Biology subjects

Bryan, J.

Publications and source records attributed to Bryan, J..

8 recordsLinked to original sources

bioRxiv2026

Air-driven aldehyde synthesis in engineered bacteria via gene deletion and aryl-alcohol oxidase profiling

Engineered bacterial routes for oxidation of non-native alcohols face three challenges: Nicotinamide-dependent enzymes are coupled to cellular redox metabolism, nicotinamide-independent aryl-alcohol oxidases (AAOs) usually express poorly in bacteria, and aldehyde products are rapidly modified by host enzymes. Here, we address these limitations by engineering aldehyde-retaining Escherichia coli for discovery and application of soluble bacterial AAOs. Screening 51 candidates revealed a high-expression sequence cluster containing enzymes that are active on diverse aromatic and furan-based alcohols. Pairing the top-performing AAO with designer pathways in aldehyde-retaining cells enabled modular C-N and C-C bond forming cascades starting from supplied alcohols. By making both the oxidase and its product compatible with the host, this work advances air-driven oxidation of diverse alcohols as a programmable entry point to aldehyde-derived chemistry in engineered bacteria.

synthetic biology↗

bioRxiv2024

Characterization of A Bronchoscopically Induced Transgenic Lung Cancer Pig Model for Human Translatability

BackgroundThere remains a need for animal models with human translatability in lung cancer (LC) research. Findings in pigs have high impact on humans due to similar anatomy and physiology. We present the characterization of a bronchoscopically-induced LC model in Oncopigs carrying inducible KRASG12D and TP53R167H mutations. MethodsTwelve Oncopigs underwent 29 injections via flexible bronchoscopy. Eighteen Adenovirus-Cre recombinase gene (AdCre) inductions were performed endobronchially (n=6) and transbronchially with a needle (n=12). Eleven control injections were performed without AdCre. Oncopigs underwent serial contrast-enhanced chest CT with clinical follow-up for 29 weeks. Following autopsy, lung and organ tissues underwent histopathology, immunohistochemistry, and RNA-sequencing with comparative analysis with The Cancer Genome Atlas (TCGA) human LC data. ResultsAll 18 sites of AdCre injections had lung consolidations on CT imaging. Transbronchial injections led to histopathologic invasive cancer and/or carcinoma in situ (CIS) in 11/12 (91.7%), and invasive cancer (excluding CIS) in 8/12 (66.6%). Endobronchial inductions led to invasive cancer in 3/6 (50%). A soft tissue metastasis was observed in one Oncopig. Immunohistochemistry confirmed expression of Pan-CK+/epithelial cancer cells, with macrophages and T cells infiltration in the tumor microenvironment. Transcriptome comparison showed 54.3% overlap with human LC (TCGA), in contrast to 29.88% overlap of KRAS-mutant mouse LC with human LC. ConclusionsThe transgenic and immunocompetent Oncopig model has a high rate of LC following bronchoscopic transbronchial induction. Overlap of the Oncopig LC transcriptome with human LC transcriptome was noted. This pig model is expected to have high clinical translatability to the human LC patient.

cancer biology↗

bioRxiv2024

One Health in practice: Multi-season survey of ixodid tick species collected from domestic dogs in Chad

Ticks are medically important vectors of pathogens, many of which are zoonotic or impact domestic animal and/or wildlife health. Climate change, landscape use, and increasing interactions between domestic animals, wildlife, and humans have resulted in changes in tick-host dynamics and the emergence of novel pathogens worldwide. Therefore, it is crucial to describe the host and geographic ranges of vector species to assess disease risk, particularly in areas where research is lacking. This task necessitates adopting a One Health approach. In sub-Saharan Africa, previous work on ticks has focused primarily on those species most relevant to domestic livestock or humans, highlighting a significant knowledge gap concerning species of ticks that infest peri-domestic animals in rural areas. The objective of this study was to investigate the species diversity of ticks on peri-domestic dogs in rural areas of Chad, Africa. From 2019-2022, we collected 3,412 ixodid ticks from 435 peri-domestic dogs from 23 villages in Chad, Africa during both dry and wet seasons. Ticks were identified to species using morphological techniques and/or molecular analyses of the 16S rRNA, 12S rRNA, and cytochrome oxidase I gene regions. We identified 11 species of ticks from dogs including Amblyomma variegatum, Amblyomma marmoreum, Haemaphysalis leachi, a Haemaphysalis sp., Hyalomma impressum, Hyalomma truncatum, Rhipicephalus decoloratus, Rhipicephalus guilhoni, Rhipicephalus muhsamae, Rhipicephalus linnaei (=R. sanguineus tropical lineage), and a Rhipicephalus sp. Several of these tick species are known vectors for important canine and zoonotic pathogens and some are more commonly associated with cattle hosts. Our results show that sampling ticks from peri-domestic dogs provides an opportunity to examine vectors that may infest domestic animals, agricultural animals, wildlife, and humans as hosts in an understudied area. HighlightsO_LITick-borne diseases are significant concern across sub-Saharan Africa C_LIO_LILimited data on ticks of animals and people in Chad, Africa C_LIO_LIA high diversity of tick species infested domestic dogs in Chad C_LIO_LIMany detected tick species associated with important pathogens C_LI

zoology↗

bioRxiv2023

Red cabbage juice-mediated gut microbiota modulation improves intestinal epithelial homeostasis and ameliorates colitis

Gut microbiota plays a crucial role in inflammatory bowel disease (IBD) and has therapeutic benefits. Thus, targeting the gut microbiota is a promising therapeutic approach for IBD treatment. We recently found that red cabbage juice (RCJ) ameliorates dextran sulfate sodium (DSS)-induced colitis in mice. However, the underlying mechanisms remain unknown. The current study investigated the modulation of gut microbiota in response to treatment with RCJ to ameliorate the DSS colitis. The initial results demonstrated that mice treated with DSS + RCJ showed increased body weight and decreased diarrhea and blood in feces compared to the DSS alone group. RCJ ameliorated colitis by regulating the intestinal barrier function by reducing the number of apoptotic cells, improving colonic protective mucin, and increasing tight junction protein in RCJ + DSS groups compared to the DSS group. Short-gun metagenomic analysis revealed significant enrichment of short-chain fatty acid (SCFAs)-producing bacteria (Butyrivibrio, Ruminococcaceae, Acetatifactor muris, Rosburia Sp. CAG:303, Dorea Sp. 5-2) increased PPAR-(C) activation, leading to repression of the nuclear factor {kappa}B (NF{kappa}B) signaling pathway, thus decreasing the production of crucial inflammatory cytokines and chemokines in the RCJ + DSS groups compared to the DSS group. Pathway abundance analysis showed an increased abundance of the SCFA pathway, reduced histidine degradation (Bacteroides sartorii, and Bacteroides caecimuris), and LCFA production in the RCJ+DSS treated group, suggesting the promotion of good colonic health. Furthermore, increased T-reg (FOXP3+) cells in the colon were due to SCFAs produced by the gut microbiota, which was corroborated by an increase in IL-10, a vital anti-inflammatory cytokine. Thus, our study provides the first evidence that RCJ ameliorates colonic inflammation by modulating the gut microbiota.

pathology↗

bioRxiv2022

Opioid receptor architecture for the modulation of brainstem functions

Opioids produce profound and diverse effects on a range of behaviors, many driven by brainstem activity; however, the presence of opioid and opioid-like receptors at this level has been poorly studied outside of nociceptive structures and components of respiratory circuitry. While previous studies identified expression of {micro}, {delta}, {kappa}, and nociceptin opioid and opioid-like receptors in the brainstem, patterns have not been fully delineated, and neither has receptor coexpression nor the behavioral implications of their expression in most structures. We aimed to elucidate expression patterns for all four receptors across somatosensory-motor, auditory, and respiratory brainstem circuits; identify recurring themes to provide insight into the mechanisms by which exogenous opioids affect broader brainstem circuits; and characterize the function of endogenous opioids in subcortical processing and behavior modulation. Using a fluorescent reporter mouse line for each receptor, we created a comprehensive atlas of brainstem receptor distribution and identified novel expression patterns in modality-specific circuits. Each receptor showed unique expression patterns across the brainstem with minimal correlation between receptors. Orofacial somatosensory-motor circuits expressed all four receptors, though generally in distinct regions, suggesting differential opiate modulation of afferent and efferent trigeminal signaling. Within the auditory circuits, receptors segregated along the vertical and horizontal processing pathways with minimal colocalization. Finally, the respiratory circuit strongly expressed the {micro} opioid receptor in multiple crucial structures with minimal presence of the other three receptors. We further assessed the functional significance of these expression patterns, using the respiratory circuitry as an example, by characterizing respiratory responses to selective opioid agonists, finding that each agonist caused unique alterations in breathing pattern and/or breath shape. Together, these results establish a comprehensive atlas of opioid and opioid-like receptor expression throughout the brainstem, laying the essential groundwork for further evaluation of opioid neuromodulation across the broad spectrum of behaviors.

neuroscience↗

bioRxiv2022

Evidence that SPIO Chain Formation is Essential for High-Resolution MPI

Magnetic Particle Imaging (MPI) is a noninvasive imaging modality that exploits the saturation properties of superparamagnetic iron oxide particles (SPIOs). A major thrust of MPI research aims to sharpen the magnetic resolution of biocompatible SPIOs, which will be crucial for affordable and safe clinical translation. We recently reported on a new class of MPI tracers --called superferromagnetic iron oxide nanoparticles (SFMIOs) -- which offer much sharper magnetic saturation curves. SFMIOs experimentally demonstrate 10-fold improvement in both resolution and sensitivity. However, superferromagnetism is a relatively unexplored branch of physics and the nanoscale physics and dynamics of SFMIOs remain a mystery. Here we show experimentally that chaining of SPIOs can explain SFMIOs boost in SNR and resolution. We show how concentration, viscosity, transmit amplitude, and pre-polarization time can all affect SPIO chain formation and SFMIO behavior. These experiments will inform strategies on SFMIO chemical synthesis as well as SFMIO data acquisition pulse sequences.

bioengineering↗

bioRxiv2022

First superferromagnetic remanence characterization and scan optimization for super-resolution Magnetic Particle Imaging

Magnetic particle imaging (MPI) is a sensitive, high contrast tracer modality that images superparamagnetic iron oxide nanoparticles (SPIOs), enabling radiation-free theranostic imaging. MPI resolution is currently limited by scanner and particle constraints. Recent tracers have experimentally shown 10x resolution and signal improvements, with dramatically sharper M-H curves. Experiments suggest that this results from interparticle interactions, conforming to literature definitions of superferromagnetism. We thus call our tracers superferromagnetic iron oxide nanoparticles (SFMIOs). While SFMIOs provide excellent signal and resolution, they exhibit hysteresis, with non-negligible remanence and coercivity. We provide the first report on MPI scanning with remanence and coercivity, including the first quantitative measurements of SFMIO remanence decay and reformation using a novel multi-echo pulse sequence. We also describe an SNR-optimized pulse sequence for SFMIOs under human electromagnetic safety limitations. The resolution from SFMIOs could enable clinical MPI with 10x reduced scanner selection fields, reducing hardware costs by up to 100x.

bioengineering↗

bioRxiv2021

Reconstruction of metagenome-assembled genomes from aquaria

We report 11 metagenome-assembled genomes (MAGs) reconstructed from freshwater and saltwater aquaria including representatives of Polynucleobacter, Anaerolinae, Roseobacter, Flavobacteriia, Octadecabacter, Mycobacterium and Candidate Phyla Radiation (CPR) members. These MAGs can serve as a resource for aquatic research and elucidating the role of CPR taxa in the built environment.

microbiology↗