Biology subjects

Woodruff, T. K.

Publications and source records attributed to Woodruff, T. K..

3 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

Inorganic profiles of preimplantation embryos reveal a role for zinc in blastocyst development

Elements such as iron, copper and zinc play essential roles in the mammalian oocyte, egg, and embryo, however among these metals, zinc plays unique regulatory roles. Temporal fluctuations in zinc concentrations drive reproductive milestones such as meiotic resumption, egg activation, and initiation of the mitotic cell cycle. Roles for zinc in late preimplantation embryo development, have not been well characterized. Using a quantitative element approach we report the inorganic profiles of mouse embryos progressing through the late blastocyst stage. We find that blastocysts, like oocytes and eggs, and distinct to somatic cells, maintain higher levels of zinc than copper and iron. All three of these essential metals are more abundant in the inner cell mass, which contains the population of pluripotent stem cells that give rise to the fetus, relative to the trophectoderm which gives rise to the placenta and extraembryonic tissues. To test whether zinc abundance was associated with mitotic progress and cell fate lineage, we perturbed zinc homeostasis during blastocyst formation by artificially raising intracellular zinc concentrations with zinc pyrithione. This treatment during the morula-to-blastocyst transition when cell fate lineages emerge resulted in an elevation of zinc in the ICM. This treatment did not impact cell number but did increase expression of the pluripotency and epiblast marker, Nanog. These results demonstrate that the inorganic profiles of the late preimplantation embryo retain elemental hallmarks of earlier developmental stages and perturbation of zinc levels alters pluripotency gene expression in the blastocyst. In BriefZinc plays important regulatory roles during oocyte maturation, fertilization and early embryo development; however, the role of zinc in the late preimplantation embryo is unknown. In this study, inorganic profiling of mouse embryos reveal zinc levels are higher than copper and iron in the late blastocyst and zinc supplementation during the morula-to-blastocyst alters expression of pluripotency marker, Nanog.

developmental biology↗

bioRxiv2025

Transcriptomic analysis of whole staged ovarian follicles reveals stage-specific folliculogenesis signatures in mice

Activation and maturation of ovarian follicles are essential for female reproduction, yet the underlying molecular and transcriptional mechanisms that govern these processes remain poorly understood. In this study, we used single follicle RNA-sequencing (RNA-seq) to identify transcriptional signatures of staged ovarian follicles, from primordial to secondary stages, to uncover the genes and pathways involved in early folliculogenesis. Our findings demonstrate that primordial follicles are transcriptionally distinct from growing follicles, with enrichment in DNA integrity and RNA processing pathways, which may play a role in preserving oocyte genomic stability and cell state during dormancy. Additionally, our analysis reveals minimal transcriptomic differences between primary and secondary follicles using traditional differential expression analysis. To better distinguish growing follicle stages, we introduce unsupervised approaches, including discrete-variable predictors of follicle stage and weighted gene co-expression analysis. We identified pathways involved in DNA integrity, meiotic arrest, and cellular metabolism that drive the transition from dormant to active follicle states, as well as pathways related to cellular growth, ECM organization, and biosynthesis in growing follicle stages. Our study offers novel insights into the molecular mechanisms governing early follicle activation and growth, providing a foundation for future research with applications in reproductive biology, contraception, and fertility preservation. Author SummaryThe development of ovarian follicles is essential for female fertility, but the molecular signals that control their growth remain unclear. In this study, we used advanced gene sequencing techniques to analyze the genetic activity of individual ovarian follicles at different stages of early development. We found that dormant follicles have unique gene expression patterns that help protect the genetic material of the egg and maintain their inactive state. In contrast, follicles that have begun to grow show increased activity in genes related to cell growth, communication, and structural changes. Interestingly, we observed that early growing follicles are more similar to each other than previously thought, prompting us to apply new analytical methods to better distinguish their developmental stages. Our findings highlight key biological pathways that regulate the transition from dormant to active follicles and uncover new genes that may play a role in this process. Understanding these mechanisms provides valuable insights into ovarian biology and could inform future research on fertility treatments, contraception, and reproductive health.

bioinformatics↗