Biology subjects

MacRenaris, K. W.

Publications and source records attributed to MacRenaris, K. W..

4 recordsLinked to original sources

bioRxiv2026

Blank Spectrum Correction as a Robust Solution to Artifacts in Quantitative X-ray Fluorescence Mapping

X-ray fluorescence microscopy (XFM) continues to develop as a powerful quantitative technique for high resolution, label-free, elemental mapping of biological, environmental, and material samples. Methods for rigorously fitting spectra, increasing throughput, accounting for background signals, and deconvoluting overlapping emission lines continue to evolve. We show here that quantitative fits of XFM data obtained after removing a baseline, calculated by connecting peak edges, can be unexpectedly dependent upon acquisition dwell-time and spectral aggregation leading to differences in apparent elemental content. Using mouse preimplantation embryos and ovarian follicles as model samples, we demonstrate how these variables influence quantitative comparisons between samples. We find that subtracting an empirically measured blank spectrum instead of a baseline provides quantitative XFM elemental mapping results that are independent of dwell time and spectral aggregation dependencies.

biophysics↗

bioRxiv2025

An All-In-One Software Solution for Automated Processing of LA-ICP-TOF-MS datasets

LA-ICP-TOF-MS provides rapid, high resolution elemental analysis of biological and non-biological samples. However, accurate real-time data analysis frequently requires the user to account for several instrumental and experimental variables that can change during data acquisition. AutoSpect is a novel software tool designed to automate the processing and fitting of LA-ICP-TOF-MS data, addressing key challenges such as time-dependent spectral drift, instrument sensitivity drift calibration inaccuracies, and peak deconvolution, enabling researchers to rapidly and accurately process complex datasets. The tool is optimized to be robustly applicable across scientific fields (e.g., geochemistry, biology, and materials science), providing a streamlined solution for end users seeking to maximize the potential of LA-ICP-TOF-MS for high-resolution elemental mapping and isotopic analysis. Significance to JAASAnalysis of fast transient signals using laser ablation inductively coupled plasma time-of-flight mass spectrometry (LA-ICP-TOF-MS) has become mainstream for elemental mapping. Advancements in LA-ICP-TOF-MS technology continue to accelerate the collective understanding of the role inorganic chemistry plays in dynamic processes. To ensure accurate quantitative results, the vast amount of complex spectral data generated requires elegant solutions to perform a variety of functions including data partitioning, peak fitting, drift correction, mass-to-charge calibration, peak profiling, and spectral fitting. AutoSpect is an all-in-one software solution that provides high level automation with a user-friendly graphical interface to perform complex data analyses for ICP-TOF-MS datasets.

scientific communication and education↗

bioRxiv2025

Autoimmune regulator deficiency causes sterile epididymitis and impacts male fertility through disruption of inorganic physiology

Autoimmune regulator (AIRE), a transcription factor expressed by medullary thymic epithelial cells, is required for shaping the self-antigen tolerant T cell receptor repertoire. Humans with mutations in AIRE suffer from Autoimmune Polyglandular Syndrome Type 1 (APS-1). Among many symptoms, men with APS-1 commonly experience testicular insufficiency and infertility, but the mechanisms causing infertility are unknown. Using an Aire-deficient mouse model, we demonstrate that male subfertility is caused by sterile epididymitis characterized by immune cell infiltration and extensive fibrosis. In addition, we reveal that the presence of autoreactive immune cells and inflammation in epididymides of Aire-deficient mice are required for iron (Fe) deposition in the interstitium, which is brought on by macrophages. We further demonstrate that male subfertility is associated with a decrease in metals zinc (Zn), copper (Cu), and selenium (Se) which serve as cofactors in several antioxidant enzymes. We also show increase in DNA damage of epididymal sperm of Aire-/- animals as a key contributing factor to subfertility. The absence of Aire results in autoimmune attack of the epididymis leading to fibrosis, Fe deposition, and Cu, Zn and Se imbalance, ultimately resulting in sperm DNA damage and subfertility. These results highlight the requirement of Aire to promote immune tolerance throughout the epididymis, disruption of which causes an imbalance of inorganic elements with resulting consequence on male fertility. Key pointsBreakdown of epididymal self-tolerance promotes disruption of inorganic elements. Autoimmunity causes interstitial fibrosis resulting in sperm DNA damage and subfertility. Elevated interstitial iron and macrophages contribute to fibrosis.

pathology↗

bioRxiv2020

Rapid isolation and profiling of a diverse panel of human monoclonal antibodies targeting the SARS-CoV-2 spike protein

Antibodies are a principal determinant of immunity for most RNA viruses and have promise to reduce infection or disease during major epidemics. The novel coronavirus SARS-CoV-2 has caused a global pandemic with millions of infections and hundreds of thousands of deaths to date1,2. In response, we used a rapid antibody discovery platform to isolate hundreds of human monoclonal antibodies (mAbs) against the SARS-CoV-2 spike (S) protein. We stratify these mAbs into five major classes based on their reactivity to subdomains of S protein as well as their cross-reactivity to SARS-CoV. Many of these mAbs inhibit infection of authentic SARS-CoV-2 virus, with most neutralizing mAbs recognizing the receptor-binding domain (RBD) of S. This work defines sites of vulnerability on SARS-CoV-2 S and demonstrates the speed and robustness of new antibody discovery methodologies.

immunology↗