

Publications and source records attributed to Benson, E..

8 recordsLinked to original sources
bioRxiv2026

Ultrastructural and Proteomic Signatures of Mechanoadaptive Fibroblast Remodeling across Microphysiological and Mesoscale Shear Platforms

Mechanobiological cues in the tissue microenvironment increasingly drive pathological fibroblast activation in inflammatory bowel disease (IBD), yet engineered platforms modeling this transition remain limited. Here, a microfluidic gut-on-a-chip microphysiological system and a mesofluidic rotary shaker are used to demonstrate that sustained fluid shear stress alone is necessary and sufficient to drive an irreversible, profibrotic phenotypic switch in primary normal human intestinal fibroblasts. Across both platforms, normal fibroblasts from small and large intestine reproducibly self-organize into three-dimensional (3D) multicellular aggregates within 72 h, independent of shear delivery format, indicating that the transition is governed by mechanical dose rather than device geometry. The resulting aggregates acquire robust -smooth muscle actin (-SMA) expression with aligned stress fibers, contrasting with the -SMA-negative parental population. Scanning electron microscopy (SEM) resolves densely packed cellular microarchitecture embedded in a microfibrillar extracellular network, while ultrastructural serial block-face 3D EM reveals expansive intercellular spaces, stochastic fibrillar extrusions, and electron-dense cytoplasmic material at cell boundaries. Proteomic profiling confirms enrichment of core matrisome components, including collagen subtypes and matrix metalloproteinases. Together, these results establish fluid shear stress as a platform-independent, sufficient mechanical trigger for fibroblast-to-mechanoadaptive transition, positioning microphysiological shear platforms as tractable tools for modeling and targeting early fibrogenesis in IBD.

bioengineering↗
bioRxiv2026

S100A9-Dependent CXCR2hi Neutrophils Mediate Systemic Immune Suppression and Checkpoint Resistance in Metastatic TNBC

Most high-dimensional studies of tumor-immune interactions focus on metastatic models, limiting insight into how immune remodeling in primary tumors shapes metastatic competence. Here, integrating single-cell RNA sequencing, CyTOF, and functional studies across metastatic (4T1) and non-invasive (EMT6) triple-negative breast cancer (TNBC) murine models, we define tumor state-specific immune programs that distinguish metastatic competence. Tumors with metastatic capacity uniquely drive early bone marrow expansion of CXCR2 neutrophils, which infiltrate primary tumors acquiring a CXCL2-producing phenotype that promotes EMT-associated cancer stem cell (CSC) plasticity. This program depends on TGF-{beta}/CEBPD-mediated induction of S100A9. Elevated CXCL2, together with G-CSF, establishes a feed-forward circuit that drives systemic neutrophil mobilization and recruitment to distant organs, where neutrophil-derived S100A8/A9 (calprotectin) promotes MET-driven CSC outgrowth and metastatic colonization. Clinically, gene signatures associated with CXCR2 neutrophils predict poor survival in TNBC patients, whereas monocyte/macrophage (CX3CR1) and T cell activation signatures correlate with improved outcomes. S100A9 ablation disrupts this cascade and enhances immunotherapy responsiveness, defining a TGF-{beta}/S100A9/CXCR2 axis linking immune remodeling, CSC plasticity and metastasis. HighlightsO_LIMetastatic TNBC engages a TGF-{beta}/C/EBP{delta}/S100A9 axis that expands CXCR2 neutrophils C_LIO_LINon-invasive EMT6 tumors retain a CX3CR1 monocyte/macrophage and T-cell landscape C_LIO_LICXCR2+ neutrophils in pre-metastatic niches suppress T cell response while promoting tumor cell proliferation C_LIO_LIS100A9 loss redirects myelopoiesis and potentiates anti-PD-L1 in TNBC models C_LI In BriefAlkan et al. dissect how tumor state programs the myeloid compartment in TNBC. Metastatic 4T1 tumors uniquely engage a TGF-{beta}/C/EBP{delta}/S100A9 axis driving CXCR2 neutrophil expansion and CXCL2/G-CSF-dependent systemic mobilization, coupling immune remodeling to EMT/MET cancer-stem-cell plasticity, while S100A9 loss restores CX3CR1 myeloid identity and unlocks checkpoint-inhibitor responsiveness.

cancer biology↗
bioRxiv2026

Evolutionary selection of DNA nanostructures for cellular uptake

DNA nanotechnology offers precise, biocompatible structures with strong potential for targeted drug delivery, yet current discovery approaches rely on testing individual designs, limiting exploration of structural diversity. Here, we introduce an evolutionary selection strategy that screens large libraries of DNA nanostructures, each folded from a single-stranded structure genome compatible with amplification and sequencing. Cellular internalization is used as the selection pressure: libraries are incubated with mammalian cells, internalized structures are recovered from lysates, and the process is iterated across multiple rounds in HEK293T and RAW264.7 cells. High-throughput sequencing of recovered structure genomes reveals cell-type-specific enrichment patterns, enabling the identification of individual nanostructures with preferential uptake. Selected candidates were synthesized and evaluated as purified structures, confirming differential internalization by quantitative flow cytometry and microscopy. Turning DNA nanostructure discovery into a selection-based process, could enable high-throughput exploration of structural diversity and provide an alternative route to identify nanostructures with cell-specific uptake properties for biomedical applications.

bioengineering↗
bioRxiv2025

cONcat: Computational reconstruction of concatenated fragments from long Oxford Nanopore reads

Synthetic combinatorial DNA libraries are widely used to produce protein variants, optimize binders, and for high throughput studies of protein - DNA interactions. The libraries can be made by researchers or vendors and high-throughput sequencing is used for both quality control and to study the outcome of selection experiments. Oxford nanopore sequencing (ONT) is well suited to this as it allows for long read lengths and can be done rapidly with low-cost instrumentation. However, it suffers from a lower overall read accuracy and an uneven error profile. No current bioinformatics tools are well suited to the challenge of deducing the composition and order of constituent members of combinatorial libraries from ONT reads. We introduce cONcat, an algorithm to identify the makeup of concatenated DNA fragments in a set of ONT sequencing reads from a pool of known fragments. cONcat uses the edit distance-based recursive covering algorithm for finding the best possible matchings between the fragments and the reads. In our experiments on simulated and experimental data, cONcat could accurately detect the correct fragment coverings given the short fragment sizes (< 20bp) and the sequencing errors present in ONT reads. However, we find that the high error rates in the start of ONT reads make it challenging to get confident coverage there, inferring a need for experimental strategies to avoid key sequence information in the start of reads.

bioinformatics↗
bioRxiv2024

Root metaxylem area influences drought tolerance and transpiration in pearl millet in a soil texture dependent manner

O_LIPearl millet is a key cereal for food security in drylands but its yield is strongly impacted by drought. We investigated how root anatomical traits contribute to mitigating the effects of vegetative drought stress in pearl millet. C_LIO_LIWe examined associations between root anatomical traits and agronomical performance in a pearl millet diversity panel under irrigated and vegetative drought stress treatments in field trials. The impact of associated anatomical traits on transpiration was assessed using subpanels grown in different soil within a greenhouse. C_LIO_LIIn the field, total metaxylem area was positively correlated with grain weight and its maintenance under drought. In the greenhouse, genotypes with larger metaxylem area grown in sandy soil exhibited a consumerist water use strategy under irrigation, which shifted to a conservative strategy under drought. Water savings was mediated by transpiration restriction under high evaporative demand. This mechanism was dependent on soil hydraulics as it was not observed in peat soil with higher hydraulic conductivity upon soil drying. C_LIO_LIWe propose that water savings under drought, mediated by large metaxylem area and its interaction with soil hydraulics, help mitigate vegetative drought stress. Our findings highlight the role of soil hydraulic properties in shaping plant hydraulics and drought tolerance. C_LI

physiology↗
bioRxiv2023

Diet-induced changes in metabolism influence immune response and viral shedding dynamics in Jamaican fruit bats

Land-use change may drive viral spillover from bats into humans, partly through dietary shifts caused by decreased availability of native foods and increased availability of cultivated foods. We manipulated diets of Jamaican fruit bats to investigate whether diet influences shedding of a virus they naturally host. To reflect dietary changes experienced by wild bats during periods of nutritional stress, bats were fed either standard or putative suboptimal diets which were deprived of protein (suboptimal-sugar) and/or supplemented with fat (suboptimal-fat). Upon H18N11 influenza A-virus infection, bats fed the suboptimal-sugar diet shed the most viral RNA for the longest period, but bats fed the suboptimal-fat diet shed the least viral RNA for the shortest period. Unlike mice and humans, bats fed the suboptimal-fat diet displayed higher pre-infection levels of metabolic markers associated with gut health. Diet-driven heterogeneity in viral shedding may influence population-level viral dynamics in wild bats and alter risk of shedding and spillover to humans.

ecology↗
bioRxiv2020

Ultrastructural view of astrocyte-astrocyte and astrocyte-synapse contacts within the hippocampus

Astrocytes branch out and make contact at their interfaces. However, the ultrastructural interactions of astrocytes and astrocytes with their surroundings, including the spatial-location selectivity of astrocyte-synapse contacts, remain unknown. Here, the branching architecture of three neighboring astrocytes, their contact interfaces, and their surrounding neurites and synapses have been traced and 3D reconstructed using serial block-face scanning electron microscopy (SBF-SEM). Our reconstructions reveal extensive reflexive, loop-like processes that serve as scaffolds to neurites and give rise to spongiform astrocytic morphology. At the astrocyte-astrocyte interface, a cluster of process-process contacts were identified, which biophysically explains the existence of low inter-astrocytic electrical resistance. Additionally, we found that synapses uniformly made contact with the entire astrocyte, from soma to terminal processes, and can be ensheathed by two neighboring astrocytes. Lastly, in contrast to densely packed vesicles at the synaptic boutons, vesicle-like structures were scant within astrocytes. Together, these ultrastructural details should expand our understanding of functional astrocyte-astrocyte and astrocyte-neuron interactions.

neuroscience↗