Biology subjects

Fredriksson, S.

Publications and source records attributed to Fredriksson, S..

3 recordsLinked to original sources

bioRxiv2025

Comparative regulomics provides novel insight into the evolution of wood formation across dicot and conifer trees

Understanding the regulatory program underlying wood formation is key to improving biomass production and carbon sequestration in trees. However, how wood formation evolved and how these programs have been rewired across lineages remains unclear. Here, we present the first high-spatial-resolution evo-devo resource spanning the wood transcriptomes of six tree species - three dicots and three conifers - capturing 250 million years of evolutionary divergence. Using orthology-aware co-expression network analysis, we identified genes with conserved and lineage-specific expression patterns. By integrating chromatin accessibility data and transcription factor motif analysis, we further inferred regulatory networks for xylem differentiation and secondary cell wall formation. We demonstrate how this dataset can be used to answer long standing questions in wood biology related to differences in acetylation of cell wall polymers and master regulators of xylem specification across dicot and conifer tree species. The data offer a foundational resource for the tree biology and evo-devo communities, and are publicly available at PlantGenIE.org.

genomics↗

bioRxiv2025

Single-Cell Protein Interactomes by the Proximity Network Assay

Cellular functions depend on dynamic interactions of proteins and their spatial organisation. While transcriptomic and proteomic methods of molecular parts-lists have enabled single-cell profiling based on abundance, scalable technologies allowing high-resolution measurements of protein organization and interactions at scale are lacking. Here we present the Proximity Network Assay (PNA), a DNA-based method for constructing three-dimensional nanoscale maps of 155 plasma membrane proteins in single cells without the use of optics. PNA employs barcoded antibodies and in situ rolling circle amplification to generate >40,000 spatial nodes per cell, which are linked through proximity-dependent gap-fill ligation and decoded by DNA sequencing forming single cell Proximity Networks. PNA captures abundance, self-clustering, and [~]12,000 pairwise colocalization relationships per single-cell, validating established protein interactions. This new modality provides a framework to uncover novel spatial biomarkers, reveal functional mechanisms, and advance translational studies in immunology, oncology, and cell therapy.

bioengineering↗

bioRxiv2023

Molecular Pixelation: Single cell spatial proteomics by sequencing

The spatial distribution of cell surface proteins govern vital processes of the immune system such as inter-cell communication and mobility. However, tools for studying these at high multiplexing scale, resolution, and throughput needed to drive novel discoveries are lacking. We present Molecular Pixelation, a DNA-sequencing based method for single cell analysis to quantify protein abundance, spatial distribution, and colocalization of targeted proteins using Antibody Oligonucleotide Conjugates (AOCs). Relative locations of AOCs are inferred by sequentially associating these into local neighborhoods using DNA-pixels containing unique pixel identifier (UPI) sequences, forming >1,000 connected spatial zones per single cell in three dimensions. DNA-sequencing reads are computationally arranged into spatial single cell maps for 76 proteins without cell compartmentalization. By studying immune cell dynamics and using spatial statistics on graph representations of the data, previously known and novel patterns of protein spatial polarization and co-localization were found in chemokine-stimulated T-cells.

immunology↗