Biology subjects

Shapiro, E.

Publications and source records attributed to Shapiro, E..

11 recordsLinked to original sources

bioRxiv2026

Longitudinal diffusion tensor imaging identifies coordinated white matter remodeling during cocaine self-administration in mice

White matter microstructural alterations are increasingly recognized as a feature of cocaine use disorder (CUD), yet the longitudinal progression and biological underpinnings of these changes remain poorly understood. Although rodent intravenous self-administration (IVSA) provides a translational model of voluntary cocaine use, longitudinal diffusion tensor imaging (DTI) has not previously been combined with cocaine IVSA in mice. Here, we established a longitudinal IVSA-DTI framework to characterize white matter microstructural remodeling during cocaine self-administration and early withdrawal. Male C57BL/6 mice underwent DTI at baseline, following 11 consecutive days of cocaine (0.5 mg/kg/infusion) or saline IVSA, and after a 7-day withdrawal period immediately following a cocaine-seeking test (n = 4/group). Fractional anisotropy (FA) was evaluated longitudinally using atlas-based region-of-interest analyses and whole-brain diffusion maps. Cocaine-treated mice acquired robust operant responding and exhibited coordinated longitudinal FA alterations across interconnected hippocampal-associated white matter pathways. The most consistent changes occurred within the bilateral dorsal hippocampal commissure, fornix, and fimbria, with cocaine-treated mice demonstrating increased FA during self-administration relative to baseline while saline controls exhibited smaller or opposing longitudinal changes. Difference-in-differences maps further demonstrated cocaine-associated FA alterations within hippocampal pathways and localized regions of the corpus callosum after accounting for longitudinal changes in saline controls. These findings establish the feasibility of combining longitudinal DTI with cocaine IVSA in mice and demonstrate coordinated white matter microstructural remodeling during voluntary cocaine exposure. This framework provides a translational platform for future studies integrating longitudinal neuroimaging with genetically modified mouse models, tractography, and histological validation to investigate the mechanisms underlying cocaine-associated white matter plasticity.

neuroscience↗

bioRxiv2025

Distinct Roles of Surface Nanostructure and Polymer Degradation in Fibroblast Response to Device Design

Fibrotic encapsulation of implanted biomedical devices represents the highest cause of device failure across numerous fields, including orthopedics, breast implants and neural electrodes. While most research has focused on the immune system for driving the foreign body response to devices, fibroblasts are emerging as another key regulator of tissue response. In the present study, we evaluated the effects of porous device design on the activation of primary human dermal fibroblasts into myofibroblasts, a contractile cell that is a hallmark of fibrosis, over four weeks in culture. In particular two factors were studied 1) the introduction of nanoparticles, as they are increasingly being used for device functionalization, and 2) the polymer matrix, which dictates chemistry, mechanics and degradation. The addition of tantalum oxide (TaOx) nanoparticles (0-20wt%) had a minimal effect on fibroblasts, significantly down-regulating expression of alpha smooth muscle actin (SMA) (0.31 {+/-} 0.1), likely driven by the increase in nanoscale surface roughness. The polymer matrix of the device caused significant changes to myofibroblast activation, with the fast degrading polymer, poly(lactide co-glycolide) (PLGA) 50:50, significantly up-regulating multiple myofibroblast markers, including SMA (5.16 {+/-} 2.5), vinculin, integrin {beta}1, and integrin {beta}5, compared to non-degrading polycaprolactone (PCL). The effect was due to the release of degradation products, namely lactic acid, which affects cellular metabolism. Together this highlights that device design affects biological response immediately post-implantation in ways that impact the ultimate success or failure of biomedical devices.

bioengineering↗

bioRxiv2024

Material Composition and Implantation Site Affect in vivo Device Degradation Rate

Successful tissue engineering requires biomedical devices that initially stabilize wounds, then degrade as tissue is regenerated. However, the material degradation rates reported in literature are often conflicting. Incorporation of in situ monitoring functionality into implanted devices would allow real time assessment of degradation and potential failure. This necessitates introduction of contrast agent as most biomedical devices are composed of polymeric materials with no inherent contrast in medical imaging modalities. In the present study, computed tomography (CT)-visible radiopaque composites were created by adding 5-20wt% tantalum oxide (TaOx) nanoparticles into polymers with distinct degradation profiles: polycaprolactone (PCL), poly(lactide-co-glycolide) (PLGA) 85:15 and PLGA 50:50, representing slow, medium and fast degrading materials respectively. Radiopaque phantoms, mimicking porous tissue engineering devices, were implanted into mice intramuscularly or intraperitoneally, and monitored via CT over 20 weeks. Changes in phantom volume, including collapse and swelling, were visualized over time. Phantom degradation profile was determined by polymer matrix, regardless of nanoparticle addition and foreign body response was dictated by the implant site. In addition, degradation kinetics were significantly affected in mid-degrading materials, transitioning from linear degradation intramuscularly to exponential degradation intraperitoneally, due to differences in inflammatory responses and fluid flow. Nanoparticle excretion from degraded phantoms lagged behind polymer, and future studies will modulate nanoparticle clearance. Utilizing in situ monitoring, this study seeks to unify literature and facilitate better tissue engineering devices, by highlighting the relative effect of composition and implant site on important materials properties.

bioengineering↗

bioRxiv2024

Device Design and Diagnostic Imaging of Radiopaque 3D Printed Tissue Engineering Scaffolds

3D printed biomaterial implants are revolutionizing personalized medicine for tissue repair, especially in orthopedics. In this study, a radiopaque Bi2O3 doped polycaprolactone (PCL) composite is developed and implemented to enable the use of diagnostic X-ray technologies, especially photon counting X-ray computed tomography (PCCT), for comprehensive in vivo device monitoring. PCL filament with homogeneous Bi2O3 nanoparticle (NP) dispersion (0.8 to 11.7 wt%) are first fabricated. Tissue engineered scaffolds (TES) are then 3D printed with the composite filament, optimizing printing parameters for small feature size and severely overhung geometries. These composite TES are characterized via micro-computed tomography ({micro}CT), tensile testing, and a cytocompatibility study, with Bi2O3 mass fractions as low as 2 wt% providing excellent radiographic distinguishability, improved tensile properties, and equivalent cytocompatibility of neat PCL. The excellent radiographic distinguishability is validated in situ by imaging 4 and 7 wt% TES in a mouse model with {micro}CT, showing excellent agreement with in vitro measurements. Subsequently, CT image-derived swine menisci are 3D printed with composite filament and re-implanted in their corresponding swine legs ex vivo. Re-imaging the swine legs via clinical CT allows facile identification of device location and alignment. Finally, the emergent technology of PCCT unambiguously distinguishes implanted menisci in situ.

bioengineering↗

bioRxiv2024

Biomaterial Degradation Products affect Regenerating Glia Independently of Surface Properties

Devices to treat peripheral nerve injury (PNI) must balance many considerations to effectively guide regenerating nerves across a gap and achieve functional recovery. To enhance efficacy, design features like luminal fillers have been explored extensively. Material choice for PNI devices is also critical, as the determining factor of device mechanics, and degradation rate and has increasingly been found to directly impact biological response. This study investigated the ways in which synthetic polymer materials impact the differentiation state and myelination potential of Schwann cells, peripheral nerve glia. Microporous substrates of polycaprolactone (PCL), poly(lactide-co-glycolide) (PLGA) 85:15, or PLGA 50:50 were chosen, as materials already used in nerve repair devices, representing a wide range of mechanics and degradation profiles. Schwann cells co-cultured with dorsal root ganglion (DRG) neurons on the substrates expressed more mature myelination proteins (MPZ) on PLGA substrates compared to PCL. Changes to myelination and differentiation state of glia were reflected in adhesion proteins expressed by glia, including {beta}-dystroglycan and integrin 6, both laminin binding proteins. Importantly, degradation products of the polymers affected glial expression independently of direct attachment. Fast degrading PLGA 50:50 substrates released measurable amounts of degradation products (lactic acid) within the culture period, which may push Schwann cells towards glycolytic metabolism, decreasing expression of early transcription factors like sox10. This study shows the importance of understanding not only material effects on attachment, but also on cellular metabolism which drives myelination responses.

bioengineering↗

bioRxiv2024

Computed Tomography of Polymeric Biomedical Implants from Bench to Bedside

Implanted biomedical devices require porosity to encourage tissue regeneration. However, characterizing porosity, which affects many functional device properties, is non-trivial. Computed tomography (CT) is a quick, versatile, and non-destructive way to gain 3D structural information. While optimization of CT for polymeric devices has been investigated at the bench on high-resolution micro-CT (CT) scanners, pre-clinical and clinical systems cannot be tuned the same way, given an overriding objective to minimize ionizing radiation exposure to living tissues. Therefore, in this study we tested feasibility of obtaining structural information in pre-clinical systems and CT under physiological conditions. The size of resolved features in porous structures is highly dependent on the resolution (voxel size) of the scan. Lower resolution underestimated porosity and overestimated pore size. With the homogeneous introduction of radiopaque nanoparticle contrast agent into both biopolymers and synthetic polymers, devices could be imaged in the hydrated state, even at high-resolution. Biopolymers had significant structural changes at the micro-scale post-hydration, including a mean increase of 130% in pore wall thickness that could potentially impact biological response. Through optimizing devices for medical imaging, CT has the potential to be a facile way to monitor devices from initial design stages through to clinical translation.

bioengineering↗

bioRxiv2023

In vivo Biomedical Imaging of Immune Tolerant, Radiopaque Nanoparticle-Embedded Polymeric Device Degradation

Biomedical implants remain an important clinical tool for restoring patient mobility and quality of life after trauma. While polymers are often used for devices, their degradation profile remains difficult to determine post-implantation. CT monitoring could be a powerful tool for in situ monitoring of devices, but polymers require the introduction of radiopaque contrast agents, like nanoparticles, to be distinguishable from native tissue. As device function is mediated by the immune system, use of radiopaque nanoparticles for serial monitoring therefore requires a minimal impact on inflammatory response. Radiopaque polymer composites were produced by incorporating 0-20wt% TaOx nanoparticles into synthetic polymers: polycaprolactone (PCL) and poly(lactide-co-glycolide) (PLGA). In vitro inflammatory response to TaOx was determined by monitoring mouse bone marrow derived macrophages on composite films. Nanoparticle addition stimulated only a slight inflammatory reaction, namely increased TNF secretion, mediated by changes to the polymer matrix properties. When devices (PLGA 50:50 + 20wt% TaOx) were implanted subcutaneously in a mouse model of chronic inflammation, no changes to device degradation were noted although macrophage number was increased over 12 weeks. Serial CT monitoring of devices post-implantation provided a detailed timeline of device structural collapse, with no burst release of the nanoparticles from the implant. Changes to the device were not significantly altered with monitoring, nor was the immune system ablated when checked via blood cell count and histology. Thus, polymer devices incorporating radiopaque TaOx NPs can be used for in situ CT monitoring, and can be readily combined with multiple medical imaging techniques, for a truly dynamic view biomaterials interaction with tissues throughout regeneration, paving the way for a more structured approach to biomedical device design.

bioengineering↗

bioRxiv2023

Incorporating Radiopacity into Implantable Polymeric Biomedical Devices for Clinical Radiological Monitoring

Longitudinal radiological monitoring of biomedical devices is increasingly important, driven by risk of device failure following implantation. Polymeric devices are poorly visualized with clinical imaging, hampering efforts to use diagnostic imaging to predict failure and enable intervention. Introducing nanoparticle contrast agents into polymers is a potential method for creating radiopaque materials that can be monitored via computed tomography. However, properties of composites may be altered with nanoparticle addition, jeopardizing device functionality. This, we investigated material and biomechanical response of model nanoparticle-doped biomedical devices (phantoms), created from 0-40wt% TaOx nanoparticles in polycaprolactone, poly(lactide-co-glycolide) 85:15 and 50:50, representing non-, slow and fast degrading systems, respectively. Phantoms degraded over 20 weeks in vitro, in simulated physiological environments: healthy tissue (pH 7.4), inflammation (pH 6.5), and lysosomal conditions (pH 5.5), while radiopacity, structural stability, mechanical strength and mass loss were monitored. The polymer matrix determined overall degradation kinetics, which increased with lower pH and higher TaOx content. Importantly, all radiopaque phantoms could be monitored for a full 20-weeks. Phantoms implanted in vivo and serially imaged, demonstrated similar results. An optimal range of 5-20wt% TaOx nanoparticles balanced radiopacity requirements with implant properties, facilitating next-generation biomedical devices.

bioengineering↗

bioRxiv2021

Intergenerational Stress Transmission is Associated with Brain Metabotranscriptome Remodeling andMitochondrial Dysfunction

Intergenerational stress increases lifetime susceptibility to depression and other psychiatric disorders. Whether intergenerational stress transmission is a consequence of in utero neurodevelopmental disruptions vs early-life mother-infant interaction is largely unknown. Here, we demonstrated that exposure to traumatic stress in mice during pregnancy, through predator scent exposure, induces in the offspring social deficits and depressive-like behavior. We found, through cross-fostering experiments, that raising of normal pups by traumatized mothers produced a similar behavioral phenotype to that induced in pups raised by their biological traumatized mothers. Good caregiving (by non-traumatized mothers), however, did not completely protect against the prenatal trauma-induced behavioral deficits. These findings support a two-hit stress mechanism of both in utero and early-life parenting (poor caregiving by the traumatized mothers) environments. Associated with the behavioral deficits, we found profound changes in brain metabolomics and transcriptomic (metabotranscriptome). Striking increases in the mitochondrial hypoxia marker and epigenetic modifier 2-hydroxyglutaric acid, in the brains of neonatal and adult pups whose mothers were exposed to stress during pregnancy, indicated mitochondrial metabolism dysfunctions and epigenetic mechanisms. Bioinformatic analyses revealed mechanisms involving stress- and hypoxia-response metabolic pathways in the brains of the neonatal mice, which appear to lead to long-lasting alterations in mitochondrial-energy metabolism, and epigenetic processes pertaining to DNA and chromatin modifications. Most strikingly, we demonstrated that an early pharmacological intervention that can correct mitochondria metabolism - lipid metabolism and epigenetic modifications with acetyl-L-carnitine (ALCAR) supplementation - produces long-lasting protection against the behavioral deficits associated with intergenerational transmission of traumatic stress. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/438868v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1fb2500org.highwire.dtl.DTLVardef@13a5c6forg.highwire.dtl.DTLVardef@8aa512org.highwire.dtl.DTLVardef@5b6906_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2017

A duplex MIPs-based biological-computational cell lineage discovery platform

Cell lineage analysis aims to uncover the developmental history of an organism back to its cell of origin1. Recently, novel in vivo methods and technologies utilizing genome editing enabled important insights into the cell lineages of animals2-8. In contrast, human cell lineage remains restricted to retrospective approaches, which still lack in resolution and cost-efficient solutions. Here we demonstrate a scalable platform for human cell lineage tracing based on Short Tandem Repeats (STRs) targeted by duplex Molecular Inversion Probes (MIPs). With this platform we accurately reproduced a known lineage of DU145 cell lines cells9 and reconstructed lineages of healthy and metastatic single cells from a melanoma patient. The reconstructed trees matched the anatomical and SNV references while adding further refinements. Our platform allowed to faithfully recapitulate lineages of developmental tissue formation in cells from healthy donors. In summary, our lineage discovery platform can profile informative STR somatic mutations efficiently and we provide a solid, high-resolution lineage reconstruction even in challenging low-mutation-rate healthy single cells.

systems biology↗

bioRxiv2017

Comparison of seven single cell Whole Genome Amplification commercial kits using targeted sequencing

Advances in biochemical technologies have led to a boost in the field of single cell genomics. Observation of the genome at a single cell resolution is currently achieved by pre-amplification using whole genome amplification (WGA) techniques that differ by their biochemical aspects and as a result by biased amplification of the original molecule. Several comparisons between commercially available single cell dedicated WGA kits (scWGA) were performed, however, these comparisons are costly, were only performed on selected scWGA kit and more notably, are limited by the number of analyzed cells, making them limited for reproducibility analysis. We benchmarked an economical assay to compare all commercially available scWGA kits that is based on targeted sequencing of thousands of genomic regions, including highly mutable genomic regions (microsatellites), from a large cohort of human single cells (125 cells in total). Using this approach, we could analyze the genome coverage, the reproducibility of genome coverage and the error rate of each kit. Our experimental design provides an affordable and reliable comparative assay that simulates a real single cell experiment. Results demonstrate the needfor a dedicated kit selection depending on the desired single cell assay.

genomics↗