Biology subjects

Brettner, L.

Publications and source records attributed to Brettner, L..

3 recordsLinked to original sources

bioRxiv2025

High-throughput single-cell transcriptomics informs mechanisms underlying cell-to-cell differences in stress responses

Cellular stress responses are central to survival, adaptation, and disease, yet individual cells experiencing the same environment can differ substantially in how they respond. Understanding which features of the stress response are shared among cells, and which vary across cells and stressors, requires resolving transcriptional responses at the level of individual cells. Here, we used ultra-high-throughput single-cell RNA sequencing to profile more than 16,000 Saccharomyces cerevisiae cells exposed to diverse stressors, including protein misfolding, nutrient limitation, and drug stress. We compared the canonical Environmental Stress Response (ESR), originally defined from population-level measurements, with stress-responsive programs identified by emphasizing expression changes that were consistent across individual cells. Although the canonical induced ESR (iESR) showed strong average activation in stressed populations, its activation varied substantially among their constituent cells. Stress-specific programs identified by our single-cell-aware analysis were more consistent predictors of individual cell stress, yet showed little overlap with the ESR or with one another across stressors. This stress-specificity was asymmetric: Induced programs varied considerably across stressors, whereas repressed programs were dominated by a conserved set of growth- and ribosome-related genes. Consequently, unstressed cells could be identified across environments much more reliably than stressed cells, revealing a transcriptional version of the Anna Karenina principle: Unstressed cells resemble one another in their shared growth programs, whereas stressed cells diverge in stress-specific ways. Single-cell resolution also revealed an alternative transcriptional state in which cells with weaker activation of canonical stress programs showed stronger transposable element (TE) expression. Although iESR and TE expression were positively associated across stressed populations, they were inversely related across individual cells, demonstrating that population averaging can obscure, and even reverse, relationships among transcriptional programs. Together, these results show that population-level and single-cell analyses capture complementary properties of stress responses. Both perspectives are important in understanding and ultimately predicting how cell populations survive and adapt under stressful conditions.

molecular biology↗

bioRxiv2025

INgen: Intracellular Genomic DNA Amplification for Downstream Applications in Sequencing and Sorting

Here, we introduce intracellular genomic amplification (INgen), a method that harnesses the cell membrane as a natural reaction chamber to amplify DNA within fixed, permeabilized cells. INgen employs a strand-displacing, isothermal polymerase together with biotinylated primers to achieve robust intracellular DNA amplification and efficient recovery of the amplified material for sequencing. This approach overcomes a long-standing barrier that has prevented important advances in single-cell and rare-cell genomics: the inability to amplify and recover sequenceable DNA from fixed cells. By pushing past this barrier, INgen provides a critical and previously inaccessible step toward scalable single-cell DNA sequencing without the need to isolate each cell into a separate reaction vessel. Using INgen, we demonstrate targeted and whole-genome amplification across diverse organisms, including Saccharomyces cerevisiae, Bacillus subtilis, and Escherichia coli. Together, these capabilities position INgen as a foundational advance that paves the way for the next generation of single cell sequencing methods including high-throughput single-cell sequencing without physical isolation, contamination-resistant amplification within intact cells, and rare-cell enrichment prior to genomic analysis.

molecular biology↗

bioRxiv2020

Proteomic changes in bacteria caused by exposure to environmental conditions can be detected by Matrix-Assisted Laser Desorption/Ionization - Time of Flight (MALDI-ToF) Mass Spectrometry

In the past decade, matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry (MS) has become a timely and cost-effective alternative to bacterial identification. The MALDI-ToF MS technique analyzes the total protein of culturable microorganisms at the species level and produces a mass spectra based on peptides which is compared to a database of identified profiles. Consequently, unique signatures of each microorganism are produced allowing identification at the species and, more importantly, strain level. Our present study proposes that the MALDI-ToF MS can be further used to screen functional and metabolic differences. While other studies applied the MALDI-ToF technique to identify subgroups within species, we investigated how various environmental factors could alter the unique bacterial signatures. We found that genetic and phenotypic differences between microorganisms belonging to the same species can be reflected in peptide-mass fingerprints generated by MALDI-ToF MS. These results suggest that MALDI-ToF MS can screen intra-species phenotypic differences of several microorganisms.

microbiology↗