Biology subjects

Dennis, A. M.

Publications and source records attributed to Dennis, A. M..

5 recordsLinked to original sources

bioRxiv2025

Elemental Composition and Degradation Rate Impact the Biocompatibility of Copper Chalcogenide Nanocrystals

Copper chalcogenide nanocrystals (NCs) are promising candidates for biophotonic applications due to their tunable optical properties. Concrete methods to examine the relationship between their degradation and toxicity are necessary to enable development of nanoconstructs with reduced toxicity. This study compares the degradation and acute cytotoxicity of three compositions of micelle-coated copper chalcogenide NCs: the fluorescent semiconductor copper indium sulfide (CuInS2), and the plasmonic semiconductors copper sulfide (Cu2-xS) and chalcopyrite copper iron sulfide (CuFeS2). We developed a quantitative degradation assay to assess ion release from these ultra-small nanocrystals, revealing that while all three particles biodegrade, CuInS2 and CuFeS2 undergo rapid degradation in artificial lysosomal fluid, leading to a burst release of indium and iron ions. In cellular toxicity assays, CuInS2 exhibited significantly higher acute cytotoxicity than Cu2-xS and CuFeS2, primarily due to indium-induced necrosis. To mitigate this toxicity, an alternative surface-binding polymer coating was introduced, effectively reducing both the degradation rate and cytotoxicity of CuInS2. These findings highlight the influence of both nanocrystal composition and coating chemistry in moderating the acute cytotoxity of degradable nanocrystals, demonstrating that tuning of composition and degradation rate can be used to moderate nanoparticle toxicity.

pharmacology and toxicology↗

bioRxiv2025

High dynamic range shortwave infrared (SWIR) imaging of mice with an InGaAs camera

SignificanceWhile shortwave infrared (SWIR) imaging provides superior tissue penetration and reduced autofluorescence for preclinical applications, quantitative fluorescence analysis is hindered by the limited dynamic range of InGaAs cameras, forcing a focus on either bright or dim anatomical features. AimWe develop a high dynamic range (HDR) imaging method specifically adapted for the high-noise characteristics of InGaAs detectors to enable quantitative fluorescence imaging across wide intensity ranges. We demonstrate that one-time camera calibration based on a series of images encompassing the range of radiance intensities enables all subsequent image processing. ApproachWe modified classical HDR algorithms with exposure-time-dependent dark current subtraction, preprocessing to exclude saturated and noisy pixels before camera response function recovery, and dynamic weighting range adjustment to account for shrinking intensity ranges at longer exposures. HDR image processing effects on preclinical imaging outcomes were analyzed using indocyanine green and SWIR-emitting PbS/CdS quantum dots in mouse models. ResultsHDR imaging achieved a 22 dB improvement in dynamic range over single exposures, enabling simultaneous quantification across more than three orders of magnitude of fluorophore concentration. In vivo studies showed improvements in contrast-to-noise ratios across all anatomical features, with improvements in vascular contrast while maintaining quantitative accuracy. After one-time camera calibrations, this approach enables rapid processing of subsequent datasets. ConclusionsThis software-based HDR SWIR imaging approach eliminates exposure parameter optimization and enables comprehensive biodistribution analysis across all anatomical structures from a single acquisition sequence, significantly streamlining preclinical imaging workflows while preserving quantitative accuracy.

bioengineering↗

bioRxiv2025

A New Type of Nonsuppressible Viremia Produced by HIV-Infected Macrophage

BackgroundHIV-1 RNA typically declines rapidly after initiation of antiretroviral therapy (ART); often reaching undetectable levels within a few weeks and remaining undetectable by standard assays. However, some patients on ART have persistent nonsuppressible viremia (NSV) that does not respond to treatment optimization or intensification. NSV can emerge at the time of ART initiation (primary NSV) or after being ART-suppressed (secondary NSV). Here, we examine mechanisms producing primary NSV in four people on ART. MethodsBlood samples were collected from four participants who, despite being adherent to ART, required approximately a year or more to become virologically suppressed. Viral RNA and proviral DNA genomes were sequenced to examine HIV-1 drug resistance, genome intactness and genetic diversity. The ability of HIV-1 Envs to facilitate efficient entry into cells expressing low levels of CD4 (a proxy for macrophage tropism) was assessed. ResultsBefore ART, the blood contained HIV-1 RNA genomes that were adapted to replication in CD4+ T cells and rapidly decayed after ART initiation. During ART, the blood contained HIV-1 genomes that were drug sensitive, genetically diverse, macrophage-tropic, not evolving and often had defects in vpr. ConclusionsOur results suggest that in individuals with primary NSV, ART stopped virus replication, but large pools of long-lived, HIV-infected macrophage continued to produce virus. This is mechanistically distinct from secondary NSV produced by CD4+ T cell clones. In addition, defects in vpr independently accumulation in macrophage-tropic lineages found in three participants, suggesting that vpr may impact survival of, or virus production from, HIV-infected macrophage. SUMMARYPeople with HIV-1 on ART can experience persistent, nonsuppressible viremia (NSV). We identified four people with a previously uncharacterized form of NSV that emerged at the time of ART initiation (primary NSV) and is notable for its genetic diversity, drug sensitivity, and macrophage tropism. This is mechanistically distinct from previously described cases of NSV produced by CD4+ T cells in people who were previously ART-suppressed (secondary NSV).

microbiology↗

bioRxiv2024

Multiplexed Short-wave Infrared Imaging Highlights Anatomical Structures in Mice

While multiplexed fluorescence imaging is frequently used for in vitro microscopy, extending the technique to whole animal imaging in vivo has remained challenging due to the attenuation and scattering of visible and traditional near infrared (NIR-I) wavelengths. Fluorescence imaging using short-wave infrared (SWIR, 1000 - 1700 nm, a.k.a. NIR-II) light enables deeper tissue penetration for preclinical imaging compared to previous methods due to reduced tissue scattering and minimal background autofluorescence in this optical window. Combining NIR-I excitation wavelengths with multiple distinct SWIR emission peaks presents a tremendous opportunity to distinguish multiple fluorophores with high precision for non-invasive, multiplexed anatomical imaging in small animal models. SWIR-emitting semiconductor quantum dots (QDs) with tunable emission peaks and optical stability have emerged as powerful contrast agents, but SWIR imaging demonstrations have yet to move beyond two-color imaging schemes. In this study, we engineered a set of three high quantum yield lead sulfide/cadmium sulfide (PbS/CdS) core/shell QDs with distinct SWIR emissions ranging from 1100 - 1550 nm and utilize these for simultaneous three-color imaging in mice. We first use QDs to non-invasively track lymphatic drainage, highlighting the detailed network of lymphatic vessels with high-resolution with a widefield imaging over a 2 hr period. We then perform multiplexed imaging with all three QDs to distinctly visualize the lymphatic system and spatially overlapping vasculature network. This work establishes optimized SWIR QDs for next-generation multiplexed preclinical imaging, moving beyond the capability of previous dual-labeling techniques. The capacity to discriminate several fluorescent labels through non-invasive NIR-I excitation and SWIR detection unlocks numerous opportunities for studies of disease progression, drug biodistribution, and cell trafficking dynamics in living organisms.

bioengineering↗

bioRxiv2021

Extending the Near Infrared Emission Range of Indium Phosphide Quantum Dots for Multiplexed In Vivo Imaging

This report of the reddest emitting indium phosphide quantum dots (InP QDs) to date demonstrates tunable, near infrared (NIR) photoluminescence and fluorescence multiplexing in the first optical tissue window with a material that avoids toxic constituents. This synthesis overcomes the InP synthesis "growth bottleneck" and extends the emission peak of InP QDs deeper into the first optical tissue window using an inverted QD heterostructure. The ZnSe/InP/ZnS core/shell/shell structure is designed to produce emission from excitons with heavy holes confined in InP shells wrapped around larger-bandgap ZnSe cores and protected by a second shell of ZnS. The InP QDs exhibit InP shell thickness-dependent tunable emission with peaks ranging from 515 - 845 nm. The high absorptivity of InP leads to effective absorbance and photoexcitation of the QDs with UV, visible, and NIR wavelengths in particles with diameters of eight nanometers or less. These nanoparticles extend the range of tunable direct-bandgap emission from InP-based nanostructures, effectively overcoming a synthetic barrier that has prevented InP-based QDs from reaching their full potential as NIR imaging agents. Multiplexed lymph node imaging in a mouse model shows the potential of the NIR-emitting InP particles for in vivo imaging.

bioengineering↗